Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-03-05 0.9.5
2013-09-26 0.8.6
2013-02-06 0.8.5
2012-01-25 0.8.4
2010-04-27 0.7.1
2010-04-09 0.7.0
2009-12-30 0.6.0
2009-05-05 0.5.1
Title: Functions for Clustering of Presence-Absence, Abundance and
Multilocus Genetic Data
Diff between prabclus versions 2.2-5 dated 2015-01-13 and 2.2-6 dated 2015-01-14
Description: Distance-based parametric bootstrap tests for clustering with
spatial neighborhood information. Some distance measures,
Clustering of presence-absence, abundance and multilocus genetical data
for species delimitation, nearest neighbor
based noise detection. Try package?prabclus for on overview.
Author: Christian Hennig
Maintainer: Christian Hennig
DESCRIPTION | 30
MD5 | 59
R/abundfunctions.R | 31
R/geodist.R | 4
R/prabclust.R | 4
data/kykladspecreg.rda |binary
data/waterdist.rda |binary
man/alleleconvert.Rd | 9
man/autoconst.Rd | 1
man/coord2dist.Rd | 1
man/crmatrix.Rd | 4
man/dicedist.Rd | 1
man/distratio.Rd | 1
man/geco.Rd | 1
man/homogen.test.Rd | 1
man/jaccard.Rd | 1
man/kulczynski.Rd | 1
man/lociplots.Rd | 3
man/piecewiselin.Rd | 1
man/pop.sim.Rd | 1
man/prab.sarestimate.Rd | 1
man/prabclust.Rd | 2
man/prabtest.Rd | 1
man/qkulczynski.Rd | 1
man/regpop.sar.Rd | 1
man/specgroups.Rd | 1
man/stressvals.Rd | 1
tests/Examples/prabclus-Ex.Rout.save | 9289 ++++++++++++++---------------------
tests/donttestexamples.R |only
tests/prabclustests.R | 3
tests/prabclustests.Rout.save | 669 +-
31 files changed, 4119 insertions(+), 6004 deletions(-)
Title: Mapping Fisheries Data and Spatial Analysis Tools
Diff between PBSmapping versions 2.67.60 dated 2014-04-05 and 2.68.68 dated 2015-01-14
Description: This software has evolved from fisheries research conducted at the
Pacific Biological Station (PBS) in Nanaimo, British Columbia, Canada. It
extends the R language to include two-dimensional plotting features similar
to those commonly available in a Geographic Information System (GIS).
Embedded C code speeds algorithms from computational geometry, such as
finding polygons that contain specified point events or converting between
longitude-latitude and Universal Transverse Mercator (UTM) coordinates.
Additionally, we include C++ code developed by Angus Johnson for the Clipper
library. PBSmapping also includes data for a global shoreline and other
data sets in the public domain. The R directory `.../library/PBSmapping/doc'
offers a complete user's guide PBSmapping-UG.pdf, which should be consulted
to use all functions in the package effectively.
Author: Jon T. Schnute
Maintainer: Rowan Haigh
DESCRIPTION | 22
MD5 | 44 -
R/PBSmapping.r | 467 ++++++-----
R/zzz.r | 6
data/bcBathymetry.rda |binary
data/pythagoras.rda |binary
data/surveyData.rda |binary
data/towData.rda |binary
inst/Utils/00ReadMe.txt | 94 +-
inst/Utils/Makefile | 37
inst/Utils/clipPolys.cpp | 1774 +++++++++++++++++++++---------------------
inst/Utils/convUL.cpp | 914 ++++++++++-----------
inst/Utils/findPolys.cpp | 1624 +++++++++++++++++++-------------------
inst/Utils/makeUtils.bat | 1
inst/doc/ChangeLog.txt | 23
inst/doc/PBSmappingIntro.pdf |binary
inst/doc/index.html | 12
man/findCells.Rd | 23
man/findPolys.Rd | 18
src/clipper.cpp | 968 +++++++++++++---------
src/clipper.h | 38
src/clipperWrapper.cpp | 35
vignettes/PBSmappingIntro.Rnw | 4
23 files changed, 3192 insertions(+), 2912 deletions(-)
Title: Spatial Oblique Decision Tree
Diff between SPODT versions 0.9 dated 2014-04-24 and 0.9-1 dated 2015-01-14
Description: SPODT is a spatial partitioning method based on oblique decision trees, in order to classify study area into zones of different risks, determining their boundaries
Author: Jean Gaudart, Nathalie Graffeo, Guillaume Barbet, Bernard Fichet, Roch Giorgi (Aix-Marseille University)
Maintainer: Jean Gaudart
DESCRIPTION | 6 +++---
MD5 | 43 ++++++++++++++++++++++---------------------
inst |only
man/SPODT-package.Rd | 1 +
man/dataBALL0.Rd | 1 +
man/dataBALL0_5.Rd | 1 +
man/dataBALL1_5.Rd | 1 +
man/dataBALL2.Rd | 1 +
man/dataCOV.Rd | 1 +
man/dataMALARIA.Rd | 1 +
man/dataSQUARE0.Rd | 1 +
man/dataSQUARE0_5.Rd | 1 +
man/dataSQUARE1_5.Rd | 1 +
man/dataSQUARE2.Rd | 1 +
man/dataV0.Rd | 1 +
man/dataV0_5.Rd | 1 +
man/dataV1_5.Rd | 1 +
man/dataV2.Rd | 1 +
man/spodt-class.Rd | 1 +
man/spodt.Rd | 1 +
man/spodt.tree.Rd | 1 +
man/spodtSpatialLines.Rd | 1 +
man/test.spodt.Rd | 1 +
23 files changed, 45 insertions(+), 24 deletions(-)
Title: Plotting (social) networks on maps
Diff between spnet versions 0.9.0.1 dated 2014-07-31 and 0.9.0.6 dated 2015-01-14
Description: The package provides methods for dealing with spatial social
networks. It allows to plot networks for which actors have a specific
location on a map (cities, participants in a political debate, etc.).
SpatialPolygons objects from the sp package are supported.
