Title: Estimation of the Structural Topic Model
Diff between stm versions 0.6.24 dated 2014-06-30 and 1.0.0 dated 2014-10-02
Description: The Structural Topic Model (STM) allows researchers
to estimate topic models with document-level covariates.
The package also includes tools for model selection, visualization,
and estimation of topic-covariate regressions.
Author: Margaret E. Roberts, Brandon M. Stewart and Dustin Tingley
Maintainer: Brandon Stewart
stm-0.6.24/stm/R/STMbetakappa.R |only
stm-0.6.24/stm/R/STMinitialize.R |only
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stm-1.0.0/stm/MD5 | 120 ++++++++------
stm-1.0.0/stm/NAMESPACE | 17 +-
stm-1.0.0/stm/R/STMconvergence.R | 54 +-----
stm-1.0.0/stm/R/STMestep.R | 67 +++-----
stm-1.0.0/stm/R/STMfunctions.R | 39 ++++
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stm-1.0.0/stm/R/STMreport.R | 48 +++--
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stm-1.0.0/stm/R/cloud.R | 89 +++++-----
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stm-1.0.0/stm/R/labelTopics.R | 2
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stm-1.0.0/stm/R/permute.R | 4
stm-1.0.0/stm/R/plot.estimateEffect.R | 21 +-
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stm-1.0.0/stm/R/semanticCoherence.R | 2
stm-1.0.0/stm/R/spectral.R |only
stm-1.0.0/stm/R/stm.R | 66 ++++---
stm-1.0.0/stm/R/stm.control.R | 226 +++++++++++++++++++--------
stm-1.0.0/stm/R/tau.R |only
stm-1.0.0/stm/R/textProcessor.R | 49 +++--
stm-1.0.0/stm/R/thetaPosterior.R | 140 ++++++++++++----
stm-1.0.0/stm/R/topicCorr.R | 25 +-
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stm-1.0.0/stm/build/vignette.rds |binary
stm-1.0.0/stm/data/gadarian.RData |binary
stm-1.0.0/stm/data/gadarianFit.RData |binary
stm-1.0.0/stm/data/poliblog5k.RData |binary
stm-1.0.0/stm/inst/NEWS.Rd | 11 +
stm-1.0.0/stm/inst/doc/stmVignette.R | 68 ++++----
stm-1.0.0/stm/inst/doc/stmVignette.Rnw | 187 +++++++++++++++-------
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stm-1.0.0/stm/vignettes/vignetteBib.bib | 45 +++++
86 files changed, 1054 insertions(+), 550 deletions(-)
Title: Graph Based Multiple Comparison Procedures
Diff between gMCP versions 0.8-7 dated 2014-08-26 and 0.8-8 dated 2014-10-02
Description: This package provides functions and a graphical user interface for graphical described multiple test procedures.
Author: Kornelius Rohmeyer [aut, cre],
Florian Klinglmueller [aut]
Maintainer: Kornelius Rohmeyer
gMCP-0.8-7/gMCP/inst/classes |only
gMCP-0.8-7/gMCP/java/org/af/gMCP/gui/datatable/CloseTabPanel.java |only
gMCP-0.8-7/gMCP/java/org/af/gMCP/gui/dialogs/PowerDialogParameterUncertainty.java |only
gMCP-0.8-7/gMCP/java/org/af/gMCP/gui/power/PDistPanel.java |only
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gMCP-0.8-8/gMCP/INSTALL | 12
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gMCP-0.8-8/gMCP/NAMESPACE | 6
gMCP-0.8-8/gMCP/NEWS | 86
gMCP-0.8-8/gMCP/R/analysis.R | 52
gMCP-0.8-8/gMCP/R/calcPower.R | 109
gMCP-0.8-8/gMCP/R/doRUnitTests.R | 39
gMCP-0.8-8/gMCP/R/exampleGraphs.R | 116 -
gMCP-0.8-8/gMCP/R/gACT-internal.R | 43
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gMCP-0.8-8/gMCP/R/generateBounds.R | 8
gMCP-0.8-8/gMCP/R/generatePvals.R | 15
gMCP-0.8-8/gMCP/R/generateTest.R | 4
gMCP-0.8-8/gMCP/R/generateWeights.R | 51
gMCP-0.8-8/gMCP/R/graph2latex.R | 41
gMCP-0.8-8/gMCP/R/graphTest.R | 9
gMCP-0.8-8/gMCP/R/helperGUI.R | 67
gMCP-0.8-8/gMCP/R/misc.R | 88
gMCP-0.8-8/gMCP/R/onLoad.R | 44
gMCP-0.8-8/gMCP/R/sampSize.R | 57
gMCP-0.8-8/gMCP/R/startGUIs.R | 5
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gMCP-0.8-8/gMCP/inst/unitTests/runit.entangled.R | 28
gMCP-0.8-8/gMCP/inst/unitTests/runit.gMCP.R | 19
gMCP-0.8-8/gMCP/inst/unitTests/runit.power.R | 4
gMCP-0.8-8/gMCP/java/build.xml | 14
gMCP-0.8-8/gMCP/java/org/af/gMCP/config/GeneralConfig.java | 75
gMCP-0.8-8/gMCP/java/org/af/gMCP/config/VersionComparator.java | 36
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/AboutDialog.java | 16
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/CreateGraphGUI.java | 48
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/ErrorDialogGMCP.java | 36
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/MenuBarMGraph.java | 169 +
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/RControl.java | 16
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/datatable/DataFramePanel.java | 77
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/datatable/DataTable.java | 1
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/datatable/EpsilonTableCellRenderer.java | 9
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/dialogs/AdjustedPValueDialog.java | 60
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/dialogs/DialogConfIntEstVar.java | 122 -
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/dialogs/GraphSendToArchiveDialog.java | 2
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/dialogs/LoadGraphFromArchiveDialog.java | 2
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/dialogs/MatrixCreationDialog.java | 19
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/dialogs/ParameterDialog.java | 2
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/dialogs/PowerOptionsPanel.java |only
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/dialogs/RObjectLoadingDialog.java | 6
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/dialogs/RearrangeNodesDialog.java | 2
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/dialogs/RejectedDialog.java | 70
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/dialogs/TellAboutOnlineUpate.java | 2
