Title: Traveling Salesperson Problem (TSP)
Diff between TSP versions 1.0-9 dated 2014-07-16 and 1.0-10 dated 2015-02-03
Description: Basic infrastructure and some algorithms for the traveling
salesperson problem (also traveling salesman problem; TSP).
The package provides some simple algorithms and
an interface to Concorde, the currently fastest TSP solver. Concorde
itself is not included in the package and has to be obtained separately.
Author: Michael Hahsler [aut, cre, cph],
Kurt Hornik [aut, cph]
Maintainer: Michael Hahsler
DESCRIPTION | 12 +++++------
MD5 | 44 ++++++++++++++++++++---------------------
R/ATSP.R | 2 -
R/TSP.R | 3 +-
R/cut_tour.R | 1
R/tsp_concorde.R | 26 +++++++++++++-----------
build/vignette.rds |binary
data/USCA312.rda |binary
data/USCA312_map.rda |binary
data/USCA50.rda |binary
inst/NEWS | 5 ++++
inst/doc/TSP.pdf |binary
man/ATSP.Rd | 1
man/Concorde.Rd | 10 +++++----
man/TOUR.Rd | 1
man/TSP.Rd | 1
man/TSPLIB.Rd | 3 +-
man/USCA312.Rd | 1
man/cut_tour.Rd | 1
man/insert_dummy.Rd | 1
man/reformulate_ATSP_as_TSP.Rd | 1
man/solve_TSP.Rd | 1
man/tour_length.Rd | 1
23 files changed, 68 insertions(+), 47 deletions(-)
Title: Quasi Variances for Factor Effects in Statistical Models
Diff between qvcalc versions 0.8-8 dated 2012-06-05 and 0.8-9 dated 2015-02-03
Description: Functions to compute quasi variances and associated measures of approximation error
Author: David Firth
Maintainer: David Firth
qvcalc-0.8-8/qvcalc/INDEX |only
qvcalc-0.8-9/qvcalc/DESCRIPTION | 19 +++++++++----------
qvcalc-0.8-9/qvcalc/MD5 | 11 +++++------
qvcalc-0.8-9/qvcalc/R/qvcalc.R | 8 +++++++-
qvcalc-0.8-9/qvcalc/man/plot.qv.Rd | 5 ++++-
qvcalc-0.8-9/qvcalc/man/qvcalc.Rd | 17 +++++++++--------
qvcalc-0.8-9/qvcalc/man/worstErrors.Rd | 2 +-
7 files changed, 35 insertions(+), 27 deletions(-)
Title: Combination of Factorial Methods and Cluster Analysis
Diff between FactoClass versions 1.1.0 dated 2013-07-18 and 1.1.1 dated 2015-02-03
Description: Multivariate exploration of a data table with factorial
analysis and cluster methods.
Author: Campo Elias Pardo
Maintainer: Campo Elias Pardo
FactoClass-1.1.0/FactoClass/FactoClass-Ex.R |only
FactoClass-1.1.1/FactoClass/DESCRIPTION | 8
FactoClass-1.1.1/FactoClass/MD5 | 17 -
FactoClass-1.1.1/FactoClass/NAMESPACE | 25 +
FactoClass-1.1.1/FactoClass/R/plot.dudi.R | 351 ++++++++++++--------------
FactoClass-1.1.1/FactoClass/R/plotfp.R | 288 ++++++++++-----------
FactoClass-1.1.1/FactoClass/R/stableclus.R | 218 ++++++++--------
FactoClass-1.1.1/FactoClass/man/Bogota.Rd | 30 +-
FactoClass-1.1.1/FactoClass/man/plotfp.Rd | 115 ++++----
FactoClass-1.1.1/FactoClass/man/stableclus.Rd | 112 ++++----
10 files changed, 590 insertions(+), 574 deletions(-)
More information about AncestryMapper at CRAN
Permanent link
Title: R Commander Plug-in for the survival Package
Diff between RcmdrPlugin.survival versions 1.0-4 dated 2013-01-17 and 1.0-5 dated 2015-02-03
More information about RcmdrPlugin.survival at CRAN
Description: This package provides an R Commander plug-in for the survival
package, with dialogs for Cox models, parametric survival regression models,
estimation of survival curves, and testing for differences in survival
curves, along with data-management facilities and a variety of tests,
diagnostics and graphs.
Author: John Fox
Maintainer: John Fox
RcmdrPlugin.survival-1.0-4/RcmdrPlugin.survival/man/anova.coxph.Rd |only
RcmdrPlugin.survival-1.0-4/RcmdrPlugin.survival/man/survQuantiles.Rd |only
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/DESCRIPTION | 20 +-
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/MD5 | 26 +--
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/NAMESPACE | 8 -
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/R/CoxModel.R | 4
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/R/Survdiff.R | 2
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/R/Survfit.R | 6
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/R/misc.R | 12 -
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/R/quantile.survfit.R | 76 +++++-----
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/R/survregModel.R | 4
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/R/unfold.R | 2
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/inst/CHANGES | 6
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/inst/etc/menus.txt | 5
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/man/RcmdrPlugin.survival-package.Rd | 4
15 files changed, 91 insertions(+), 84 deletions(-)
Permanent link
Title: Genetic Analysis of Populations With Mixed Reproduction
Diff between poppr versions 1.1.2 dated 2014-07-29 and 1.1.3 dated 2015-02-03
Description: Population genetic analyses for hierarchical analysis of partially
clonal populations built upon the architecture of the adegenet package.