Author: Emmanuel Rousseaux, Marion Deville, Gilbert Ritschard
Maintainer: Emmanuel Rousseaux
spnet-0.9.0.1/spnet/R/room.create.grid.r |only
spnet-0.9.0.1/spnet/man/room.create.grid.Rd |only
spnet-0.9.0.1/spnet/man/room.create.u.Rd |only
spnet-0.9.0.1/spnet/man/spnet.network.arrow.head.length-set.Rd |only
spnet-0.9.0.1/spnet/man/spnet.network.arrow.head.length.Rd |only
spnet-0.9.0.1/spnet/man/spnet.network.arrow.shortening-set.Rd |only
spnet-0.9.0.1/spnet/man/spnet.network.arrow.shortening.Rd |only
spnet-0.9.0.1/spnet/man/spnet.network.arrow.translate.x-set.Rd |only
spnet-0.9.0.1/spnet/man/spnet.network.arrow.translate.x.Rd |only
spnet-0.9.0.1/spnet/man/spnet.network.arrow.translate.y-set.Rd |only
spnet-0.9.0.1/spnet/man/spnet.network.arrow.translate.y.Rd |only
spnet-0.9.0.1/spnet/man/spnet.symbol.translate.x-set.Rd |only
spnet-0.9.0.1/spnet/man/spnet.symbol.translate.x.Rd |only
spnet-0.9.0.1/spnet/man/spnet.symbol.translate.y-set.Rd |only
spnet-0.9.0.1/spnet/man/spnet.symbol.translate.y.Rd |only
spnet-0.9.0.6/spnet/DESCRIPTION | 20
spnet-0.9.0.6/spnet/MD5 | 220 +-
spnet-0.9.0.6/spnet/NAMESPACE | 47
spnet-0.9.0.6/spnet/R/SpatialNetwork.r | 1028 +++++++---
spnet-0.9.0.6/spnet/R/plot.position.r | 20
spnet-0.9.0.6/spnet/R/spnet.example.basic.r | 81
spnet-0.9.0.6/spnet/R/world.map.simplified.r |only
spnet-0.9.0.6/spnet/R/zzz.r | 2
spnet-0.9.0.6/spnet/data |only
spnet-0.9.0.6/spnet/inst/CITATION | 43
spnet-0.9.0.6/spnet/inst/doc/spnet-overview.pdf |binary
spnet-0.9.0.6/spnet/man/SpatialNetwork.Rd | 8
spnet-0.9.0.6/spnet/man/extract-methods.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.barplot.bgcolor-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.barplot.bgcolor.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.barplot.bound.lower-set.Rd | 7
spnet-0.9.0.6/spnet/man/spnet.barplot.bound.lower.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.barplot.bound.upper-set.Rd | 7
spnet-0.9.0.6/spnet/man/spnet.barplot.bound.upper.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.barplot.fgcolor-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.barplot.fgcolor.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.barplot.list-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.barplot.list.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.barplot.variable-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.barplot.variable.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.barplot.width-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.barplot.width.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.color.background-set.Rd |only
spnet-0.9.0.6/spnet/man/spnet.color.background.Rd |only
spnet-0.9.0.6/spnet/man/spnet.color.border-set.Rd |only
spnet-0.9.0.6/spnet/man/spnet.color.border.Rd |only
spnet-0.9.0.6/spnet/man/spnet.color.legend-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.color.legend.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.color.list-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.color.list.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.color.node-set.Rd |only
spnet-0.9.0.6/spnet/man/spnet.color.node.Rd |only
spnet-0.9.0.6/spnet/man/spnet.color.region-set.Rd |only
spnet-0.9.0.6/spnet/man/spnet.color.region.Rd |only
spnet-0.9.0.6/spnet/man/spnet.color.variable-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.color.variable.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.create.Rd | 37
spnet-0.9.0.6/spnet/man/spnet.example.basic.Rd | 8
spnet-0.9.0.6/spnet/man/spnet.get.local.user.manual.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.label.cex-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.label.cex.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.label.color-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.label.color.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.label.list-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.label.list.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.label.variable-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.label.variable.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.layout.list-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.layout.list.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.legend.cex-set.Rd |only
spnet-0.9.0.6/spnet/man/spnet.legend.cex.Rd |only
spnet-0.9.0.6/spnet/man/spnet.legend.horiz-set.Rd |only
spnet-0.9.0.6/spnet/man/spnet.legend.horiz.Rd |only
spnet-0.9.0.6/spnet/man/spnet.legend.line.width-set.Rd |only
spnet-0.9.0.6/spnet/man/spnet.legend.line.width.Rd |only
spnet-0.9.0.6/spnet/man/spnet.legend.list-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.legend.list.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.legend.ncol-set.Rd |only
spnet-0.9.0.6/spnet/man/spnet.legend.ncol.Rd |only
spnet-0.9.0.6/spnet/man/spnet.legend.print-set.Rd |only
spnet-0.9.0.6/spnet/man/spnet.legend.print.Rd |only
spnet-0.9.0.6/spnet/man/spnet.map-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.map.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.map.plot.position.Rd | 26
spnet-0.9.0.6/spnet/man/spnet.network.arrow.color-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.network.arrow.color.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.network.arrow.head.lth-set.Rd |only
spnet-0.9.0.6/spnet/man/spnet.network.arrow.head.lth.Rd |only
spnet-0.9.0.6/spnet/man/spnet.network.arrow.head.type-set.Rd | 7
spnet-0.9.0.6/spnet/man/spnet.network.arrow.head.type.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.network.arrow.opacity-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.network.arrow.opacity.Rd | 9
spnet-0.9.0.6/spnet/man/spnet.network.arrow.shift.x-set.Rd |only
spnet-0.9.0.6/spnet/man/spnet.network.arrow.shift.x.Rd |only
spnet-0.9.0.6/spnet/man/spnet.network.arrow.shift.y-set.Rd |only
spnet-0.9.0.6/spnet/man/spnet.network.arrow.shift.y.Rd |only
spnet-0.9.0.6/spnet/man/spnet.network.arrow.shorten-set.Rd |only
spnet-0.9.0.6/spnet/man/spnet.network.arrow.shorten.Rd |only
spnet-0.9.0.6/spnet/man/spnet.network.arrow.thickness-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.network.arrow.thickness.Rd | 9
spnet-0.9.0.6/spnet/man/spnet.network.data-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.network.data.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.network.exists.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.network.label-set.Rd | 7
spnet-0.9.0.6/spnet/man/spnet.network.label.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.network.list-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.network.list.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.networks.add-set.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.networks.list-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.networks.list.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.networks.remove-set.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.par.list-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.par.list.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.symbol.cex-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.symbol.cex.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.symbol.color-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.symbol.color.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.symbol.legend-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.symbol.legend.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.symbol.list-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.symbol.list.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.symbol.shift.x-set.Rd |only
spnet-0.9.0.6/spnet/man/spnet.symbol.shift.x.Rd |only
spnet-0.9.0.6/spnet/man/spnet.symbol.shift.y-set.Rd |only
spnet-0.9.0.6/spnet/man/spnet.symbol.shift.y.Rd |only
spnet-0.9.0.6/spnet/man/spnet.symbol.variable-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.symbol.variable.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.title.list-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.title.list.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.title.main-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.title.main.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.title.sub-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.title.sub.Rd | 3
spnet-0.9.0.6/spnet/man/world.map.simplified.Rd |only
135 files changed, 1221 insertions(+), 637 deletions(-)
Title: Geostatistical Modelling of Spatially Referenced Prevalence Data
Diff between PrevMap versions 1.1.3 dated 2014-12-11 and 1.1.4 dated 2015-01-14
Description: It provides functions for both likelihood-based
and Bayesian analysis of spatially referenced prevalence data. 'PrevMap' is
also an extension of the 'geoR' package which should be installed first
together with the 'maxLik', 'raster' and 'pdist' packages.