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/dialogs/VariableDialog.java | 4
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/graph/DView.java | 3
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/graph/Edge.java | 4
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/graph/EdgeWeight.java | 41
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/graph/GraphMCP.java | 7
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/graph/GraphView.java | 66
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/graph/LaTeXTool.java | 38
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/graph/NetList.java | 1131 +++-------
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/graph/NetListPanel.java |only
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/graph/NetListSelectionPopUpMenu.java | 12
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/graph/Node.java | 66
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/graph/PPanel.java | 70
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/graph/PView.java | 98
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/graph/PrintableObject.java | 2
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/graph/annotations/Annotation.java |only
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/graph/annotations/AnnotationPanel.java |only
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/graph/annotations/Ellipse.java | 73
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/graph/annotations/Legend.java |only
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/graph/annotations/Line.java | 44
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/graph/annotations/Note.java | 38
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/graph/annotations/Rectangle.java | 60
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/graph/annotations/Text.java | 66
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gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/options/GeneralPanel.java | 61
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/options/NumericPanel.java | 59
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/pdf/PDFGenerator.java | 7
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/power/CVPanel.java |only
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gMCP-0.8-8/gMCP/java/org/af/gMCP/tests/ThreadExceptionTest.java |only
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gMCP-0.8-8/gMCP/java/tests/RJavaUTF.java |only
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gMCP-0.8-8/gMCP/man/corMatWizard.Rd | 31
gMCP-0.8-8/gMCP/man/doInterim.Rd | 91
gMCP-0.8-8/gMCP/man/exampleGraphs.Rd | 265 +-
gMCP-0.8-8/gMCP/man/extractPower.Rd | 33
gMCP-0.8-8/gMCP/man/gMCP-package.Rd | 14
gMCP-0.8-8/gMCP/man/gMCP.Rd | 272 +-
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gMCP-0.8-8/gMCP/man/generatePvals.Rd | 191 -
gMCP-0.8-8/gMCP/man/generateTest.Rd | 141 -
gMCP-0.8-8/gMCP/man/generateWeights.Rd | 52
gMCP-0.8-8/gMCP/man/getJavaInfo.Rd | 17
gMCP-0.8-8/gMCP/man/graph2latex.Rd | 138 -
gMCP-0.8-8/gMCP/man/graphAnalysis.Rd | 32
gMCP-0.8-8/gMCP/man/graphGUI.Rd | 82
gMCP-0.8-8/gMCP/man/graphTest.Rd | 112
gMCP-0.8-8/gMCP/man/joinGraphs.Rd | 43
gMCP-0.8-8/gMCP/man/matrix2graph.Rd | 33
gMCP-0.8-8/gMCP/man/placeNodes.Rd | 40
gMCP-0.8-8/gMCP/man/plotSimCI.Rd | 15
gMCP-0.8-8/gMCP/man/rejectNode.Rd | 41
gMCP-0.8-8/gMCP/man/replaceVariables.Rd | 37
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gMCP-0.8-8/gMCP/man/secondStageTest.Rd | 97
gMCP-0.8-8/gMCP/man/subgraph.Rd | 19
gMCP-0.8-8/gMCP/man/substituteEps.Rd | 21
gMCP-0.8-8/gMCP/man/unitTestsGMCP.Rd | 63
gMCP-0.8-8/gMCP/src/mcp.c | 6
gMCP-0.8-8/gMCP/vignettes/gMCP.Rnw | 274 +-
gMCP-0.8-8/gMCP/vignettes/literatur.bib | 38
gMCP-0.8-8/gMCP/vignettes/parametric.Rnw | 2
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167 files changed, 3994 insertions(+), 3077 deletions(-)
Title: Discriminant analysis with additional information
Diff between dawai versions 1.0 dated 2014-02-05 and 1.1 dated 2014-10-02
Description: This package performs linear and quadratic discriminant analysis with additional information expressed as inequality restrictions among the populations means and computes several estimations of the true error rate
Author: David Conde, Miguel A. Fernandez, Bonifacio Salvador
Maintainer: David Conde
DESCRIPTION | 8 +-
MD5 | 52 ++++++-------
R/bootstrapsamples.R | 2
R/checks.R | 80 +++++++++------------
R/classify.R | 11 +-
R/err.est.R | 4 -
R/getmeans.R | 2
R/getvariances.R | 2
R/posterior.R | 11 +-
R/resmatrix.R | 12 +--
R/rest.est.R | 10 +-
R/restrictions.R | 20 ++---
R/rlda.R | 189 +++++++++++++++++++++++++-------------------------
R/rqda.R | 190 +++++++++++++++++++++++++--------------------------
data/Vehicle2.rda |binary
inst/doc/dawai.R | 27 +++----
inst/doc/dawai.Rnw | 27 +++----
inst/doc/dawai.pdf |binary
man/Vehicle2.Rd | 77 ++++++++++----------
man/dawai-package.Rd | 5 -
man/err.est.rlda.Rd | 15 ++--
man/err.est.rqda.Rd | 33 ++++----
man/predict.rlda.Rd | 57 +++++++--------
man/predict.rqda.Rd | 39 +++++-----
man/rlda.Rd | 57 ++++++---------
man/rqda.Rd | 40 +++++-----
vignettes/dawai.Rnw | 27 +++----
27 files changed, 489 insertions(+), 508 deletions(-)
Title: Cross-platform Perl based R function to create Excel 2003 (XLS)
and Excel 2007 (XLSX) files
Diff between WriteXLS versions 3.5.0 dated 2014-03-18 and 3.5.1 dated 2014-10-02
Description: Cross-platform Perl based R function to create Excel 2003 (XLS) and Excel 2007 (XLSX)
files from one or more data frames. Each data frame will be
written to a separate named worksheet in the Excel spreadsheet.
