Title: Merging linkage maps by linear programming
Diff between LPmerge versions 1.5 dated 2014-01-06 and 1.6 dated 2014-08-16
Description: LPmerge creates a consensus genetic map by merging linkage maps from different populations. The software uses linear programming (LP) to efficiently minimize the mean absolute error between the consensus map and the linkage maps. This minimization is performed subject to linear inequality constraints that ensure the ordering of the markers in the linkage maps is preserved. When marker order is inconsistent between linkage maps, a minimum set of ordinal constraints is deleted to resolve the conflicts.
Author: Jeffrey Endelman
Maintainer: Jeffrey Endelman
DESCRIPTION | 6 +++---
MD5 | 8 ++++----
R/LPmerge.R | 22 ++++++++++++++++------
inst/CITATION | 8 +++++---
man/LPmerge.Rd | 2 +-
5 files changed, 29 insertions(+), 17 deletions(-)
Title: Cultural Consensus Theory applications to data
Diff between CCTpack versions 1.2 dated 2014-06-10 and 1.3 dated 2014-08-16
Description: A user-friendly GUI for the application of Cultural Consensus Theory (CCT) models and methods to consensus data. The models are applied using hierarchical Bayesian inference. The current package version supports binary, ordinal, and continuous data formats.
Author: Royce Anders
Maintainer: Royce Anders
CCTpack-1.2/CCTpack/man/print.occult.Rd |only
CCTpack-1.3/CCTpack/DESCRIPTION | 10
CCTpack-1.3/CCTpack/MD5 | 21
CCTpack-1.3/CCTpack/NAMESPACE | 3
CCTpack-1.3/CCTpack/R/cctgui.r | 5801 ++++++++++++++---------------
CCTpack-1.3/CCTpack/man/CCTpack-package.Rd | 12
CCTpack-1.3/CCTpack/man/cctapply.Rd | 14
CCTpack-1.3/CCTpack/man/cctexport.Rd | 4
CCTpack-1.3/CCTpack/man/cctgui.Rd | 4
CCTpack-1.3/CCTpack/man/cctppc.Rd | 8
CCTpack-1.3/CCTpack/man/cctresults.Rd | 4
CCTpack-1.3/CCTpack/man/cctscree.Rd | 2
12 files changed, 2944 insertions(+), 2939 deletions(-)
Title: Multilayer optics
Diff between planar versions 1.5 dated 2013-12-16 and 1.5.2 dated 2014-08-16
Description: Solves the electromagnetic problem of reflection and transmission
of a plane wave or a gaussian beam, at a planar multilayer interface. Also
computed are the decay rates and emission profile for a dipolar emitter
near a multilayer structure.
Author: Baptiste Auguie [aut, cre] (Some functions ported from the original
Matlab SPLAC code by E.C. Le Ru and P. G. Etchegoin),
Steven Johnson [aut, cph] (C code for the cubature library)
Maintainer: Baptiste Auguie
planar-1.5.2/planar/DESCRIPTION | 23
planar-1.5.2/planar/MD5 | 162 ++--
planar-1.5.2/planar/NAMESPACE | 13
planar-1.5.2/planar/NEWS | 19
planar-1.5.2/planar/R/collection.r |only
planar-1.5.2/planar/R/dipole.r | 8
planar-1.5.2/planar/R/dipole_integrand.r | 10
planar-1.5.2/planar/R/gaussian.r | 127 ++-
planar-1.5.2/planar/R/internal_field.r |only
planar-1.5.2/planar/R/multilayer.r | 155 +++-
planar-1.5.2/planar/R/planar-package.r | 7