Author: Emanuele Giorgi, Peter J. Diggle
Maintainer: Emanuele Giorgi
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/foo.R | 21 ++++++++++++---------
man/spatial.pred.binomial.MCML.Rd | 2 +-
4 files changed, 20 insertions(+), 17 deletions(-)
Title: Tools for Ecological Network Analysis (ena)
Diff between enaR versions 2.8 dated 2014-11-01 and 2.8.1 dated 2015-01-14
Description: Functions for the analysis of ecological networks
Author: M.K. Lau, S.R. Borrett, D.E. Hines, P. Singh
Maintainer: Matthew K. Lau
DESCRIPTION | 12 +--
MD5 | 92 ++++++++++++-------------
R/read.scor.R | 3
man/TES.Rd | 2
man/TET.Rd | 2
man/as.extended.Rd | 2
man/bal.Rd | 2
man/balance.Rd | 2
man/bcratio.Rd | 2
man/cycliv.Rd | 2
man/eigenCentrality.Rd | 2
man/enaAll.Rd | 2
man/enaAscendency.Rd | 156 +++++++++++++++++++++-----------------------
man/enaControl.Rd | 2
man/enaCycle.Rd | 2
man/enaEnviron.Rd | 2
man/enaFlow.Rd | 2
man/enaMTI.Rd | 2
man/enaModelInfo.Rd | 2
man/enaModels.Rd | 2
man/enaR-package.Rd | 6 +
man/enaStorage.Rd | 2
man/enaStructure.Rd | 2
man/enaTroAgg.Rd | 2
man/enaUtility.Rd | 2
man/environCentrality.Rd | 2
man/findPathLength.Rd | 2
man/force.balance.Rd | 2
man/get.ns.Rd | 2
man/get.orient.Rd | 2
man/m.list.Rd | 2
man/mExp.Rd | 2
man/netOrder.Rd | 2
man/oyster.Rd | 2
man/pack.Rd | 2
man/read.enam.Rd | 2
man/read.nea.Rd | 2
man/read.scor.Rd | 2
man/read.wand.Rd | 2
man/scc.Rd | 2
man/scifix.Rd | 2
man/set.orient.Rd | 2
man/ssCheck.Rd | 2
man/structure.statistics.Rd | 2
man/troModels.Rd | 2
man/unpack.Rd | 6 -
man/write.nea.Rd | 2
47 files changed, 176 insertions(+), 181 deletions(-)
Title: Extended hierarchical logistic regression (Huisman-Olff-Fresco)
models
Diff between eHOF versions 1.5.4 dated 2014-11-01 and 1.5.7 dated 2015-01-14
Description: Extended and enhanced hierarchical logistic regression models, so-called Huisman-Olff-Fresco models. Response curves along one-dimensional gradients including no response, monotone, plateau, unimodal and bimodal models.
Author: Florian Jansen, Jari Oksanen
Maintainer: Florian Jansen
DESCRIPTION | 18 ++++++------
MD5 | 54 +++++++++++++++++++++++---------------
R/HOF.fun.r | 9 +-----
R/HOF.model.r | 8 ++---
R/Para.deriv.r | 13 +++++----
R/Para.opt.r | 75 ++++++++++++++++++++++++++---------------------------
R/autolayout.r | 10 ++++---
R/coef.HOF.r | 27 +++++++------------
R/pick.model.r | 34 ++++++++++++++----------
R/plot.HOF.list.r | 10 ++-----
R/plot.HOF.r | 8 ++---
R/print.HOF.list.r | 2 -
R/print.HOF.r | 25 +++++++----------
R/zzz.r | 4 ++
build/vignette.rds |binary
inst/ChangeLog | 6 ++++
inst/doc/eHOF.R | 7 ++--
inst/doc/eHOF.Rnw | 11 ++++---
inst/doc/eHOF.pdf |binary
man/HOF.Rd | 7 ++--
man/autolayout.Rd | 6 ++--
vignettes/eHOF.Rnw | 11 ++++---
vignettes/figure |only
23 files changed, 184 insertions(+), 161 deletions(-)
Title: Bayesian Inference on Causal Genetic Variants using Affected
Sib-Pairs Data
Diff between ASPBay versions 1.1 dated 2014-12-09 and 1.2 dated 2015-01-14
Description: This package allows to make inference on the properties of causal genetic
variants in linkage disequilibrium with genotyped markers. In a first step,
we select a subset of variants using a score statistic for affected
sib-pairs. In a second step, on the selected subset, we make
inference on causal genetic variants in the considered region.