Author: Zhian N. Kamvar [cre, aut],
Javier F. Tabima [aut],
Niklaus J. Grunwald [ths]
Maintainer: Zhian N. Kamvar
DESCRIPTION | 29 ++-
MD5 | 222 +++++++++++++++--------------
NAMESPACE | 2
NEWS | 19 ++
R/Index_calculations.r | 8 -
R/amova.r | 14 -
R/bruvo.r | 99 +++++++-----
R/data_subset.r | 40 ++++-
R/distances.r | 29 ++-
R/file_handling.r | 5
R/internal.r | 38 +++-
R/methods.r | 3
R/mlg.r | 5
R/poppr.R | 2
R/sandbox.r | 24 +--
R/visualizations.r | 172 ++++++++++++++--------
R/zzz.r | 2
README.md | 16 --
build/vignette.rds |binary
data/Aeut.rda |binary
data/Pinf.rda |binary
data/monpop.rda |binary
data/partial_clone.rda |binary
inst/doc/algo.R | 4
inst/doc/algo.Rnw | 27 +++
inst/doc/algo.pdf |binary
inst/doc/poppr_manual.R | 36 ++--
inst/doc/poppr_manual.Rnw | 48 +++---
inst/doc/poppr_manual.pdf |binary
man/Aeut.Rd | 3
man/Pinf.Rd | 3
man/aboot.Rd | 13 +
man/bootgen-class.Rd | 3
man/bootgen-methods.Rd | 10 -
man/bruvo.boot.Rd | 3
man/bruvo.dist.Rd | 95 ++++++------
man/bruvo.msn.Rd | 3
man/bruvomat-class.Rd | 3
man/bruvomat-methods.Rd | 3
man/clonecorrect.Rd | 3
man/coercion-methods.Rd | 3
man/diss.dist.Rd | 3
man/genclone-class.Rd | 3
man/genclone-method.Rd | 7
man/genetic_distance.Rd | 3
man/genind2genalex.Rd | 3
man/genotype_curve.Rd | 3
man/getfile.Rd | 3
man/greycurve.Rd | 3
man/hierarchy-methods.Rd | 3
man/ia.Rd | 9 -
man/info_table.Rd | 9 -
man/informloci.Rd | 3
man/is.genclone.Rd | 3
man/locus_table.Rd | 3
man/missingno.Rd | 3
man/mlg.Rd | 15 +
man/monpop.Rd | 3
man/partial_clone.Rd | 3
man/plot_poppr_msn.Rd | 127 +++++++++-------
man/poppr-package.Rd | 5
man/poppr.Rd | 3
man/poppr.all.Rd | 3
man/poppr.amova.Rd | 5
man/poppr.msn.Rd | 14 +
man/popsub.Rd | 3
man/population-methods.Rd | 3
man/private_alleles.Rd | 5
man/read.genalex.Rd | 3
man/recode_polyploids.Rd | 5
man/shufflepop.Rd | 3
man/splitcombine.Rd | 7
src/poppr_distance.c | 2
tests/testthat/test-amova.R | 19 ++
tests/testthat/test-colors.R |only
tests/testthat/test-distpop.R | 7
tests/testthat/test-import.R |only
tests/testthat/test-values.R | 30 +++
vignettes/algo-concordance.tex | 2
vignettes/algo.Rnw | 27 +++
vignettes/figure/Aeut_MLG_Ahena-1.pdf |only
vignettes/figure/Aeut_MLG_Ahena.pdf |binary
vignettes/figure/Aeut_MLG_Ahena1.pdf |only
vignettes/figure/Aeut_MLG_Ahena2.pdf |only
vignettes/figure/Aeut_MLG_black-1.pdf |only
vignettes/figure/Aeut_MLG_black.pdf |binary
vignettes/figure/Aeut_MLG_title-1.pdf |only
vignettes/figure/Aeut_MLG_title.pdf |binary
vignettes/figure/bd_histogram-1.pdf |only
vignettes/figure/bd_histogram.pdf |binary
vignettes/figure/bruvo_msn.pdf |binary
vignettes/figure/bruvo_tree.pdf |binary
vignettes/figure/ex_data_picture-1.pdf |only
vignettes/figure/ex_data_picture.pdf |binary
vignettes/figure/ggplotchart.pdf |binary
vignettes/figure/greycurve_normal.pdf |binary
vignettes/figure/greycurve_small_heavy.pdf |binary
vignettes/figure/greywidth_inverse.pdf |binary
vignettes/figure/greywidth_large_heavy.pdf |binary
vignettes/figure/initializing_poppr-1.pdf |only
vignettes/figure/initializing_poppr.pdf |binary
vignettes/figure/mantel.pdf |binary
vignettes/figure/mlgbarplot-1.pdf |only
vignettes/figure/mlgbarplot.pdf |binary
vignettes/figure/mlgrareplot-1.pdf |only
vignettes/figure/mlgrareplot.pdf |binary
vignettes/figure/popcompare_bruvo2.pdf |binary
vignettes/figure/poppr_msn_fig.pdf |binary
vignettes/figure/subnor-1.pdf |only
vignettes/figure/subnor.pdf |binary
vignettes/figure/unnamed-chunk-3-1.pdf |only
vignettes/figure/unnamed-chunk-3.pdf |binary
vignettes/figure/unnamed-chunk-4.pdf |binary
vignettes/figure/unnamed-chunk-5.pdf |binary
vignettes/figure/unnamed-chunk-6.pdf |binary
vignettes/figure/unnamed-chunk-7.pdf |binary
vignettes/figure/unnamed-chunk-8.pdf |only
vignettes/figure/unnamed-chunk-9.pdf |only
vignettes/poppr_manual-concordance.tex | 4
vignettes/poppr_manual.Rnw | 48 +++---
120 files changed, 862 insertions(+), 534 deletions(-)
Title: Confidence Intervals with Poisson Double Sampling
Diff between poisDoubleSamp versions 1.0 dated 2015-02-02 and 1.1 dated 2015-02-03
More information about poisDoubleSamp at CRAN
Description: Functions to create confidence intervals for ratios of Poisson
rates under misclassification using double sampling.