The worksheet name will be the name of the data frame it contains
or can be specified by the user.
Author: Marc Schwartz
Maintainer: Marc Schwartz
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/WriteXLS.R | 11 +++++++++--
man/WriteXLS.Rd | 7 +++++++
4 files changed, 23 insertions(+), 9 deletions(-)
Title: Global, Parameterwise and Joint Post-Estimation Shrinkage
Diff between shrink versions 1.1 dated 2013-10-21 and 1.2.0 dated 2014-10-02
Description: Post-estimation shrinkage of regression coefficients in statistical modeling can be
used to correct for the overestimation of regression coefficients caused by variable selection.
While global shrinkage modifies all regression coefficients by the same factor, parameterwise
shrinkage factors differ between regression coefficients. With variables which are either
highly correlated or associated with regard to contents, such as several columns of a design
matrix describing a nonlinear effect, parameterwise shrinkage factors are not interpretable
and a compromise between global and parameterwise shrinkage, termed 'joint shrinkage', is a
useful extension.
A computational shortcut to resampling-based shrinkage factor estimation based on DFBETA
residuals can be applied.
Global, parameterwise and joint shrinkage for models fitted by lm, glm, coxph, or (for
R <= 3.1.0) mfp is available.
Author: Daniela Dunkler, Georg Heinze
Maintainer: Daniela Dunkler
shrink-1.1/shrink/tests |only
shrink-1.2.0/shrink/Changelog | 31 +-
shrink-1.2.0/shrink/DESCRIPTION | 27 +-
shrink-1.2.0/shrink/MD5 | 38 +-
shrink-1.2.0/shrink/NAMESPACE | 12
shrink-1.2.0/shrink/R/additionalfunctions.r | 10
shrink-1.2.0/shrink/R/coef.shrink.r | 25 +
shrink-1.2.0/shrink/R/predict.shrink.r | 74 +++--
shrink-1.2.0/shrink/R/print.shrink.r | 48 ++-
shrink-1.2.0/shrink/R/shrink.coxph.r |only
shrink-1.2.0/shrink/R/shrink.glm.r |only
shrink-1.2.0/shrink/R/shrink.lm.r |only
shrink-1.2.0/shrink/R/shrink.r | 356 +++-------------------------
shrink-1.2.0/shrink/R/summary.shrink.r |only
shrink-1.2.0/shrink/R/vcov.shrink.r |only
shrink-1.2.0/shrink/data/GBSG.txt.gz |only
shrink-1.2.0/shrink/man/GBSG.Rd |only
shrink-1.2.0/shrink/man/coef.shrink.Rd | 11
shrink-1.2.0/shrink/man/deepvein.Rd | 31 +-
shrink-1.2.0/shrink/man/predict.shrink.Rd | 64 +----
shrink-1.2.0/shrink/man/print.shrink.Rd | 9
shrink-1.2.0/shrink/man/shrink-package.Rd | 42 +--
shrink-1.2.0/shrink/man/shrink.Rd | 216 +++++++++-------
shrink-1.2.0/shrink/man/summary.shrink.Rd |only
shrink-1.2.0/shrink/man/vcov.shrink.Rd |only
25 files changed, 416 insertions(+), 578 deletions(-)
Title: Geostatistics using SpatialPoints and rasters
Diff between geostatsp versions 1.0.1 dated 2014-09-18 and 1.1.0 dated 2014-10-02
Description: This package provides to geostatistical modelling facilities using raster and SpatialPoints objects. Non-Gaussian models are fit using INLA, obtainable from http://www.r-inla.org.
Author: Patrick Brown
Maintainer: Patrick Brown
DESCRIPTION | 16 +--
MD5 | 61 +++++++------
NAMESPACE | 17 ++-
R/0gm.R |only
R/RFsimulate.R | 30 +++++-
R/asImRaster.R | 3
R/conditionalGmrf.R |only
R/formulaLhs.R | 67 +++++++++++++++
R/glgm.R |only
R/grfConditional.R | 8 +
R/krige.R | 214 ++++++++++++++++++++++++++++++++++++-------------
R/lgcp.R |only
R/lgm.R | 203 +++++++++++++++++++++++-----------------------
R/lgm.Raster.R | 159 +++++++++++++++++++++---------------
R/logLikGradient.R | 4
R/loglikGmrf.R | 27 ++----
R/utils.R | 17 +++
R/variog.R | 14 +--
man/RFsimulate.Rd | 3
man/asImRaster.Rd | 3
man/excProb.Rd | 4
man/glgm.Rd |only
man/krige.Rd | 35 ++++----
man/lgm.Rd | 82 ++++++++++++++----
man/profLlgm.Rd | 2
tests/RFsimulate.R | 4
tests/glgm.R |only
tests/krige.R | 10 +-
tests/lgcp.R |only
tests/lgm.R | 18 ++--
tests/lgmRaster.R | 14 ++-
tests/likfitLgm.R | 7 +
tests/matern.R | 3
tests/maternGmrfPrec.R | 2
tests/profLlgm.R | 2
35 files changed, 670 insertions(+), 359 deletions(-)
Title: Model-Based Boosting
Diff between mboost versions 2.3-0 dated 2014-06-26 and 2.4-0 dated 2014-10-02
Description: Functional gradient descent algorithm
(boosting) for optimizing general risk functions utilizing
component-wise (penalised) least squares estimates or regression
trees as base-learners for fitting generalized linear, additive
and interaction models to potentially high-dimensional data.