Author: Claire Dandine-Roulland
Maintainer: Claire Dandine-Roulland
DESCRIPTION | 6 +++---
MD5 | 20 ++++++++++----------
R/ASP.Bayesian.R | 12 ++++++------
R/ASP.Score.R | 8 ++++----
R/Graphs.Bayesian.R | 14 +++++++-------
R/cred_int.R | 2 +-
R/graph_cred_int.R | 21 +++------------------
inst/doc/ASPBay.pdf |binary
man/ASP.Bayesian.Rd | 3 ++-
src/MH.cpp | 6 +++---
src/RcppExports.cpp | 7 ++++---
11 files changed, 43 insertions(+), 56 deletions(-)
Title: Automatic Generation of Exams in R
Diff between exams versions 2.0-1 dated 2014-12-26 and 2.0-2 dated 2015-01-14
Description: Sweave-based automatic generation of exams including multiple-choice
questions and arithmetic problems. Exams can be produced in various formats, including
PDF, HTML, Moodle XML, QTI 1.2 (for OLAT/OpenOLAT), QTI 2.1.
Author: Achim Zeileis [aut, cre],
Bettina Gruen [aut],
Friedrich Leisch [aut],
Nikolaus Umlauf [aut],
Dominik Ernst [ctb]
Maintainer: Achim Zeileis
DESCRIPTION | 10 +++++-----
MD5 | 20 ++++++++++----------
NEWS | 7 +++++++
R/exams2pdf.R | 6 +++---
R/exams2qti21.R | 1 -
R/exams_skeleton.R | 7 ++++++-
R/transformers.R | 9 ++++++---
build/vignette.rds |binary
inst/doc/exams.pdf |binary
inst/doc/exams2.pdf |binary
man/exams2pdf.Rd | 6 ++++--
11 files changed, 41 insertions(+), 25 deletions(-)
Title: Basic Robust Statistics
Diff between robustbase versions 0.92-2 dated 2014-11-22 and 0.92-3 dated 2015-01-14
Description: "Essential" Robust Statistics.
Tools allowing to analyze data with robust methods. This includes
regression methodology including model selections and multivariate
statistics where we strive to cover the book "Robust Statistics,
Theory and Methods" by Maronna, Martin and Yohai; Wiley 2006.
Author: Original code by many authors, notably
Peter Rousseeuw and Christophe Croux, see file 'Copyrights';
Valentin Todorov
Maintainer: Martin Maechler
ChangeLog | 32 +++++++
DESCRIPTION | 13 +--
MD5 | 117 +++++++++++++++-------------
NAMESPACE | 7 +
R/AAA.R | 3
R/adjoutlyingness.R | 49 ++++++------
R/comedian.R |only
R/covMcd.R | 166 +++++++++++++++++++++++++++--------------
R/covPlot.R | 4
R/detmcd.R | 51 +++++-------
R/glmrob.R | 4
R/ltsPlot.R | 4
R/ltsReg.R | 5 -
R/mc.R | 15 ++-
R/nlrob.R | 2
R/rrcov.control.R | 19 ++--
R/tolEllipse.R | 4
TODO | 2
build/vignette.rds |binary
inst/doc/fastMcd-kmini.pdf |binary
inst/doc/lmrob_simulation.R | 24 +++--
inst/doc/lmrob_simulation.Rnw | 15 ++-
inst/doc/lmrob_simulation.pdf |binary
inst/doc/psi_functions.Rnw | 4
inst/doc/psi_functions.pdf |binary
inst/xtraR/ex-funs.R | 24 -----
inst/xtraR/plot-psiFun.R | 2
inst/xtraR/test_MCD.R | 3
man/M.psi.Rd | 15 +++
man/adjOutlyingness.Rd | 15 ++-
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man/mc.Rd | 6 -
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man/rrcov.control.Rd | 19 +++-
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src/mc.c | 26 +++---
src/rffastmcd.f | 21 ++---
src/rob-utils.c |only
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src/rowMedians.c |only
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src/templates-types_undef.h |only
tests/comedian-tst.R |only
tests/glmrob-1.R | 2
tests/lmrob-psifns.R | 1
tests/lmrob-psifns.Rout.save | 14 +--
tests/m-s-estimator.R | 1
tests/mc-strict.R | 106 +++++++++++++++++++++++---
tests/nlregrob-tst.R | 3
tests/nlrob-tst.R | 2
vignettes/lmrob_simulation.Rnw | 15 ++-
vignettes/psi-GGW.pdf |binary
vignettes/psi-Hampel.pdf |binary
vignettes/psi-Huber.pdf |binary
vignettes/psi-LQQ.pdf |binary
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vignettes/psi-optimal.pdf |binary
vignettes/psi_functions.Rnw | 4
65 files changed, 580 insertions(+), 317 deletions(-)
Title: Inference on High Dimensional Max-Stable Distributions
Diff between HiDimMaxStable versions 0.1 dated 2014-10-08 and 0.1.1 dated 2015-01-14
More information about HiDimMaxStable at CRAN
Description: Inference of high dimensional max-stable
distributions, from the paper "Likelihood based inference for
high-dimensional extreme value distributions", by A. Bienvenüe
and C. Robert, arXiv:1403.0065 [stat.AP].