Author: David Kahle [aut, cre],
Phil Young [aut],
Dean Young [aut]
Maintainer: David Kahle
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
src/unNormedMargLogLikeCpp.cpp | 4 ++--
src/unNormedMargLogLikeMaxLogTermCpp.cpp | 8 ++++----
4 files changed, 13 insertions(+), 13 deletions(-)
Permanent link
Title: Tools for Reading and Handling Spatial Objects
Diff between maptools versions 0.8-30 dated 2014-06-05 and 0.8-34 dated 2015-02-03
Description: Set of tools for manipulating and reading geographic data, in particular ESRI shapefiles; C code used from shapelib. It includes binary access to GSHHG shoreline files. The package also provides interface wrappers for exchanging spatial objects with packages such as PBSmapping, spatstat, maps, RArcInfo, Stata tmap, WinBUGS, Mondrian, and others.
Author: Roger Bivand [cre, aut],
Nicholas Lewin-Koh [aut],
Edzer Pebesma [ctb],
Eric Archer [ctb],
Adrian Baddeley [ctb],
Hans-Jörg Bibiko [ctb],
Steven Brey [ctb],
Jonathan Callahan [ctb],
German Carrillo [ctb],
Stéphane Dray [ctb],
David Forrest [ctb],
Michael Friendly [ctb],
Patrick Giraudoux [ctb],
Duncan Golicher [ctb],
Virgilio Gómez Rubio [ctb],
Patrick Hausmann [ctb],
Karl Ove Hufthammer [ctb],
Thomas Jagger [ctb],
Sebastian Luque [ctb],
Don MacQueen [ctb],
Andrew Niccolai [ctb],
Edzer Pebesma [ctb],
Oscar Perpiñán Lamigueiro [ctb],
Tom Short [ctb],
Greg Snow [ctb],
Ben Stabler [ctb],
Murray Stokely [ctb],
Rolf Turner [ctb]
Maintainer: Roger Bivand
ChangeLog | 872 ++++++++++++++++++++++++++++++++++++++++++
DESCRIPTION | 12
MD5 | 54 +-
R/DP.R | 6
R/Rgshhs.R | 14
R/SP2owin.R | 14
R/checkHoles.R | 36 +
R/nowrapRecenter.R | 26 -
R/point_line_distance.R | 10
R/sp2pbs.R | 26 -
R/sp_spat1.R | 12
R/spatstat1.R | 95 ++--
R/spmaps.R | 16
R/union.R | 16
build/vignette.rds |binary
inst/ChangeLog | 872 ++++++++++++++++++++++++++++++++++++++++++
inst/doc/combine_maptools.pdf |binary
man/GE_SpatialGrid.Rd | 4
man/SpatialLines2PolySet.Rd | 5
man/dotsInPolys.Rd | 3
man/map2SpatialPolygons.Rd | 3
man/readGPS.Rd | 32 -
man/readSplus.Rd | 2
man/sp2WB.Rd | 4
man/sp2tmap.Rd | 2
man/symbolsInPolys.Rd | 3
src/Rgshhs.c | 10
src/shapefil.h | 14
28 files changed, 1983 insertions(+), 180 deletions(-)
Title: Leveraging Learning to Automatically Manage Algorithms
Diff between llama versions 0.8 dated 2015-01-31 and 0.8.1 dated 2015-02-03
Description: Provides functionality to train and evaluate algorithm selection models for portfolios.