planar-1.5.2/planar/R/recursive_fresnel.r | 2
planar-1.5.2/planar/R/utils.r | 77 +-
planar-1.5.2/planar/R/zzz.r | 2
planar-1.5.2/planar/TODO | 6
planar-1.5.2/planar/build/vignette.rds |binary
planar-1.5.2/planar/demo |only
planar-1.5.2/planar/inst/doc/decay_rates.Rmd |only
planar-1.5.2/planar/inst/doc/decay_rates.html |only
planar-1.5.2/planar/inst/doc/fresnel.Rmd |only
planar-1.5.2/planar/inst/doc/fresnel.html |only
planar-1.5.2/planar/inst/doc/gaussian.R |only
planar-1.5.2/planar/inst/doc/gaussian.Rmd |only
planar-1.5.2/planar/inst/doc/gaussian.html |only
planar-1.5.2/planar/inst/wiki/LFIEF_patterns.rmd | 109 ---
planar-1.5.2/planar/inst/wiki/RTA_consistency.rmd | 69 -
planar-1.5.2/planar/inst/wiki/SPP_dispersion.rmd | 72 --
planar-1.5.2/planar/inst/wiki/bragg_stack.rmd | 36 -
planar-1.5.2/planar/inst/wiki/decay_rates.rmd | 57 -
planar-1.5.2/planar/inst/wiki/demos.r | 8
planar-1.5.2/planar/inst/wiki/dipole_integrand.rmd | 59 -
planar-1.5.2/planar/inst/wiki/field_multilayer.rmd | 40 -
planar-1.5.2/planar/inst/wiki/fluorescence_enhancement.rmd | 144 ----
planar-1.5.2/planar/inst/wiki/gaussian_beam.rmd | 128 ---
planar-1.5.2/planar/inst/wiki/internal_field_comparison.rmd |only
planar-1.5.2/planar/inst/wiki/kretschmann_reflectivity.rmd | 86 --
planar-1.5.2/planar/inst/wiki/kretschmann_sensing.rmd | 69 -
planar-1.5.2/planar/man/classify.Rd | 15
planar-1.5.2/planar/man/collection_ml.Rd |only
planar-1.5.2/planar/man/dipole.Rd | 27
planar-1.5.2/planar/man/dipole_direct.Rd | 27
planar-1.5.2/planar/man/epsilon_dispersion.Rd |only
planar-1.5.2/planar/man/epsilon_label.Rd |only
planar-1.5.2/planar/man/gaussian.Rd | 6
planar-1.5.2/planar/man/gaussian_near_field_layer.Rd |only
planar-1.5.2/planar/man/gaussian_near_field_ml.Rd |only
planar-1.5.2/planar/man/integrand_mtot.Rd | 17
planar-1.5.2/planar/man/integrand_nr1.Rd | 25
planar-1.5.2/planar/man/integrand_nr2.Rd | 25
planar-1.5.2/planar/man/integrand_nr3.Rd | 27
planar-1.5.2/planar/man/integrand_rad.Rd | 23
planar-1.5.2/planar/man/internal_field.Rd |only
planar-1.5.2/planar/man/invert_stack.Rd | 11
planar-1.5.2/planar/man/lfief.Rd |only
planar-1.5.2/planar/man/modify_levels.Rd | 10
planar-1.5.2/planar/man/multilayer.Rd | 32
planar-1.5.2/planar/man/multilayercpp.Rd | 21
planar-1.5.2/planar/man/multilayerfull.Rd |only
planar-1.5.2/planar/man/planar-package.Rd | 13
planar-1.5.2/planar/man/planar.Rd | 10
planar-1.5.2/planar/man/raman_shift.Rd | 7
planar-1.5.2/planar/man/recursive_fresnel.Rd | 22
planar-1.5.2/planar/man/recursive_fresnelcpp.Rd | 22
planar-1.5.2/planar/man/transmission.Rd | 7
planar-1.5.2/planar/src/clencurt.h |only
planar-1.5.2/planar/src/collection.cpp |only
planar-1.5.2/planar/src/converged.h |only
planar-1.5.2/planar/src/cubature.h |only
planar-1.5.2/planar/src/gaussian.h |only
planar-1.5.2/planar/src/gaussian_beam.cpp | 415 +++++++++++-
planar-1.5.2/planar/src/hcubature.c |only
planar-1.5.2/planar/src/multilayer.cpp | 377 ++++++++++