Author: Alexis Bienvenüe [aut, cre],
Christian Robert [aut]
Maintainer: Alexis Bienvenüe
DESCRIPTION | 8 ++++----
MD5 | 14 +++++++-------
man/dens.grid.Rd | 31 ++++++++++++++++++-------------
man/excess.censor.Rd | 2 +-
man/excess.l.Rd | 2 ++
man/maxgrid.Rd | 4 ++--
man/maxlik.Rd | 50 +++++++++++++++++++++++++++++---------------------
man/simultoccur.l.Rd | 4 +++-
8 files changed, 66 insertions(+), 49 deletions(-)
Permanent link
Title: Simulation and Analysis of Random Fields
Diff between RandomFields versions 3.0.44 dated 2014-10-01 and 3.0.55 dated 2015-01-14
Description: Simulation of Gaussian and extreme value random fields;
conditional simulation; kriging; maximum likelihood estimation
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], Peter Menck [ctr], Sebastian Gross [aut], 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
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RandomFields-3.0.55/RandomFields/R/Crossvalidation.R | 6
RandomFields-3.0.55/RandomFields/R/D.H.R | 33
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RandomFields-3.0.55/RandomFields/R/convert.R | 213 +-
RandomFields-3.0.55/RandomFields/R/fitgauss.R | 432 ++--
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RandomFields-3.0.55/RandomFields/man/RFgetModelNames.Rd | 54
RandomFields-3.0.55/RandomFields/man/RFgridDataFrame-class.Rd | 8
RandomFields-3.0.55/RandomFields/man/RFinterpolate.Rd | 40
RandomFields-3.0.55/RandomFields/man/RFoptions.Rd | 798 ++++----
RandomFields-3.0.55/RandomFields/man/RFpointsDataFrame-class.Rd | 16
RandomFields-3.0.55/RandomFields/man/RFratiotest.Rd | 9
RandomFields-3.0.55/RandomFields/man/RFsimulate.Rd | 41
RandomFields-3.0.55/RandomFields/man/RFsimulate.more.examples.Rd | 2
RandomFields-3.0.55/RandomFields/man/RFsimulateAdvanced.Rd | 2
RandomFields-3.0.55/RandomFields/man/RFspatialGridDataFrame-class.Rd | 8
RandomFields-3.0.55/RandomFields/man/RFspatialPointsDataFrame-class.Rd | 16
RandomFields-3.0.55/RandomFields/man/RMS.Rd | 2
RandomFields-3.0.55/RandomFields/man/RMbcw.Rd | 7
RandomFields-3.0.55/RandomFields/man/RMcutoff.Rd | 2
RandomFields-3.0.55/RandomFields/man/RMgneiting.Rd | 2
RandomFields-3.0.55/RandomFields/man/RMkolmogorov.Rd | 4
RandomFields-3.0.55/RandomFields/man/RMmodel.Rd | 4
RandomFields-3.0.55/RandomFields/man/RMmodelgenerator-class.Rd | 2
RandomFields-3.0.55/RandomFields/man/RMmodelsAuxiliary.Rd | 3
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RandomFields-3.0.55/RandomFields/man/RMspheric.Rd | 8
RandomFields-3.0.55/RandomFields/man/RMtrafo.Rd | 49
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RandomFields-3.0.55/RandomFields/man/conventional2RFspDataFrame.Rd | 36
RandomFields-3.0.55/RandomFields/man/internal.Rd | 23
RandomFields-3.0.55/RandomFields/man/obsolete.Rd | 13
RandomFields-3.0.55/RandomFields/man/papers.SBS14.Rd | 25
RandomFields-3.0.55/RandomFields/man/papers.jss14.Rd | 39
RandomFields-3.0.55/RandomFields/man/plot-method.Rd | 25
RandomFields-3.0.55/RandomFields/man/soil.Rd | 12
RandomFields-3.0.55/RandomFields/man/weather.Rd | 1
RandomFields-3.0.55/RandomFields/src/AutoRandomFields.cc |only
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RandomFields-3.0.55/RandomFields/src/Brown.cc | 185 -
RandomFields-3.0.55/RandomFields/src/Coordinate_systems.cc |only
RandomFields-3.0.55/RandomFields/src/Covariance.h | 110 -
RandomFields-3.0.55/RandomFields/src/Families.h |only
RandomFields-3.0.55/RandomFields/src/Gneiting.cc | 36
RandomFields-3.0.55/RandomFields/src/Huetchen.cc | 352 ++-
RandomFields-3.0.55/RandomFields/src/InternalCov.cc | 791 ++------
RandomFields-3.0.55/RandomFields/src/KeyInfo.cc | 253 +-
RandomFields-3.0.55/RandomFields/src/MLE.cc | 115 -
RandomFields-3.0.55/RandomFields/src/Makevars.in | 2
RandomFields-3.0.55/RandomFields/src/Primitive.cc | 489 ++---
RandomFields-3.0.55/RandomFields/src/RF.h | 767 +++-----
RandomFields-3.0.55/RandomFields/src/RandomFields.h | 32
RandomFields-3.0.55/RandomFields/src/Specific.cc | 10
RandomFields-3.0.55/RandomFields/src/SpherModels.cc |only
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RandomFields-3.0.55/RandomFields/src/auxiliary.cc | 392 ++++
RandomFields-3.0.55/RandomFields/src/auxiliary.h | 37
RandomFields-3.0.55/RandomFields/src/avltr_modified.cc | 2
RandomFields-3.0.55/RandomFields/src/basic.h | 42
RandomFields-3.0.55/RandomFields/src/circulant.cc | 151 -
RandomFields-3.0.55/RandomFields/src/direct.cc | 67
RandomFields-3.0.55/RandomFields/src/empvario.cc | 2
RandomFields-3.0.55/RandomFields/src/error.h | 10
RandomFields-3.0.55/RandomFields/src/extremes.cc | 945 ++++------
RandomFields-3.0.55/RandomFields/src/families.cc |only
RandomFields-3.0.55/RandomFields/src/fftVario.cc | 2
RandomFields-3.0.55/RandomFields/src/gauss.cc | 134 -
RandomFields-3.0.55/RandomFields/src/getNset.cc | 677 +++----
RandomFields-3.0.55/RandomFields/src/hilfsdateien.cc |only
RandomFields-3.0.55/RandomFields/src/hyperplan.cc | 114 -
RandomFields-3.0.55/RandomFields/src/initNerror.cc | 731 ++++---
RandomFields-3.0.55/RandomFields/src/initNerrorSpherModels.h |only
RandomFields-3.0.55/RandomFields/src/kriging.cc | 6
RandomFields-3.0.55/RandomFields/src/nugget.cc | 43
RandomFields-3.0.55/RandomFields/src/operator.cc | 511 ++++-
RandomFields-3.0.55/RandomFields/src/plusmalS.cc | 496 ++---
RandomFields-3.0.55/RandomFields/src/primitive.h | 38
RandomFields-3.0.55/RandomFields/src/rf_interfaces.cc |only
RandomFields-3.0.55/RandomFields/src/sequential.cc | 100 -
RandomFields-3.0.55/RandomFields/src/shape_processes.h |only
RandomFields-3.0.55/RandomFields/src/spectral.cc | 32
RandomFields-3.0.55/RandomFields/src/startGetNset.cc | 150 -
RandomFields-3.0.55/RandomFields/src/tbm.cc | 156 -
RandomFields-3.0.55/RandomFields/src/trend.cc | 103 -
RandomFields-3.0.55/RandomFields/src/userinterfaces.cc | 696 ++-----
RandomFields-3.0.55/RandomFields/src/variogramAndCo.cc | 233 --
RandomFields-3.0.55/RandomFields/src/variogramAndCo.h |only
155 files changed, 7147 insertions(+), 6146 deletions(-)
Title: A Grammar of Data Manipulation
Diff between dplyr versions 0.4.0 dated 2015-01-08 and 0.4.1 dated 2015-01-14
Description: A fast, consistent tool for working with data frame like objects,
both in memory and out of memory.