Author: Torsten Hothorn [aut, cre],
Peter Buehlmann [aut],
Thomas Kneib [aut],
Matthias Schmid [aut],
Benjamin Hofner [aut],
Fabian Sobotka [ctb],
Fabian Scheipl [ctb]
Maintainer: Torsten Hothorn
mboost-2.3-0/mboost/NEWS |only
mboost-2.3-0/mboost/R/inference.R |only
mboost-2.3-0/mboost/inst/CHANGES |only
mboost-2.3-0/mboost/vignettes/auto |only
mboost-2.4-0/mboost/DESCRIPTION | 10 -
mboost-2.4-0/mboost/MD5 | 56 ++++----
mboost-2.4-0/mboost/NAMESPACE | 18 +-
mboost-2.4-0/mboost/R/bmrf.R | 11 -
mboost-2.4-0/mboost/R/brad.R | 23 ++-
mboost-2.4-0/mboost/R/btree.R | 6
mboost-2.4-0/mboost/R/confint.R |only
mboost-2.4-0/mboost/R/mboost.R | 116 +++++++++++++++---
mboost-2.4-0/mboost/R/methods.R | 9 -
mboost-2.4-0/mboost/R/plot.R | 48 +++++--
mboost-2.4-0/mboost/R/stabsel.R |only
mboost-2.4-0/mboost/build/vignette.rds |binary
mboost-2.4-0/mboost/inst/NEWS.Rd |only
mboost-2.4-0/mboost/inst/doc/SurvivalEnsembles.pdf |binary
mboost-2.4-0/mboost/inst/doc/mboost.pdf |binary
mboost-2.4-0/mboost/inst/doc/mboost_illustrations.pdf |binary
mboost-2.4-0/mboost/inst/doc/mboost_tutorial.R | 27 ++--
mboost-2.4-0/mboost/inst/doc/mboost_tutorial.Rnw | 42 +++---
mboost-2.4-0/mboost/inst/doc/mboost_tutorial.pdf |binary
mboost-2.4-0/mboost/man/FP.Rd | 3
mboost-2.4-0/mboost/man/baselearners.Rd | 26 ++--
mboost-2.4-0/mboost/man/blackboost.Rd | 13 --
mboost-2.4-0/mboost/man/confint.Rd |only
mboost-2.4-0/mboost/man/mboost.Rd | 12 +
mboost-2.4-0/mboost/man/mboost_package.Rd | 19 ++
mboost-2.4-0/mboost/man/methods.Rd | 1
mboost-2.4-0/mboost/man/stabsel.Rd | 88 ++++---------
mboost-2.4-0/mboost/vignettes/mboost_tutorial.Rnw | 42 +++---
mboost-2.4-0/mboost/vignettes/mboost_tutorial.bib | 17 ++
33 files changed, 367 insertions(+), 220 deletions(-)
Title: Flexible procedures for clustering
Diff between fpc versions 2.1-8 dated 2014-09-09 and 2.1-9 dated 2014-10-02
Description: Various methods for clustering and cluster validation.
Fixed point clustering. Linear regression clustering. Clustering by
merging Gaussian mixture components. Symmetric
and asymmetric discriminant projections for visualisation of the
separation of groupings. Cluster validation statistics
for distance based clustering including corrected Rand index.
Cluster-wise cluster stability assessment. Methods for estimation of
the number of clusters: Calinski-Harabasz, Tibshirani and Walther's
prediction strength, Fang and Wang's bootstrap stability.
Gaussian/multinomial mixture fitting for mixed
continuous/categorical variables. Variable-wise statistics for cluster
interpretation. DBSCAN clustering. Interface functions for many
clustering methods implemented in R, including estimating the number of
clusters with kmeans, pam and clara. Modality diagnosis for Gaussian
mixtures. For an overview see package?fpc.
Author: Christian Hennig
Maintainer: Christian Hennig
DESCRIPTION | 8 +++---
MD5 | 8 +++---
R/addclustermethods.R | 6 ++---
tests/Examples/fpc-Ex.Rout.save | 23 +++++++++++--------
tests/fpctests.Rout.save | 47 +++++++++++++---------------------------
5 files changed, 41 insertions(+), 51 deletions(-)
Title: Linear regression based on linear structure between covariates
Diff between CorReg versions 0.15.6 dated 2014-09-12 and 0.15.7 dated 2014-10-02
Description: Linear regression based on a recursive structural equation model
(explicit correlations) found by a MCMC algorithm. It permits to face
highly correlated covariates. Variable selection is included (by lasso,
elasticnet, etc.). It also provides some graphical tools for basic
statistics.
Author: Clement THERY [aut, cre],
Christophe BIERNACKI [ctb],
Gaetan LORIDANT [ctb],
Florian WATRIN [ctb],
Quentin GRIMONPREZ [ctb],
Vincent KUBICKI [ctb],
Samuel BLANCK [ctb],
Jeremie KELLNER [ctb]
Maintainer: Clement THERY
DESCRIPTION | 13 ++++++++-----
MD5 | 16 ++++++++--------
R/CorReg-package.R | 6 ++++--
R/R2Z.R | 2 +-
man/CorReg-package.Rd | 4 +++-
src/rechercheZ.cpp | 12 ++++++------
src/rechercheZ_rejet.cpp | 10 +++++-----
src/rechercheZ_relax.cpp | 12 ++++++------
src/rechercheZ_sparse_relax.cpp | 10 +++++-----
9 files changed, 46 insertions(+), 39 deletions(-)
Title: Replicability Analysis for Multiple Studies of High Dimension
Diff between repfdr versions 1.0 dated 2014-01-08 and 1.1 dated 2014-10-02
Description: Estimation of Bayes and local Bayes false discovery rates for
replicability analysis.