Author: Lars Kotthoff [aut,cre],
Bernd Bischl [aut],
Barry Hurley [ctb],
Talal Rahwan [ctb]
Maintainer: Lars Kotthoff
DESCRIPTION | 8 +++----
MD5 | 38 +++++++++++++++++------------------
R/helpers.R | 6 +++++
inst/manual/llama.pdf |binary
man/analysis.Rd | 2 -
man/classify.Rd | 2 -
man/classifyPairs.Rd | 2 -
man/cluster.Rd | 2 -
man/imputeCensored.Rd | 2 -
man/llama-package.Rd | 2 -
man/misc.Rd | 2 -
man/misclassificationPenalties.Rd | 2 -
man/normalize.Rd | 2 -
man/parscores.Rd | 2 -
man/plot.Rd | 2 -
man/regression.Rd | 2 -
man/regressionPairs.Rd | 2 -
man/successes.Rd | 2 -
tests/testthat/helper_mockLearners.R | 6 ++---
tests/testthat/test.satsolvers.R | 14 ++++++------
20 files changed, 53 insertions(+), 47 deletions(-)
More information about RPPairwiseDesign at CRAN
Permanent link
Title: Relative Contribution of Effects in a Regression Model
Diff between relimp versions 1.0-3 dated 2011-10-17 and 1.0-4 dated 2015-02-03
Description: Functions to facilitate inference on the relative importance of predictors in a linear or generalized linear model, and a couple of useful Tcl/Tk widgets.
Author: David Firth with contributions from Heather Turner
Maintainer: David Firth
DESCRIPTION | 17 +--
MD5 | 13 +-
NAMESPACE | 2
R/Tcl-utilities.R |only
R/pickFrom.R | 165 ++++++++++++++++++-----------------
R/relimp.R | 40 ++++----
R/showData.R | 249 +++++++++++++++++++++++++++---------------------------
man/relimp.Rd | 5 -
8 files changed, 250 insertions(+), 241 deletions(-)
Title: R Commander
Diff between Rcmdr versions 2.1-5 dated 2014-12-10 and 2.1-6 dated 2015-02-03
Description:
A platform-independent basic-statistics GUI (graphical user interface) for R, based on the tcltk package.
Author: John Fox [aut, cre],
Milan Bouchet-Valat [aut],
Liviu Andronic [ctb],
Michael Ash [ctb],
Theophilius Boye [ctb],
Stefano Calza [ctb],
Andy Chang [ctb],
Philippe Grosjean [ctb],
Richard Heiberger [ctb],
Kosar Karimi Pour [ctb],
G. Jay Kerns [ctb],
Renaud Lancelot [ctb],
Matthieu Lesnoff [ctb],
Uwe Ligges [ctb],
Samir Messad [ctb],
Martin Maechler [ctb],
Robert Muenchen [ctb],
Duncan Murdoch [ctb],
Erich Neuwirth [ctb],
Dan Putler [ctb],
Brian Ripley [ctb],
Miroslav Ristic [ctb],
Peter Wolf [ctb],
Kevin Wright [ctb]
Maintainer: John Fox
DESCRIPTION | 13
MD5 | 14
NAMESPACE | 10
NEWS | 4
R/model-menu.R | 6
R/utilities.R | 5994 +++++++++++++++++++++++++--------------------------
man/Confint.Rd | 10
man/Rcmdr-package.Rd | 4
8 files changed, 3043 insertions(+), 3012 deletions(-)
Title: Helpers for Parameters in Black-Box Optimization, Tuning and
Machine Learning.
Diff between ParamHelpers versions 1.4 dated 2014-10-10 and 1.5 dated 2015-02-03
Description: Functions for parameter descriptions and operations in black-box optimization, tuning
and machine learning. Parameters can be described (type, constraints, defaults, etc.),
combined to parameter sets and can in general be programmed on.
A useful OptPath object (archive) to log function evaluations is also provided.
Author: Bernd Bischl [aut, cre],
Michel Lang [aut],
Jakob Bossek [aut],
Daniel Horn [aut]
Maintainer: Bernd Bischl
DESCRIPTION | 19 +--
MD5 | 142 +++++++++++++--------------
NAMESPACE | 2
NEWS | 6 -
R/OptPath.R | 7 -
R/OptPath_getter.R | 2
R/OptPath_setter.R | 3
R/ParamSet.R | 8 -
R/aParam.R | 4
R/convertParamSetToIrace.R | 4
R/generateDesign.R | 2
R/getDefaults.R | 21 ++-
R/isMissingValue.R | 3
R/removeMissingValues.R | 4
man/LearnerParam.Rd | 3
man/OptPath.Rd | 5
man/Param.Rd | 3
man/addOptPathEl.Rd | 6 -
man/as.data.frame.OptPathDF.Rd | 3
man/convertParamSetToIrace.Rd | 3
man/dfRowsToList.Rd | 3
man/discreteNameToValue.Rd | 3
man/discreteValueToName.Rd | 3
man/dropParams.Rd | 3
man/extractParamSetFromSooFunction.Rd | 3
man/filterParams.Rd | 3
man/generateDesign.Rd | 3
man/generateGridDesign.Rd | 3
man/generateRandomDesign.Rd | 3
man/getDefaults.Rd | 11 +-
man/getLower.Rd | 3
man/getOptPathBestIndex.Rd | 3
man/getOptPathCol.Rd | 3
man/getOptPathCols.Rd | 3
man/getOptPathDOB.Rd | 3
man/getOptPathEOL.Rd | 3
man/getOptPathEl.Rd | 3
man/getOptPathErrorMessages.Rd | 3
man/getOptPathExecTimes.Rd | 3
man/getOptPathLength.Rd | 3