Author: Hadley Wickham [aut, cre],
Romain Francois [aut],
RStudio [cph]
Maintainer: Hadley Wickham
DESCRIPTION | 16 ++++-----
MD5 | 42 +++++++++++++-------------
R/funs.R | 4 +-
inst/doc/data_frames.html | 58 ++++++++++++++++++------------------
inst/doc/databases.html | 24 +++++++-------
inst/doc/hybrid-evaluation.html | 4 +-
inst/doc/introduction.html | 20 ++++++------
inst/doc/new-sql-backend.html | 4 +-
inst/doc/nse.html | 4 +-
inst/doc/two-table.html | 4 +-
inst/doc/window-functions.html | 16 ++++-----
man/funs.Rd | 4 +-
src/RcppExports.cpp | 1
src/group_indices.cpp | 2 +
tests/testthat/helper-data.r | 4 --
tests/testthat/test-filter.r | 2 -
tests/testthat/test-group-by.r | 6 +--
tests/testthat/test-group-indices.R | 11 ++++++
tests/testthat/test-joins.r | 16 ++++-----
tests/testthat/test-mutate.r | 2 -
tests/testthat/test-sample.R | 4 +-
tests/testthat/test-select.r | 2 -
22 files changed, 130 insertions(+), 120 deletions(-)
Title: Interface to PHAST Software for Comparative Genomics
Diff between rphast versions 1.5 dated 2013-12-13 and 1.6 dated 2015-01-14
Description: RPHAST is an R interface to the PHAST software
(Phylogenetic Analysis with Space/Time Models). It can be used for
many types of analysis in comparative and evolutionary genomics,
such as estimating models of evolution from sequence data, scoring
alignments for conservation or acceleration, and predicting
elements based on conservation or custom phylogenetic hidden Markov
models. It can also perform many basic operations on multiple
sequence alignments and phylogenetic trees.
Author: Melissa Hubisz, Katherine Pollard, and Adam Siepel
Maintainer: Melissa Hubisz
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rphast-1.5/rphast/inst/doc/vignette2.pdf |only
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rphast-1.6/rphast/DESCRIPTION | 19
rphast-1.6/rphast/LICENSE | 4
rphast-1.6/rphast/MD5 | 403 +--
rphast-1.6/rphast/NAMESPACE | 82
rphast-1.6/rphast/build/vignette.rds |binary
rphast-1.6/rphast/cleanup | 2
rphast-1.6/rphast/configure | 2744 ++-------------------
rphast-1.6/rphast/configure.ac | 518 ---
rphast-1.6/rphast/inst/doc/vignette1.Rnw | 2
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rphast-1.6/rphast/man/add.signals.feat.Rd | 27
rphast-1.6/rphast/man/alphabet.msa.Rd | 12
rphast-1.6/rphast/man/apply.bgc.sel.Rd | 21
rphast-1.6/rphast/man/as.data.frame.feat.Rd | 30
rphast-1.6/rphast/man/as.list.tm.Rd | 15
rphast-1.6/rphast/man/as.pointer.feat.Rd | 20
rphast-1.6/rphast/man/as.pointer.msa.Rd | 17
rphast-1.6/rphast/man/as.track.feat.Rd | 38
rphast-1.6/rphast/man/as.track.msa.Rd | 69
rphast-1.6/rphast/man/as.track.wig.Rd | 60
rphast-1.6/rphast/man/base.freq.msa.Rd | 37
rphast-1.6/rphast/man/bgc.informative.Rd | 45
rphast-1.6/rphast/man/bgc.nucleotide.tests.Rd | 41
rphast-1.6/rphast/man/bgc.sel.factor.Rd | 20
rphast-1.6/rphast/man/branchlength.tree.Rd | 14
rphast-1.6/rphast/man/classify.muts.bgc.Rd | 22
rphast-1.6/rphast/man/codon.clean.msa.Rd | 50
rphast-1.6/rphast/man/col.expected.subs.msa.Rd | 18
rphast-1.6/rphast/man/complement.Rd | 15
rphast-1.6/rphast/man/composition.feat.Rd | 32
rphast-1.6/rphast/man/concat.msa.Rd | 32
rphast-1.6/rphast/man/convert.coords.feat.Rd | 71
rphast-1.6/rphast/man/coord.range.msa.Rd | 22
rphast-1.6/rphast/man/copy.feat.Rd | 21
rphast-1.6/rphast/man/copy.msa.Rd | 22
rphast-1.6/rphast/man/coverage.feat.Rd | 54
rphast-1.6/rphast/man/density.feat.Rd | 22
rphast-1.6/rphast/man/depth.tree.Rd | 20
rphast-1.6/rphast/man/dim.feat.Rd | 14
rphast-1.6/rphast/man/dim.msa.Rd | 15
rphast-1.6/rphast/man/enrichment.feat.Rd | 42
rphast-1.6/rphast/man/expected.subs.msa.Rd | 19
rphast-1.6/rphast/man/extract.feature.msa.Rd | 40
rphast-1.6/rphast/man/feat.Rd | 83
rphast-1.6/rphast/man/fix.semicolon.tree.Rd | 19
rphast-1.6/rphast/man/fix.start.stop.feat.Rd | 31
rphast-1.6/rphast/man/flatten.feat.Rd | 18
rphast-1.6/rphast/man/freq3x4.msa.Rd | 18
rphast-1.6/rphast/man/from.pointer.feat.Rd | 16
rphast-1.6/rphast/man/from.pointer.msa.Rd | 17