planar-1.5.2/planar/src/multilayer.h |only
planar-1.5.2/planar/src/vwrapper.h |only
planar-1.5.2/planar/vignettes/decay_rates.Rmd |only
planar-1.5.2/planar/vignettes/frames.png |only
planar-1.5.2/planar/vignettes/fresnel.Rmd |only
planar-1.5.2/planar/vignettes/gaussian.Rmd |only
planar-1.5.2/planar/vignettes/interface.png |only
planar-1.5.2/planar/vignettes/stack.png |only
planar-1.5/planar/inst/doc/decay_rates.Rnw |only
planar-1.5/planar/inst/doc/decay_rates.pdf |only
planar-1.5/planar/inst/doc/fresnel.pdf |only
planar-1.5/planar/inst/doc/fresnel.rnw |only
planar-1.5/planar/inst/doc/gaussian.pdf |only
planar-1.5/planar/inst/doc/gaussian.rnw |only
planar-1.5/planar/inst/wiki/LFIEF_patterns.R |only
planar-1.5/planar/inst/wiki/RTA_consistency.R |only
planar-1.5/planar/inst/wiki/SPP_dispersion.R |only
planar-1.5/planar/inst/wiki/bragg_stack.R |only
planar-1.5/planar/inst/wiki/decay_rates.R |only
planar-1.5/planar/inst/wiki/dipole_integrand.R |only
planar-1.5/planar/inst/wiki/field_multilayer.R |only
planar-1.5/planar/inst/wiki/fluorescence_enhancement.R |only
planar-1.5/planar/inst/wiki/gaussian_beam.R |only
planar-1.5/planar/inst/wiki/kretschmann_reflectivity.R |only
planar-1.5/planar/inst/wiki/kretschmann_sensing.R |only
planar-1.5/planar/man/field_profile.Rd |only
planar-1.5/planar/man/gaussian_near_field.Rd |only
planar-1.5/planar/vignettes/decay_rates.Rnw |only
planar-1.5/planar/vignettes/frames.pdf |only
planar-1.5/planar/vignettes/fresnel.rnw |only
planar-1.5/planar/vignettes/gaussian.rnw |only
planar-1.5/planar/vignettes/interface.pdf |only
planar-1.5/planar/vignettes/stack.pdf |only
105 files changed, 1374 insertions(+), 1253 deletions(-)
Title: Teitz and Bart p-median algorithm
Diff between tbart versions 0.9 dated 2013-06-19 and 0.9.1 dated 2014-08-16
Description: Solves Teitz and Bart's p-median problem - given a set of
points attempts to find subset of size p such that summed distances of any
point in the set to the nearest point in p is minimised. Although
generally effective, this algorithm does not guarantee that a globally
optimal subset is found.
Author: Chris Brunsdon
Maintainer: Chris Brunsdon
DESCRIPTION | 18 ++++++-------
MD5 | 18 ++++++-------
NAMESPACE | 1
man/allocate.Rd | 27 ++++++--------------
man/euc.dists.Rd | 19 +++++---------
man/star.diagram.Rd | 15 ++++-------
man/tb.Rd | 27 ++++++--------------
man/tb.raw.Rd | 16 +++++-------
man/tbart-package.Rd | 18 ++++++-------
src/RcppExports.cpp | 66 +++++++++++++++++++++++++++++++++------------------
10 files changed, 108 insertions(+), 117 deletions(-)
More information about RGoogleAnalytics at CRAN
Permanent link
Title: Companion to Applied Regression
Diff between car versions 2.0-20 dated 2014-04-28 and 2.0-21 dated 2014-08-16
Description:
This package accompanies J. Fox and S. Weisberg, An R Companion to Applied Regression,
Second Edition, Sage, 2011.