man/getOptPathParetoFront.Rd | 3
man/getOptPathX.Rd | 3
man/getOptPathY.Rd | 3
man/getParamIds.Rd | 3
man/getParamLengths.Rd | 3
man/getParamNr.Rd | 3
man/getParamTypeCounts.Rd | 3
man/getParamTypes.Rd | 3
man/hasFiniteBoxConstraints.Rd | 3
man/hasForbidden.Rd | 3
man/hasRequires.Rd | 3
man/hasTrafo.Rd | 3
man/hasType.Rd | 3
man/isEmpty.Rd | 3
man/isFeasible.Rd | 3
man/isForbidden.Rd | 3
man/isType.Rd | 3
man/makeParamSet.Rd | 3
man/paramValueToString.Rd | 3
man/removeMissingValues.Rd | 3
man/repairPoint.Rd | 3
man/sampleValue.Rd | 3
man/sampleValues.Rd | 3
man/setOptPathElDOB.Rd | 3
man/setOptPathElEOL.Rd | 3
man/setValueCNames.Rd | 3
man/trafoOptPath.Rd | 3
man/trafoValue.Rd | 3
tests/testthat/test_OptPath.R | 6 -
tests/testthat/test_convertParamSetToIrace.R | 16 ++-
tests/testthat/test_generateDesign.R | 11 +-
tests/testthat/test_getDefaults.R | 15 ++
72 files changed, 278 insertions(+), 172 deletions(-)
Title: Numerical Methods and Optimization in Finance
Diff between NMOF versions 0.34-0 dated 2014-11-05 and 0.34-1 dated 2015-02-03
Description: Functions, examples and data from the book
'Numerical Methods and Optimization in Finance' by M.
Gilli, D. Maringer and E. Schumann. The package provides
implementations of several optimisation heuristics, such as
Differential Evolution, Genetic Algorithms and Threshold
Accepting. There are also functions for the valuation of
financial instruments, such as bonds and options, and
functions that help with stochastic simulations.
Author: Enrico Schumann [aut, cre]
Maintainer: Enrico Schumann
DESCRIPTION | 8
MD5 | 65 ++---
build/vignette.rds |binary
inst/NMOFex/NMOFman.R | 538 +++++++++++++++++++++++-----------------------
inst/doc/An_overview.R | 14 -
inst/doc/An_overview.Rnw | 3
inst/doc/An_overview.pdf |binary
inst/doc/DEnss.R | 60 ++---
inst/doc/DEnss.Rnw | 5
inst/doc/DEnss.pdf |binary
inst/doc/LSselect.R | 24 +-
inst/doc/LSselect.Rnw | 3
inst/doc/LSselect.pdf |binary
inst/doc/NMOF.bib |only
inst/doc/PSlms.R | 20 -
inst/doc/PSlms.Rnw | 2
inst/doc/PSlms.pdf |binary
inst/doc/TAportfolio.R | 40 +--
inst/doc/TAportfolio.Rnw | 5
inst/doc/TAportfolio.pdf |binary
inst/doc/qTableEx.Rnw | 2
inst/doc/qTableEx.pdf |binary
inst/doc/repair.R | 30 +-
inst/doc/repair.Rnw | 4
inst/doc/repair.pdf |binary
inst/doc/vectorise.pdf |binary
inst/unitTests/report.txt | 26 +-
vignettes/.install_extras |only
vignettes/An_overview.Rnw | 3
vignettes/DEnss.Rnw | 5
vignettes/LSselect.Rnw | 3
vignettes/PSlms.Rnw | 2
vignettes/TAportfolio.Rnw | 5
vignettes/qTableEx.Rnw | 2
vignettes/repair.Rnw | 4
35 files changed, 451 insertions(+), 422 deletions(-)
Title: Nested Association Mapping analysis
Diff between NAM versions 1.0.2.1 dated 2015-01-24 and 1.0.2.2 dated 2015-02-03
Description: Package designed for association studies in nested association mapping (NAM) panels, but it also can handle biparental and random populations. It includes functions for genome-wide associations mapping of multiple populations, marker quality control, solving mixed models and finding variance components through REML.
Author: Alencar Xavier, William Muir, Katy Rainey, Tiago Pimenta, Qishan Wang, Shizhong Xu.
Maintainer: Alencar Xavier
DESCRIPTION | 10 +++++-----
MD5 | 9 +++++----
R/gwas.R | 9 +++++----
R/gwas2.R |only
man/NAM-package.Rd | 6 +++---
man/gwas.Rd | 3 +++
6 files changed, 21 insertions(+), 16 deletions(-)
Title: Miscellaneous Functions from M. Kohl
Diff between MKmisc versions 0.96 dated 2013-11-17 and 0.97 dated 2015-02-03
Description: Miscellaneous Functions from M. Kohl
Author: Matthias Kohl [aut, cre]
Maintainer: Matthias Kohl
DESCRIPTION | 15 ++--
MD5 | 18 ++--
NAMESPACE | 1
NEWS | 9 ++
R/or2rr.R |only
R/quantileCI.R | 11 ++
R/repMeans.R | 182 +++++++++++++++++++++++--------------------------
inst/CITATION | 16 +---
man/0MKmisc-package.Rd | 6 -
man/or2rr.Rd |only
man/quantileCI.Rd | 19 +++--
11 files changed, 146 insertions(+), 131 deletions(-)
Title: Distributions To Be Used For GAMLSS Modelling
Diff between gamlss.dist versions 4.3-1 dated 2014-09-17 and 4.3-4 dated 2015-02-03
Description: This package contains the distributions for GAMLSS
modelling.