rphast-1.6/rphast/man/gc.content.msa.Rd | 26
rphast-1.6/rphast/man/get.rate.matrix.params.tm.Rd | 26
rphast-1.6/rphast/man/get4d.msa.Rd | 34
rphast-1.6/rphast/man/guess.format.msa.Rd | 28
rphast-1.6/rphast/man/hist.feat.Rd | 18
rphast-1.6/rphast/man/hmm.Rd | 32
rphast-1.6/rphast/man/informative.regions.msa.Rd | 67
rphast-1.6/rphast/man/inverse.feat.Rd | 28
rphast-1.6/rphast/man/is.format.msa.Rd | 24
rphast-1.6/rphast/man/is.msa.Rd | 12
rphast-1.6/rphast/man/is.ordered.msa.Rd | 13
rphast-1.6/rphast/man/is.subst.mod.tm.Rd | 16
rphast-1.6/rphast/man/is.tm.Rd | 12
rphast-1.6/rphast/man/is.track.Rd | 14
rphast-1.6/rphast/man/label.branches.Rd | 30
rphast-1.6/rphast/man/label.subtree.Rd | 31
rphast-1.6/rphast/man/leafnames.tree.Rd | 15
rphast-1.6/rphast/man/likelihood.msa.Rd | 40
rphast-1.6/rphast/man/mod.backgd.tm.Rd | 27
rphast-1.6/rphast/man/msa.Rd | 111
rphast-1.6/rphast/man/name.ancestors.Rd | 15
rphast-1.6/rphast/man/names.msa.Rd | 14
rphast-1.6/rphast/man/ncol.feat.Rd | 17
rphast-1.6/rphast/man/ncol.msa.Rd | 23
rphast-1.6/rphast/man/ninf.msa.Rd | 19
rphast-1.6/rphast/man/nothanks.rphast.Rd | 17
rphast-1.6/rphast/man/nrow.feat.Rd | 13
rphast-1.6/rphast/man/nrow.msa.Rd | 15
rphast-1.6/rphast/man/nstate.hmm.Rd | 12
rphast-1.6/rphast/man/numleaf.tree.Rd | 14
rphast-1.6/rphast/man/numnodes.tree.Rd | 14
rphast-1.6/rphast/man/offset.msa.Rd | 16
rphast-1.6/rphast/man/optim.rphast.Rd | 86
rphast-1.6/rphast/man/overlap.feat.Rd | 81
rphast-1.6/rphast/man/pairwise.diff.msa.Rd | 47
rphast-1.6/rphast/man/phastBias.Rd | 118
rphast-1.6/rphast/man/phastCons.Rd | 237 -
rphast-1.6/rphast/man/phyloFit.Rd | 283 --
rphast-1.6/rphast/man/phyloP.Rd | 135 -
rphast-1.6/rphast/man/phyloP.prior.Rd | 73
rphast-1.6/rphast/man/phyloP.sph.Rd | 156 -
rphast-1.6/rphast/man/plot.feat.Rd | 63
rphast-1.6/rphast/man/plot.gene.Rd | 42
rphast-1.6/rphast/man/plot.lsmodel.tm.Rd | 80
rphast-1.6/rphast/man/plot.msa.Rd | 64
rphast-1.6/rphast/man/plot.rate.matrix.Rd | 81
rphast-1.6/rphast/man/plot.tm.Rd | 74
rphast-1.6/rphast/man/plot.track.Rd | 77
rphast-1.6/rphast/man/postprob.msa.Rd | 25
rphast-1.6/rphast/man/print.feat.Rd | 15
rphast-1.6/rphast/man/print.msa.Rd | 50
rphast-1.6/rphast/man/print.phastBiasResult.Rd | 13
rphast-1.6/rphast/man/print.tm.Rd | 19
rphast-1.6/rphast/man/prune.tree.Rd | 21
rphast-1.6/rphast/man/range.feat.Rd | 17
rphast-1.6/rphast/man/range.track.Rd | 20
rphast-1.6/rphast/man/rbind.feat.Rd | 15
rphast-1.6/rphast/man/read.feat.Rd | 46
rphast-1.6/rphast/man/read.hmm.Rd | 16
rphast-1.6/rphast/man/read.msa.Rd | 140 -
rphast-1.6/rphast/man/read.newick.tree.Rd | 14
rphast-1.6/rphast/man/read.tm.Rd | 14
rphast-1.6/rphast/man/read.wig.Rd | 16
rphast-1.6/rphast/man/reflect.phylo.hmm.Rd | 34
rphast-1.6/rphast/man/register.rphast.Rd | 49
rphast-1.6/rphast/man/rename.tree.Rd | 23
rphast-1.6/rphast/man/rescale.tree.Rd | 28
rphast-1.6/rphast/man/reverse.complement.msa.Rd | 21
rphast-1.6/rphast/man/rphast-package.Rd | 17
rphast-1.6/rphast/man/sample.msa.Rd | 38
rphast-1.6/rphast/man/score.hmm.Rd | 114
rphast-1.6/rphast/man/set.rate.matrix.tm.Rd | 120
rphast-1.6/rphast/man/setup.branch.site.tm.Rd | 60
rphast-1.6/rphast/man/simulate.msa.Rd | 80
rphast-1.6/rphast/man/smooth.wig.Rd | 22
rphast-1.6/rphast/man/sort.feat.Rd | 23
rphast-1.6/rphast/man/split.by.feature.msa.Rd | 31
rphast-1.6/rphast/man/split.feat.Rd | 49
rphast-1.6/rphast/man/square-bracket-assign-msa.Rd | 54
rphast-1.6/rphast/man/square-bracket-msa.Rd | 60
rphast-1.6/rphast/man/state.freq.msa.Rd | 17
rphast-1.6/rphast/man/strip.gaps.msa.Rd | 44
rphast-1.6/rphast/man/sub.msa.Rd | 44
rphast-1.6/rphast/man/subst.mods.Rd | 12
rphast-1.6/rphast/man/subtree.Rd | 28
rphast-1.6/rphast/man/summary.feat.Rd | 13
rphast-1.6/rphast/man/summary.msa.Rd | 27
rphast-1.6/rphast/man/summary.tm.Rd | 15
rphast-1.6/rphast/man/summary.tree.Rd | 22
rphast-1.6/rphast/man/tagval.Rd | 34
rphast-1.6/rphast/man/tagval.feat.Rd | 38
rphast-1.6/rphast/man/tm.Rd | 101
rphast-1.6/rphast/man/total.expected.subs.msa.Rd | 17
rphast-1.6/rphast/man/translate.msa.Rd | 48