Author: Ruth Heller, Shachar Kaufman, Shay Yaacoby, Daniel Yekutieli
Maintainer: Ruth Heller
repfdr-1.0/repfdr/data/simzmat.RData |only
repfdr-1.0/repfdr/data/zmat.RData |only
repfdr-1.0/repfdr/man/simzmat.Rd |only
repfdr-1.0/repfdr/man/zmat.Rd |only
repfdr-1.1/repfdr/DESCRIPTION | 12 +-
repfdr-1.1/repfdr/MD5 | 37 ++++----
repfdr-1.1/repfdr/NAMESPACE | 1
repfdr-1.1/repfdr/R/ztobins.R | 101 ++++++++++++----------
repfdr-1.1/repfdr/data/Pi.RData |binary
repfdr-1.1/repfdr/data/SNPlocations.RData |binary
repfdr-1.1/repfdr/data/binned_zmat.RData |only
repfdr-1.1/repfdr/data/binned_zmat_sim.RData |only
repfdr-1.1/repfdr/data/datalist | 7 +
repfdr-1.1/repfdr/data/hmat_sim.RData |only
repfdr-1.1/repfdr/data/zmat_sim.RData |only
repfdr-1.1/repfdr/man/SNPlocations.Rd |only
repfdr-1.1/repfdr/man/binned_zmat.Rd |only
repfdr-1.1/repfdr/man/binned_zmat_sim.Rd |only
repfdr-1.1/repfdr/man/em.control.Rd | 8 -
repfdr-1.1/repfdr/man/hconfigs.Rd | 8 -
repfdr-1.1/repfdr/man/hmat_sim.Rd |only
repfdr-1.1/repfdr/man/ldr.Rd | 21 +---
repfdr-1.1/repfdr/man/piem.Rd | 25 +++--
repfdr-1.1/repfdr/man/repfdr.Rd | 121 +++++++++++++--------------
repfdr-1.1/repfdr/man/zmat_sim.Rd |only
repfdr-1.1/repfdr/man/ztobins.Rd | 43 +++------
26 files changed, 192 insertions(+), 192 deletions(-)
Title: DDI with R
Diff between DDIwR versions 0.1-0 dated 2014-07-30 and 0.2-0 dated 2014-10-02
Description: This package provides useful functions for various DDI (Data Documentation Initiative) related outputs.
Author: Adrian Dusa [aut, cre]
Maintainer: Adrian Dusa
DESCRIPTION | 12 -
MD5 | 24 +--
NAMESPACE | 1
R/getDelimiter.R |only
R/getFiles.R | 11 +
R/getMetadata.R | 20 +-
R/setupfile.R | 343 +++++++++++++++++++++++++-------------------------
R/treatPath.R | 6
data |only
inst/ChangeLog | 12 +
man/DDIwR-internal.Rd | 2
man/DDIwR.package.Rd | 6
man/getMetadata.Rd | 8 -
man/setupfile.Rd | 109 ++++++++-------
14 files changed, 291 insertions(+), 263 deletions(-)
Title: Multivariate Dependence with Copulas
Diff between copula versions 0.999-11 dated 2014-09-05 and 0.999-12 dated 2014-10-02
Description: Classes (S4) of commonly used elliptical, Archimedean, extreme
value and some more copula families. Methods for density, distribution,
random number generation, bivariate dependence measures, perspective and
contour plots. Fitting copula models including variance estimates.
Independence and serial (univariate and multivariate) independence tests,
and other copula related tests. Empirical copula and multivariate CDF.
Goodness-of-fit tests for copulas based on multipliers, the parametric
bootstrap with several transformation options.
Merged former package 'nacopula' for nested Archimedean copulas: Efficient
sampling algorithms, various estimators, goodness-of-fit tests and related
tools and special functions.
Author: Marius Hofert
Maintainer: Martin Maechler
DESCRIPTION | 10 ++--
MD5 | 30 ++++++------
R/derCdfPdf.R | 6 +-
R/fitCopula.R | 4 -
R/gofTests.R | 108 ++++++++++++++++++++--------------------------
inst/NEWS.Rd | 17 ++++++-
inst/doc/Frank-Rmpfr.pdf |binary
inst/doc/nacopula-pkg.pdf |binary
inst/doc/rhoAMH-dilog.pdf |binary
man/fitMvdc.Rd | 12 +++--
man/gofCopula.Rd | 48 +++++++++++---------
man/gofTrafos.Rd | 5 +-
man/gofTstat.Rd | 11 ++--
man/mvdc-class.Rd | 2
src/gof.c | 79 ++++++++++++++++-----------------
src/gof.h | 4 -
16 files changed, 176 insertions(+), 160 deletions(-)
Title: R interface to X-13ARIMA-SEATS
Diff between seasonal versions 0.60.0 dated 2014-05-09 and 0.70.1 dated 2014-10-02
Description: seasonal is an easy-to-use and full-featured R-interface
to X-13ARIMA-SEATS, the newest seasonal adjustment software from
the United States Census Bureau. See the README file or the vignette for
installation notes.