Author: Mikis Stasinopoulos
Maintainer: Mikis Stasinopoulos
gamlss.dist-4.3-1/gamlss.dist/R/WA1.R |only
gamlss.dist-4.3-1/gamlss.dist/R/WARING.r |only
gamlss.dist-4.3-4/gamlss.dist/DESCRIPTION | 10
gamlss.dist-4.3-4/gamlss.dist/MD5 | 26
gamlss.dist-4.3-4/gamlss.dist/NAMESPACE | 3
gamlss.dist-4.3-4/gamlss.dist/R/BEOI.r | 550 +++++++-------
gamlss.dist-4.3-4/gamlss.dist/R/BEZI.r | 544 ++++++-------
gamlss.dist-4.3-4/gamlss.dist/R/DoublePoisson-30-12-14.R |only
gamlss.dist-4.3-4/gamlss.dist/R/NO.r | 280 +++----
gamlss.dist-4.3-4/gamlss.dist/R/WARING_BOB.r |only
gamlss.dist-4.3-4/gamlss.dist/R/ZAGA.R | 10
gamlss.dist-4.3-4/gamlss.dist/R/make-link-gamlss-4-4-13.R | 344 ++++----
gamlss.dist-4.3-4/gamlss.dist/man/DPO.Rd |only
gamlss.dist-4.3-4/gamlss.dist/man/WARING.Rd | 132 +--
gamlss.dist-4.3-4/gamlss.dist/man/ZAGA.Rd | 227 ++---
gamlss.dist-4.3-4/gamlss.dist/src/dDPOgetC5_C.c |only
gamlss.dist-4.3-4/gamlss.dist/src/tofyHead.h | 2
17 files changed, 1071 insertions(+), 1057 deletions(-)
Title: Tools for Analysis of Diversity and Similarity in Biological
Systems
Diff between divo versions 0.1 dated 2015-01-29 and 0.1.1 dated 2015-02-03
Description: A set of tools for empirical analysis of diversity (a number and frequency of different types in population) and similarity (a number and frequency of shared types in two populations) in biological or ecological systems.
Author: Maciej Pietrzak, Michal Seweryn, Grzegorz Rempala
Maintainer: Maciej Pietrzak
DESCRIPTION | 8 ++---
MD5 | 15 +++++----
R/divo.R | 72 +++++++++++++++++++++++++++++++++-------------
inst/DivO_DP.py | 54 +++++++++++++++++++---------------
inst/DivO_EnvCheck.py |only
inst/DivO_Overlap.py | 13 +++-----
inst/doc/divo-Manual.Rnw | 2 -
inst/doc/divo-Manual.pdf |binary
vignettes/divo-Manual.Rnw | 2 -
9 files changed, 101 insertions(+), 65 deletions(-)
Title: Documentation for Packages distr, distrEx, distrSim, distrTEst,
distrTeach, distrMod, and distrEllipse
Diff between distrDoc versions 2.5 dated 2013-09-13 and 2.5.1 dated 2015-02-03
Description: provides documentation in form of a common vignette to packages distr, distrEx,
distrMod, distrSim, distrTEst, distrTeach, and distrEllipse
Author: Florian Camphausen [ctb] (contributed as student to the documented
packages in the initial phase --2005),
Matthias Kohl [aut, cph],
Peter Ruckdeschel [cre, cph],
Thomas Stabla [ctb] (contributed as student to the documented packages
in the initial phase --2005)
Maintainer: Peter Ruckdeschel
DESCRIPTION | 31 ++++++++++++++++++++-----------
MD5 | 15 ++++++++-------
build |only
inst/CITATION | 22 +++++++++++++++++++++-
inst/NEWS | 9 +++++++++
inst/doc/distr.R | 3 ++-
inst/doc/distr.Rnw | 10 ++++++----
inst/doc/distr.pdf |binary
vignettes/distr.Rnw | 10 ++++++----
9 files changed, 72 insertions(+), 28 deletions(-)
Title: Global Value Chains Decomposition (Wang-Wei-Zhu and Leontief)
Diff between decompr versions 2.0 dated 2015-01-27 and 2.1.0 dated 2015-02-03
Description: Two Global Value Chains decompositions are implemented. Firstly,
the Wang-Wei-Zhu (Wang, Wei, and Zhu 2013) algorithm splits bilateral gross
exports into 16 value added components. Secondly, the Leontief decomposition
(default) derives the value added origin of exports by country and
industry, which is also based on Wang, Wei, and Zhu (2013).