rphast-1.6/rphast/man/unapply.bgc.sel.Rd | 20
rphast-1.6/rphast/man/unique.feat.Rd | 60
rphast-1.6/rphast/man/write.feat.Rd | 15
rphast-1.6/rphast/man/write.hmm.Rd | 18
rphast-1.6/rphast/man/write.msa.Rd | 33
rphast-1.6/rphast/man/write.tm.Rd | 20
rphast-1.6/rphast/man/write.wig.Rd | 33
rphast-1.6/rphast/man/write.wig.feat.Rd | 32
rphast-1.6/rphast/src/Makevars.in | 126
rphast-1.6/rphast/src/Makevars.win | 126
rphast-1.6/rphast/src/complex_matrix.c | 34
rphast-1.6/rphast/src/eigen.c | 38
rphast-1.6/rphast/src/fit_column.c | 454 +--
rphast-1.6/rphast/src/fit_column.h | 74
rphast-1.6/rphast/src/fit_feature.c | 2
rphast-1.6/rphast/src/maf.c | 274 +-
rphast-1.6/rphast/src/markov_matrix.c | 98
rphast-1.6/rphast/src/matrix.c | 38
rphast-1.6/rphast/src/misc.c | 6
rphast-1.6/rphast/src/misc.h | 159 -
rphast-1.6/rphast/src/phast_cons.c | 298 +-
rphast-1.6/rphast/src/phylo_fit.c | 322 +-
rphast-1.6/rphast/src/phylo_p_print.c | 207 -
rphast-1.6/rphast/src/prob_matrix.c | 6
rphast-1.6/rphast/src/rph_trees.c | 38
rphast-1.6/rphast/src/subst_mods.c | 635 ++--
rphast-1.6/rphast/src/tree_likelihoods.c | 250 -
rphast-1.6/rphast/src/trees.c | 224 -
rphast-1.6/rphast/vignettes/vignette1.Rnw | 2
rphast-1.6/rphast/vignettes/vignette2-source.pdf |only
rphast-1.6/rphast/vignettes/vignette3.Rnw | 30
rphast-1.6/rphast/vignettes/vignette4.Rnw | 5
188 files changed, 5082 insertions(+), 8084 deletions(-)
Title: Process Rhea, KEGG, MetaCyc, Unipathway biochemical reaction
data
Diff between RbioRXN versions 1.3.1 dated 2014-07-30 and 1.5 dated 2015-01-14
Description: RbioRXN facilitates retrieving and processing biochemical reaction data such as Rhea, MetaCyc, KEGG and Unipathway. The package provides the functions to download and parse data, instantiate generic reaction and check mass-balance. The package aims to construct an integrated metabolic network and genome-scale metabolic model.
Author: Byoungnam Min, Byeonghyuk Park, Kyoung Heon Kim and In-Geol Choi
Maintainer: Byoungnam Min
DESCRIPTION | 16 ++++++------
MD5 | 18 ++++++-------
NAMESPACE | 2 -
R/RbioRXN-internal.R | 2 -
R/get.metacyc.all.R | 16 +++++++++++-
R/get.metacyc.reaction.byId.R | 51 ++++++++++++++++++++++++---------------
R/instantiate.rhea.R | 15 ++++++++---
man/RbioRXN-package.Rd | 4 +--
man/get.metacyc.all.Rd | 2 +
man/get.metacyc.reaction.byId.Rd | 2 +
10 files changed, 83 insertions(+), 45 deletions(-)
Title: Modelling with Sparse And Dense Matrices
Diff between MatrixModels versions 0.3-1.1 dated 2014-02-12 and 0.4-0 dated 2015-01-14
Description: Modelling with sparse and dense 'Matrix' matrices, using
modular prediction and response module classes.
Author: Douglas Bates
Maintainer: Martin Maechler
DESCRIPTION | 22 +++++++++++-----------
MD5 | 12 ++++++------
NAMESPACE | 45 ++++++++++++++++++++++++++-------------------
R/modelMatrix.R | 5 ++---
man/glm4.Rd | 8 ++++----
man/lm.fit.sparse.Rd | 19 ++++++++++---------
man/model.Matrix.Rd | 2 +-
7 files changed, 60 insertions(+), 53 deletions(-)
Title: Interactive Exploration of Contour Data
Diff between exCon versions 0.1-0 dated 2014-10-29 and 0.1-3 dated 2015-01-14
Description: exCon is an interactive tool to explore topographic-like data
sets. Such data sets take the form of a matrix in which the rows and
columns provide location/frequency information, and the matrix elements
contain altitude/response information. Such data is found in cartography,
2D spectroscopy and chemometrics. exCon creates an interactive web page
showing the contoured data set along with slices from the original matrix
parallel to each dimension. The page is written in d3/javascript.
Author: Bryan Hanson [aut, cre],
Kristina Mulry [ctb]
Maintainer: Bryan Hanson
DESCRIPTION | 10 +++---
MD5 | 15 ++++-----
NAMESPACE | 2 -
NEWS | 22 +++++++++++++
R/exCon.R | 66 ++++++++++++++++++++++++++--------------
inst/extdata/eC_brushNguides.js | 5 +--
inst/extdata/exCon.js |only
man/exCon-package.Rd | 3 +
man/exCon.Rd | 35 +++++++++++++++------
9 files changed, 109 insertions(+), 49 deletions(-)