Author: Christoph Sax
Maintainer: Christoph Sax
seasonal-0.60.0/seasonal/vignettes/seas-concordance.tex |only
seasonal-0.60.0/seasonal/vignettes/seas.tex |only
seasonal-0.70.1/seasonal/DESCRIPTION | 21
seasonal-0.70.1/seasonal/MD5 | 101 ++--
seasonal-0.70.1/seasonal/NAMESPACE | 4
seasonal-0.70.1/seasonal/NEWS | 32 +
seasonal-0.70.1/seasonal/R/base.methods.R | 11
seasonal-0.70.1/seasonal/R/checkX13.R | 121 +++--
seasonal-0.70.1/seasonal/R/deparse.R | 2
seasonal-0.70.1/seasonal/R/detect.R | 133 ++++-
seasonal-0.70.1/seasonal/R/diagnostics.R | 61 ++
seasonal-0.70.1/seasonal/R/genhol.R | 10
seasonal-0.70.1/seasonal/R/inspect.R | 274 +++++++-----
seasonal-0.70.1/seasonal/R/out.R | 92 +---
seasonal-0.70.1/seasonal/R/plot.R | 27 +
seasonal-0.70.1/seasonal/R/read_est.R | 5
seasonal-0.70.1/seasonal/R/read_mdl.R | 9
seasonal-0.70.1/seasonal/R/read_series.R | 19
seasonal-0.70.1/seasonal/R/read_udg.R |only
seasonal-0.70.1/seasonal/R/reeval.R | 2
seasonal-0.70.1/seasonal/R/seas.R | 227 +++++-----
seasonal-0.70.1/seasonal/R/seasonal-package.R | 8
seasonal-0.70.1/seasonal/R/series.R | 14
seasonal-0.70.1/seasonal/R/spclist.R | 22
seasonal-0.70.1/seasonal/R/startup.R | 2
seasonal-0.70.1/seasonal/R/static.R | 6
seasonal-0.70.1/seasonal/R/summary.R | 30 -
seasonal-0.70.1/seasonal/README.md | 50 +-
seasonal-0.70.1/seasonal/build/vignette.rds |binary
seasonal-0.70.1/seasonal/inst/doc/seas.Rnw | 4
seasonal-0.70.1/seasonal/inst/doc/seas.pdf |binary
seasonal-0.70.1/seasonal/man/SPECS.Rd | 9
seasonal-0.70.1/seasonal/man/checkX13.Rd | 23 -
seasonal-0.70.1/seasonal/man/cpi.Rd | 5
seasonal-0.70.1/seasonal/man/easter.Rd | 2
seasonal-0.70.1/seasonal/man/exp.Rd | 5
seasonal-0.70.1/seasonal/man/final.Rd | 30 -
seasonal-0.70.1/seasonal/man/genhol.Rd | 75 +--
seasonal-0.70.1/seasonal/man/identify.seas.Rd | 18
seasonal-0.70.1/seasonal/man/inspect.Rd | 54 +-
seasonal-0.70.1/seasonal/man/na.x13.Rd | 8
seasonal-0.70.1/seasonal/man/out.Rd | 72 +--
seasonal-0.70.1/seasonal/man/outlier.Rd | 12
seasonal-0.70.1/seasonal/man/plot.seas.Rd | 49 +-
seasonal-0.70.1/seasonal/man/qs.Rd | 64 +-
seasonal-0.70.1/seasonal/man/seas.Rd | 212 ++++-----
seasonal-0.70.1/seasonal/man/seasonal-deprecated.Rd | 8
seasonal-0.70.1/seasonal/man/seasonal-package.Rd | 21
seasonal-0.70.1/seasonal/man/series.Rd | 362 ++++++++--------
seasonal-0.70.1/seasonal/man/static.Rd | 45 -
seasonal-0.70.1/seasonal/man/summary.seas.Rd | 36 -
seasonal-0.70.1/seasonal/vignettes/README.tex | 97 ++--
seasonal-0.70.1/seasonal/vignettes/seas.Rnw | 4
53 files changed, 1398 insertions(+), 1100 deletions(-)
Title: Turbulence Time Series Event Detection and Classification
Diff between TED versions 1.1 dated 2014-10-01 and 1.1.1 dated 2014-10-02
Description: TED performs Turbulence time series Event Detection and classification.
Author: Yanfei Kang, Danijel Belusic and Kate Smith-Miles
Maintainer: Yanfei Kang
DESCRIPTION | 15 ++++++++-------
MD5 | 10 +++++-----
NAMESPACE | 2 +-
R/noiseTests.R | 4 +++-
man/noiseTests.Rd | 2 ++
man/ted-package.Rd | 2 +-
6 files changed, 20 insertions(+), 15 deletions(-)
Title: Spatio-Temporal Bayesian Modelling Using R
Diff between spTimer versions 1.0-2 dated 2014-06-23 and 1.0-3 dated 2014-10-02
Description: The package is able to fit, spatially predict and temporally forecast large amounts of space-time data using [1] Bayesian Gaussian Process (GP) Models, [2] Bayesian Auto-Regressive (AR) Models, and [3] Bayesian Gaussian Predictive Processes (GPP) based AR Models for big-n problem.
Author: K. Shuvo Bakar & Sujit K. Sahu
Maintainer: Shuvo Bakar
spTimer-1.0-2/spTimer/man/as.forecast.object.Rd |only
spTimer-1.0-3/spTimer/DESCRIPTION | 10 -
spTimer-1.0-3/spTimer/MD5 | 43 +++----
spTimer-1.0-3/spTimer/NAMESPACE | 3
spTimer-1.0-3/spTimer/R/spTimer.R | 3
spTimer-1.0-3/spTimer/man/predict.spT.Rd | 3
spTimer-1.0-3/spTimer/man/spT.Gibbs.Rd | 2
spTimer-1.0-3/spTimer/man/spTimer-internal.Rd | 1
spTimer-1.0-3/spTimer/man/spTimer-package.Rd | 2
spTimer-1.0-3/spTimer/src/common.c | 140 ++++++++++++------------
spTimer-1.0-3/spTimer/src/equation_xb_ar.c | 72 ++++++------
spTimer-1.0-3/spTimer/src/equation_xb_gp.c | 92 +++++++--------
spTimer-1.0-3/spTimer/src/equation_xb_gpp.c | 70 ++++++------
spTimer-1.0-3/spTimer/src/forecast_xb_ar.c | 4
spTimer-1.0-3/spTimer/src/forecast_xb_gp.c | 45 ++++---
spTimer-1.0-3/spTimer/src/forecast_xb_gpp.c | 4
spTimer-1.0-3/spTimer/src/gibbs_ar.c | 14 +-
spTimer-1.0-3/spTimer/src/gibbs_gp.c | 35 +++---
spTimer-1.0-3/spTimer/src/gibbs_gpp.c | 16 +-
spTimer-1.0-3/spTimer/src/mathematics.c | 4
spTimer-1.0-3/spTimer/src/prediction_xb_ar.c | 4
spTimer-1.0-3/spTimer/src/prediction_xb_gp.c | 62 +++++-----
spTimer-1.0-3/spTimer/src/prediction_xb_gpp.c | 12 +-
23 files changed, 328 insertions(+), 313 deletions(-)
Title: Response-surface analysis
Diff between rsm versions 2.06 dated 2014-04-18 and 2.07 dated 2014-10-02
Description: Provides functions to generate response-surface designs, fit first- and second-order response-surface models, make surface plots, obtain the path of steepest ascent, and do canonical analysis.