Author: Bastiaan Quast [aut, cre],
Fei Wang [aut],
Victor Kummritz [aut]
Maintainer: Bastiaan Quast
DESCRIPTION | 8 +++----
MD5 | 19 +++++++++---------
NAMESPACE | 1
NEWS | 26 +++++++++++++++++-------
R/decomp.R | 10 ++++++++-
R/leontief.R | 51 ++++++++++++++++++++++++++++++++++++++++++++++---
README.md | 26 +++++++-----------------
man/decomp.Rd | 4 +--
man/kung_fu.Rd | 4 +--
man/leontief.Rd | 2 -
man/leontief_output.Rd |only
11 files changed, 103 insertions(+), 48 deletions(-)
Title: GAMLSS Utilities
Diff between gamlss.util versions 4.2-7 dated 2013-07-03 and 4.3-2 dated 2015-02-03
Description: Extra Functions For GAMLSS And Others Models
Author: Mikis Stasinopoulos
Maintainer: Mikis Stasinopoulos
gamlss.util-4.2-7/gamlss.util/R/createLags.R |only
gamlss.util-4.2-7/gamlss.util/R/flexDist.r |only
gamlss.util-4.2-7/gamlss.util/R/movMean.R |only
gamlss.util-4.2-7/gamlss.util/R/penLS.R |only
gamlss.util-4.2-7/gamlss.util/man/Locmean.Rd |only
gamlss.util-4.2-7/gamlss.util/man/flexDist.Rd |only
gamlss.util-4.2-7/gamlss.util/man/penLS.Rd |only
gamlss.util-4.3-2/gamlss.util/DESCRIPTION | 20
gamlss.util-4.3-2/gamlss.util/MD5 | 29 -
gamlss.util-4.3-2/gamlss.util/NAMESPACE | 56 +-
gamlss.util-4.3-2/gamlss.util/R/PenRegQ.R | 28 -
gamlss.util-4.3-2/gamlss.util/R/centiles-ts.R | 289 +++++++-------
gamlss.util-4.3-2/gamlss.util/R/garmaFit.R | 166 +++++---
gamlss.util-4.3-2/gamlss.util/R/plotSimpleGamlss-3-7-13.R | 7
gamlss.util-4.3-2/gamlss.util/R/scattersmooth.r | 257 ++++++------
gamlss.util-4.3-2/gamlss.util/man/garmaFit.Rd | 6
gamlss.util-4.3-2/gamlss.util/man/penReg.Rd | 26 -
gamlss.util-4.3-2/gamlss.util/man/plotSimpleGamlss.Rd | 2
gamlss.util-4.3-2/gamlss.util/man/scattersmooth.Rd | 28 +
19 files changed, 486 insertions(+), 428 deletions(-)
Title: Generating and fitting truncated (gamlss.family) distributions
Diff between gamlss.tr versions 4.2-7 dated 2014-01-18 and 4.3-1 dated 2015-02-03
Description: This is an add on package to GAMLSS. The purpose of this
package is to allow users to defined truncated distributions in
GAMLSS models. The main function gen.trun() generates truncated
version of an existing GAMLSS family distribution.
Author: Mikis Stasinopoulos
Maintainer: Mikis Stasinopoulos
DESCRIPTION | 10 +++++-----
MD5 | 6 +++---
NAMESPACE | 4 +++-
man/fitTail.Rd | 3 ++-
4 files changed, 13 insertions(+), 10 deletions(-)
Title: Generalised Additive Models for Location Scale and Shape.
Diff between gamlss versions 4.3-1 dated 2014-09-17 and 4.3-4 dated 2015-02-03
Description: The Library For Fitting GAMLSS Models
Author: Mikis Stasinopoulos
Maintainer: Mikis Stasinopoulos
gamlss-4.3-1/gamlss/R/SUMMARY-15-06-13.R |only
gamlss-4.3-1/gamlss/R/gamlss-01-05-13.R |only
gamlss-4.3-1/gamlss/R/vcoc-gamlss-03-10-13.R |only
gamlss-4.3-4/gamlss/DESCRIPTION | 10
gamlss-4.3-4/gamlss/MD5 | 47 +--
gamlss-4.3-4/gamlss/NAMESPACE | 1
gamlss-4.3-4/gamlss/R/SUMMARY.R |only
gamlss-4.3-4/gamlss/R/cubicSplines-10-08-12.R | 184 +++++------
gamlss-4.3-4/gamlss/R/extra.R | 119 ++++---
gamlss-4.3-4/gamlss/R/gamlss.R |only
gamlss-4.3-4/gamlss/R/lms.R | 6
gamlss-4.3-4/gamlss/R/lo_new.R | 18 -
gamlss-4.3-4/gamlss/R/lpred.R | 332 ++++++++++-----------
gamlss-4.3-4/gamlss/R/pb_03-02-2014.R | 14
gamlss-4.3-4/gamlss/R/pb_new.R |only
gamlss-4.3-4/gamlss/R/predict.gamlss.R | 2
gamlss-4.3-4/gamlss/R/pvc.R | 17 -
gamlss-4.3-4/gamlss/R/qstats-29-12-12.R | 13
gamlss-4.3-4/gamlss/R/quantSheets.R | 19 -
gamlss-4.3-4/gamlss/R/stepGAIC-03-10-13..R | 19 +
gamlss-4.3-4/gamlss/R/term-plot.R | 402 ++++++++++++++++++--------
gamlss-4.3-4/gamlss/R/vcov-gamlss.R |only
gamlss-4.3-4/gamlss/inst/doc/NEWS.txt | 44 ++
gamlss-4.3-4/gamlss/man/Q.stats.Rd | 102 +++---
gamlss-4.3-4/gamlss/man/gamlss.ps.Rd | 4
gamlss-4.3-4/gamlss/man/ps.Rd | 13
gamlss-4.3-4/gamlss/man/summary.gamlss.Rd | 6
gamlss-4.3-4/gamlss/man/term.plot.Rd | 66 ++--
28 files changed, 850 insertions(+), 588 deletions(-)
Title: Miscellaneous Helper Functions for B. Bischl
Diff between BBmisc versions 1.8 dated 2014-10-30 and 1.9 dated 2015-02-03
Description: Miscellaneous helper functions for and from B. Bischl and
some other guys at TU Dortmund, mainly for package development.