Author: John Fox [aut, cre],
Sanford Weisberg [aut],
Daniel Adler [ctb],
Douglas Bates [ctb],
Gabriel Baud-Bovy [ctb],
Steve Ellison [ctb],
David Firth [ctb],
Michael Friendly [ctb],
Gregor Gorjanc [ctb],
Spencer Graves [ctb],
Richard Heiberger [ctb],
Rafael Laboissiere [ctb],
Georges Monette [ctb],
Duncan Murdoch [ctb],
Henric Nilsson [ctb],
Derek Ogle [ctb],
Brian Ripley [ctb],
William Venables [ctb],
Achim Zeileis [ctb],
R-Core [ctb]
Maintainer: John Fox
DESCRIPTION | 12 -
MD5 | 136 ++++++++---------
NAMESPACE | 6
NEWS | 16 ++
R/Anova.R | 8 -
R/recode.R | 122 +++++++++------
R/residualPlots.R | 23 +-
R/scatter3d.R | 5
R/scatterplotMatrix.R | 352 +++++++++++++++++++++++---------------------
R/scatterplotSmoothers.R | 20 +-
R/utility-functions.R | 6
R/vif.R | 90 +++++++----
build/vignette.rds |binary
data/AMSsurvey.rda |binary
data/Adler.rda |binary
data/Angell.rda |binary
data/Anscombe.rda |binary
data/Baumann.rda |binary
data/Bfox.rda |binary
data/Blackmoor.rda |binary
data/Burt.rda |binary
data/CanPop.rda |binary
data/Chile.rda |binary
data/Chirot.rda |binary
data/Cowles.rda |binary
data/Davis.rda |binary
data/DavisThin.rda |binary
data/Depredations.rda |binary
data/Duncan.rda |binary
data/Ericksen.rda |binary
data/Florida.rda |binary
data/Freedman.rda |binary
data/Friendly.rda |binary
data/Ginzberg.rda |binary
data/Greene.rda |binary
data/Guyer.rda |binary
data/Hartnagel.rda |binary
data/Highway1.rda |binary
data/Leinhardt.rda |binary
data/Mandel.rda |binary
data/Migration.rda |binary
data/Moore.rda |binary
data/Mroz.rda |binary
data/OBrienKaiser.rda |binary
data/Ornstein.rda |binary
data/Pottery.rda |binary
data/Prestige.rda |binary
data/Quartet.rda |binary
data/Robey.rda |binary
data/SLID.rda |binary
data/Sahlins.rda |binary
data/Salaries.rda |binary
data/Soils.rda |binary
data/States.rda |binary
data/Transact.rda |binary
data/UN.rda |binary
data/USPop.rda |binary
data/Vocab.rda |binary
data/WeightLoss.rda |binary
data/Womenlf.rda |binary
data/Wool.rda |binary
inst/doc/embedding.pdf |binary
man/Anova.Rd | 9 -
man/ScatterplotSmoothers.Rd | 12 -
man/car-package.Rd | 4
man/recode.Rd | 2
man/scatter3d.Rd | 10 -
man/scatterplotMatrix.Rd | 8 -
man/vif.Rd | 10 -
69 files changed, 485 insertions(+), 366 deletions(-)
Title: ELT - A package to build Experience Life Tables
Diff between ELT versions 1.2 dated 2014-06-01 and 1.3 dated 2014-08-16
Description: The package is meant to help actuaries to build experience life tables. It contains functions to calculate exposure and number of deaths, smoothing following four different methods, and validation following three criteria.