Author: Russell V. Lenth
Maintainer: Russell V Lenth
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
R/contour-lm.R | 20 ++++++++++++++------
build/vignette.rds |binary
inst/NEWS | 4 ++++
5 files changed, 26 insertions(+), 14 deletions(-)
Title: Simultaneous Inference in General Parametric Models
Diff between multcomp versions 1.3-6 dated 2014-08-18 and 1.3-7 dated 2014-10-02
Description: Simultaneous tests and confidence intervals
for general linear hypotheses in parametric models, including
linear, generalized linear, linear mixed effects, and survival models.
The package includes demos reproducing analyzes presented
in the book "Multiple Comparisons Using R" (Bretz, Hothorn,
Westfall, 2010, CRC Press).
Author: Torsten Hothorn [aut, cre],
Frank Bretz [aut],
Peter Westfall [aut],
Richard M. Heiberger [ctb],
Andre Schuetzenmeister [ctb]
Maintainer: Torsten Hothorn
DESCRIPTION | 12 ++++++------
MD5 | 24 ++++++++++++------------
demo/Ch_Appl.R | 2 +-
inst/NEWS | 4 ++++
inst/doc/chfls1.pdf |binary
inst/doc/generalsiminf.R | 4 ++--
inst/doc/generalsiminf.Rnw | 6 +++---
inst/doc/generalsiminf.pdf |binary
inst/doc/multcomp-examples.R | 2 +-
inst/doc/multcomp-examples.Rnw | 2 +-
inst/doc/multcomp-examples.pdf |binary
vignettes/generalsiminf.Rnw | 6 +++---
vignettes/multcomp-examples.Rnw | 2 +-
13 files changed, 34 insertions(+), 30 deletions(-)
Title: Missing Data Imputation and Model Checking
Diff between mi versions 0.09-18.03 dated 2013-08-26 and 0.09-19 dated 2014-10-02
Description: Missing-data imputation and model checking
Author:
Andrew Gelman
Maintainer: Yu-Sung Su
CHANGELOG | 190 +++++++++++++++++++++++++++++----------------------------
DESCRIPTION | 8 +-
MD5 | 12 +--
NAMESPACE | 12 +++
R/AllGeneric.R | 16 ++--
R/mi.binary.R | 26 +++----
man/mi.Rd | 51 +++++++--------
7 files changed, 164 insertions(+), 151 deletions(-)
Title: Extension of data.frame
Diff between data.table versions 1.9.2 dated 2014-02-27 and 1.9.4 dated 2014-10-02
Description: Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns and a fast file reader (fread). Offers a natural and flexible syntax, for faster development.
Author: M Dowle, T Short, S Lianoglou, A Srinivasan with contributions from R Saporta, E Antonyan
Maintainer: Matt Dowle
data.table-1.9.2/data.table/NEWS |only
data.table-1.9.2/data.table/inst/doc/datatable-timings.R |only
data.table-1.9.2/data.table/inst/doc/datatable-timings.Rnw |only
data.table-1.9.2/data.table/inst/doc/datatable-timings.pdf |only
data.table-1.9.2/data.table/inst/tests/df.txt |only
data.table-1.9.2/data.table/vignettes/datatable-timings.Rnw |only
data.table-1.9.4/data.table/DESCRIPTION | 17
data.table-1.9.4/data.table/MD5 | 129
data.table-1.9.4/data.table/NAMESPACE | 9
data.table-1.9.4/data.table/R/IDateTime.R | 59
data.table-1.9.4/data.table/R/bmerge.R |only
data.table-1.9.4/data.table/R/c.factor.R | 2
data.table-1.9.4/data.table/R/cedta.R | 17
data.table-1.9.4/data.table/R/check_for_seq.r |only
data.table-1.9.4/data.table/R/data.table.R | 1581 ++++----
data.table-1.9.4/data.table/R/duplicated.R | 37
data.table-1.9.4/data.table/R/fcast.R | 118
data.table-1.9.4/data.table/R/fmelt.R | 15
data.table-1.9.4/data.table/R/foverlaps.R |only
data.table-1.9.4/data.table/R/fread.R | 15
data.table-1.9.4/data.table/R/merge.R | 19
data.table-1.9.4/data.table/R/onAttach.R | 3
data.table-1.9.4/data.table/R/onLoad.R | 12
data.table-1.9.4/data.table/R/setkey.R | 285 +
data.table-1.9.4/data.table/R/setops.R |only
data.table-1.9.4/data.table/R/tables.R | 31
data.table-1.9.4/data.table/R/test.data.table.R | 147
data.table-1.9.4/data.table/README.md |only
data.table-1.9.4/data.table/build/vignette.rds |binary
data.table-1.9.4/data.table/inst/doc/datatable-faq.R | 42
data.table-1.9.4/data.table/inst/doc/datatable-faq.Rnw | 123
data.table-1.9.4/data.table/inst/doc/datatable-faq.pdf |binary
data.table-1.9.4/data.table/inst/doc/datatable-intro.R | 66
data.table-1.9.4/data.table/inst/doc/datatable-intro.Rnw | 125
data.table-1.9.4/data.table/inst/doc/datatable-intro.pdf |binary
data.table-1.9.4/data.table/inst/tests/russellCRCRLF.csv |only
data.table-1.9.4/data.table/inst/tests/russellCRLF.csv |only
data.table-1.9.4/data.table/inst/tests/tests.Rraw | 2203 +++++++++---
data.table-1.9.4/data.table/man/copy.Rd |only
data.table-1.9.4/data.table/man/data.table.Rd | 51
data.table-1.9.4/data.table/man/dcast.data.table.Rd | 25
data.table-1.9.4/data.table/man/duplicated.Rd | 36
data.table-1.9.4/data.table/man/foverlaps.Rd |only
data.table-1.9.4/data.table/man/fread.Rd | 12
data.table-1.9.4/data.table/man/melt.data.table.Rd | 8
data.table-1.9.4/data.table/man/rbindlist.Rd | 44
data.table-1.9.4/data.table/man/setDF.Rd |only
data.table-1.9.4/data.table/man/setDT.Rd |only
data.table-1.9.4/data.table/man/setNumericRounding.Rd |only
data.table-1.9.4/data.table/man/setattr.Rd |only
data.table-1.9.4/data.table/man/setkey.Rd | 124
data.table-1.9.4/data.table/man/setorder.Rd |only
data.table-1.9.4/data.table/man/test.data.table.Rd | 3
data.table-1.9.4/data.table/src/assign.c | 141
data.table-1.9.4/data.table/src/bmerge.c | 70
data.table-1.9.4/data.table/src/chmatch.c | 20
data.table-1.9.4/data.table/src/data.table.h |only
data.table-1.9.4/data.table/src/dogroups.c | 161
data.table-1.9.4/data.table/src/fastmean.c | 6
data.table-1.9.4/data.table/src/fastradixdouble.c | 19
data.table-1.9.4/data.table/src/fastradixint.c | 13
data.table-1.9.4/data.table/src/fcast.c | 481 +-
data.table-1.9.4/data.table/src/fmelt.c | 91
data.table-1.9.4/data.table/src/forder.c | 1030 +++--
data.table-1.9.4/data.table/src/frank.c |only
data.table-1.9.4/data.table/src/fread.c | 196 -
data.table-1.9.4/data.table/src/gsumm.c | 236 +
data.table-1.9.4/data.table/src/ijoin.c |only
data.table-1.9.4/data.table/src/init.c | 47
data.table-1.9.4/data.table/src/rbindlist.c | 605 ++-
data.table-1.9.4/data.table/src/reorder.c | 13
data.table-1.9.4/data.table/src/uniqlist.c | 22
data.table-1.9.4/data.table/src/vecseq.c | 5
data.table-1.9.4/data.table/src/wrappers.c | 4
data.table-1.9.4/data.table/tests/tests.R | 1
data.table-1.9.4/data.table/vignettes/datatable-faq.Rnw | 123
data.table-1.9.4/data.table/vignettes/datatable-intro.Rnw | 125
77 files changed, 5890 insertions(+), 2877 deletions(-)
Title: Optimisation with Continuous Convex Piecewise (Linear and
Quadratic) Functions
Diff between ConConPiWiFun versions 0.4.3 dated 2014-10-01 and 0.4.4 dated 2014-10-02
Description: Continuous convex piecewise linear (ccpl) resp. quadratic (ccpq) functions can be implemented with sorted breakpoints and slopes. This includes functions that are ccpl (resp. ccpq) on a convex set (i.e. an interval or a point) and infinite out of the domain. These functions can be very useful for a large class of optimisation problems. Efficient manipulation (such as log(N) insertion) of such data structure is obtained with map standard template library of C++ (that hides balanced trees). This package is a wrapper on such a class based on Rcpp modules.
Author: Robin Girard
Maintainer: Robin Girard
DESCRIPTION | 6 +++---
MD5 | 4 ++--
src/Makevars | 2 +-
3 files changed, 6 insertions(+), 6 deletions(-)
Title: Estimation of the number of fatalities from carcass searches
Diff between carcass versions 1.2 dated 2014-06-10 and 1.3 dated 2014-10-02
Description: The number of bird or bat fatalities from collisions with buildings, towers or wind energy turbines can be estimated based on carcass searches and experimentally assessed carcass persistence times and searcher efficiency. This package provides diverse functions for estimating the probability that a bird or bat that died is found by a searcher. It further provides a function to obtain a posterior distribution of the number of fatalities based on the number of carcasses found and the estimated detection probability.
Author: Fraenzi Korner-Nievergelt, Ivo Niermann, Oliver Behr, Matthew A. Etterson, Robert Brinkmann, Pius Korner, Barbara Hellriegel, Tobias Roth, Manuela M. P. Huso, Dan Dalthorp
Maintainer: Fraenzi Korner-Nievergelt
DESCRIPTION | 14 -
MD5 | 24 +-
NAMESPACE | 2
R/estimateN.r | 103 +++++++++-
R/integrate.persistence.r |only
R/pkorner.R | 142 +++++++-------
R/search.efficiency.r | 410 ++++++++++++++++++++++---------------------
R/shapeparameter.R | 4
man/carcass-package.Rd | 15 +
man/estimateN.Rd | 30 ++-
man/integrate.persistence.Rd |only
man/phuso.Rd | 15 +
man/pkorner.Rd | 5
man/search.efficiency.Rd | 2
14 files changed, 458 insertions(+), 308 deletions(-)