Author: Julien Tomas, Frederic Planchet, Wassim Youssef
Maintainer: Wassim Youssef
DESCRIPTION | 8 ++---
MD5 | 46 +++++++++++++++++-----------------
R/SGraphics.R | 21 +++++++--------
man/AddReference.Rd | 16 ++++-------
man/ComparisonMethods.Rd | 62 +++++++++++++++-------------------------------
man/CompletionA.Rd | 38 +++++++++-------------------
man/CompletionB.Rd | 24 +++++++----------
man/Dispersion.Rd | 23 +++++------------
man/ELT-package.Rd | 14 ++++++++--
man/FctMethod1.Rd | 23 +++++++----------
man/FctMethod2.Rd | 23 +++++++----------
man/FctMethod3.Rd | 23 +++++++----------
man/FctMethod4_1stPart.Rd | 22 ++++++----------
man/FctMethod4_2ndPart.Rd | 29 ++++++++-------------
man/Method1.Rd | 21 +++++----------
man/Method2.Rd | 21 +++++----------
man/Method3.Rd | 21 +++++----------
man/Method4A.Rd | 18 +++++--------
man/Method4B.Rd | 32 ++++++++---------------
man/ReadHistory.Rd | 54 +++++++++++++++++-----------------------
man/SurfacePlot.Rd | 16 +++++------
man/ValidationLevel1.Rd | 33 ++++++++----------------
man/ValidationLevel2.Rd | 25 +++++-------------
man/ValidationLevel3.Rd | 26 ++++++-------------
24 files changed, 256 insertions(+), 383 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-03-20 1.0.2.13
2009-10-02 1.0.1.27
More information about RootsExtremaInflections at CRAN
Permanent link
Title: Modelling Competitive Exclusion and Limited Dispersal in a
Statistical Phylogeographic Framework
Diff between phyloland versions 1.0 dated 2014-03-07 and 1.1 dated 2014-08-16
Description: Phyloland package models a space colonization process mapped onto a phylogeny, it aims at estimating limited dispersal and ecological competitive exclusion in a Bayesian MCMC statistical phylogeographic framework (please refer to phyloland-package help for details.)
Author: Louis Ranjard, Marie Paturel
Maintainer: Louis Ranjard
DESCRIPTION | 14
MD5 | 8
NAMESPACE | 2
R/pack_Phylogeo_Functions_g.R | 1146 ++++++++++++++++++++++--------------------
man/phyloland-internal.Rd | 1
5 files changed, 627 insertions(+), 544 deletions(-)
Title: Paleontological and Phylogenetic Analyses of Evolution
Diff between paleotree versions 2.0 dated 2014-02-04 and 2.1 dated 2014-08-16
Description: Analyzes, time-scales and simulates phylogenies of extinct/fossil
lineages, along with calculation of diversity curves. Also fits likelihood
models to estimate sampling rates from stratigraphic ranges.
Author: David W. Bapst
Maintainer: David W. Bapst
CHANGELOG | 14
DESCRIPTION | 6
MD5 | 108 +++---
NAMESPACE | 4
R/cal3TimePaleoPhy.R | 23 +
R/dateNodes.R | 2
R/freqRat.R | 59 ++-
R/perfectParsCharTree.R |only
R/sampleRanges.R | 40 +-
R/seqTimeList.R |only
R/simFossilTaxa.R | 4
R/simPaleoTrees.R | 24 +
R/timePaleoPhy.R | 38 +-
man/DiversityCurves.Rd | 249 ++++++--------
man/SamplingConv.Rd | 150 +++-----
man/binTimeData.Rd | 103 ++----
man/branchClasses.Rd | 51 +--
man/cal3TimePaleoPhy.Rd | 709 ++++++++++++++++++------------------------
man/cladogeneticTraitCont.Rd | 97 ++---
man/compareTimescaling.Rd | 130 +++----
man/constrainParPaleo.Rd | 418 ++++++++++--------------
man/dateNodes.Rd | 66 +--
man/degradeTree.Rd | 95 ++---
man/depthRainbow.Rd | 19 -
man/durationFreq.Rd | 272 ++++++----------
man/expandTaxonTree.Rd | 117 +++---
man/footeValues.Rd | 154 ++++-----
man/freqRat.Rd | 136 ++++----
man/getSampProbDisc.Rd | 299 +++++++----------
man/getSampRateCont.Rd | 260 ++++++---------
man/horizonSampRate.Rd | 90 ++---
man/inverseSurv.Rd | 467 +++++++++++----------------
man/modelMethods.Rd | 107 ++----
man/modifyTerminalBranches.Rd | 101 ++---
man/multiDiv.Rd | 197 +++++------
man/optimPaleo.Rd | 29 -
man/paleotree-package.Rd | 47 +-
man/perCapitaRates.Rd | 155 ++++-----
man/perfectParsCharTree.Rd |only
man/plotTraitgram.Rd | 45 +-
man/pqr2Ps.Rd | 131 +++----
man/probAnc.Rd | 118 +++---
man/retiolitinae.Rd | 31 -
man/reverseList.Rd | 37 +-
man/rootSplit.Rd | 19 -
man/sampleRanges.Rd | 309 ++++++++----------
man/seqTimeList.Rd |only
man/simFossilTaxa.Rd | 423 +++++++++++--------------
man/simFossilTaxa_SRCond.Rd | 239 ++++++--------
man/simPaleoTrees.Rd | 163 ++++-----
man/taxa2cladogram.Rd | 111 +++---
man/taxa2phylo.Rd | 112 +++---
man/termTaxa.Rd | 268 +++++++--------
man/timeLadderTree.Rd | 42 +-
man/timePaleoPhy.Rd | 622 ++++++++++++++++--------------------
man/timeSliceTree.Rd | 61 +--
man/unitLengthTree.Rd | 23 -
57 files changed, 3447 insertions(+), 4147 deletions(-)
Title: Full factorials, orthogonal arrays and base utilities for DoE
packages
Diff between DoE.base versions 0.26-1 dated 2014-04-09 and 0.26-2 dated 2014-08-16
Description: This package creates full factorial experimental designs and designs based on orthogonal arrays for (industrial) experiments. Additionally, it provides some utility functions used also by other DoE packages.
Author: Ulrike Groemping [aut, cre],
Boyko Amarov [ctb],
Hongquan Xu [ctb]
Maintainer: Ulrike Groemping
DESCRIPTION | 8 +-
MD5 | 14 ++--
NAMESPACE | 2
R/ME.Lenth.R | 57 ++++++++++------
R/halfnormal.R | 189 ++++++++++++++++++++++++++++++++++++++++--------------
R/sysdata.rda |binary
inst/NEWS | 33 +++++++++
man/halfnormal.Rd | 76 +++++++++++++++++----
8 files changed, 286 insertions(+), 93 deletions(-)
Title: Interface between R and Google Charts
Diff between googleVis versions 0.5.4 dated 2014-07-20 and 0.5.5 dated 2014-08-16
Description: The googleVis package provides an interface between R
and the Google Charts API. It allows users to create web pages
with interactive charts based on R data frames, using the Google
Charts API. The package provides plot methods in R to display
the charts locally with the R HTTP help server without uploading
the data to Google. A modern browser with Internet connection is
required and for some charts Flash.
Author: Markus Gesmann [aut, cre],
Diego de Castillo [aut],
Joe Cheng [ctb]
Maintainer: Markus Gesmann
DESCRIPTION | 21
MD5 | 50
NEWS | 19
R/gvisCoreCharts.R | 20
README.md | 13
THANKS | 2
build/googleVis.pdf |binary
demo/Trendlines.R | 8
inst/doc/Using_Roles_via_googleVis.Rmd | 22
inst/doc/Using_Roles_via_googleVis.html | 244 ++--
inst/doc/Using_Trendlines_with_googleVis.R | 9
inst/doc/Using_Trendlines_with_googleVis.Rmd | 2
inst/doc/Using_Trendlines_with_googleVis.html | 112 --
inst/doc/Using_googleVis_with_knitr.Rmd | 9
inst/doc/Using_googleVis_with_knitr.html | 87 -
inst/doc/googleVis.pdf |binary
inst/doc/googleVis_examples.R | 86 -
inst/doc/googleVis_examples.Rmd | 31
inst/doc/googleVis_examples.html | 1447 ++++++++++++--------------
man/googleVis-package.Rd | 18
man/gvisMerge.Rd | 48
vignettes/Using_Roles_via_googleVis.Rmd | 22
vignettes/Using_Trendlines_with_googleVis.Rmd | 2
vignettes/Using_googleVis_with_knitr.Rmd | 9
vignettes/googleVis.bib | 2
vignettes/googleVis_examples.Rmd | 31
26 files changed, 1184 insertions(+), 1130 deletions(-)