Author: Bernd Bischl [aut, cre],
Michel Lang [aut],
Jakob Bossek [aut],
Daniel Horn [aut],
Jakob Richter [aut]
Maintainer: Bernd Bischl
DESCRIPTION | 10 -
MD5 | 215 +++++++++++++++++-----------------
NAMESPACE | 3
NEWS | 35 +++--
R/load2.R | 2
R/mapValues.R |only
R/messagef.R | 10 -
R/normalize.R | 11 +
R/optimizeSubInts.R | 21 ++-
R/pause.R | 2
R/requirePackages.R | 60 ++++++---
R/save2.R | 2
R/setClasses.R | 2
man/addClasses.Rd | 3
man/argsAsNamedList.Rd | 3
man/asMatrixCols.Rd | 3
man/asQuoted.Rd | 3
man/binPack.Rd | 3
man/btwn.Rd | 3
man/cFactor.Rd | 3
man/catf.Rd | 3
man/checkArg.Rd | 3
man/checkListElementClass.Rd | 3
man/chunk.Rd | 3
man/clipString.Rd | 3
man/coalesce.Rd | 3
man/collapse.Rd | 3
man/collapsef.Rd | 3
man/computeMode.Rd | 3
man/convertDataFrameCols.Rd | 3
man/convertInteger.Rd | 3
man/convertIntegers.Rd | 3
man/convertListOfRowsToDataFrame.Rd | 3
man/convertMatrixType.Rd | 3
man/convertRowsToList.Rd | 3
man/convertToShortString.Rd | 3
man/dapply.Rd | 3
man/deprecated.Rd | 3
man/do.call2.Rd | 3
man/dropNamed.Rd | 3
man/ensureVector.Rd | 3
man/explode.Rd | 3
man/extractSubList.Rd | 3
man/filterNull.Rd | 3
man/getAttributeNames.Rd | 3
man/getClass1.Rd | 3
man/getFirst.Rd | 3
man/getMaxIndex.Rd | 3
man/getMaxIndexOfRows.Rd | 3
man/getOperatingSystem.Rd | 3
man/getRelativePath.Rd | 3
man/getUnixTime.Rd | 3
man/getUsedFactorLevels.Rd | 3
man/hasAttributes.Rd | 3
man/insert.Rd | 3
man/is.error.Rd | 3
man/isDirectory.Rd | 3
man/isEmptyDirectory.Rd | 3
man/isExpensiveExampleOk.Rd | 3
man/isFALSE.Rd | 3
man/isProperlyNamed.Rd | 3
man/isScalarNA.Rd | 3
man/isScalarValue.Rd | 3
man/isSubset.Rd | 3
man/isSuperset.Rd | 3
man/isValidName.Rd | 3
man/itostr.Rd | 3
man/lib.Rd | 3
man/load2.Rd | 3
man/lsort.Rd | 3
man/makeDataFrame.Rd | 3
man/makeFileCache.Rd | 3
man/makeProgressBar.Rd | 3
man/makeS3Obj.Rd | 3
man/makeSimpleFileLogger.Rd | 3
man/mapValues.Rd |only
man/messagef.Rd | 8 -
man/namedList.Rd | 3
man/names2.Rd | 3
man/nin.Rd | 3
man/normalize.Rd | 5
man/optimizeSubInts.Rd | 6
man/pause.Rd | 3
man/printStrToChar.Rd | 3
man/printToChar.Rd | 3
man/rangeVal.Rd | 3
man/requirePackages.Rd | 26 ++--
man/rowLapply.Rd | 3
man/save2.Rd | 3
man/seq_row.Rd | 3
man/setAttribute.Rd | 3
man/setClasses.Rd | 3
man/setRowNames.Rd | 3
man/setValue.Rd | 3
man/sortByCol.Rd | 3
man/splitPath.Rd | 3
man/splitTime.Rd | 3
man/stopf.Rd | 3
man/strrepeat.Rd | 3
man/suppressAll.Rd | 3
man/symdiff.Rd | 3
man/system3.Rd | 3
man/toRangeStr.Rd | 3
man/vlapply.Rd | 3
man/warningf.Rd | 3
man/which.first.Rd | 3
tests/testthat/test_mapValues.R |only
tests/testthat/test_normalize.R | 14 ++
tests/testthat/test_optimizeSubInts.R | 6
tests/testthat/test_requirePackages.R | 25 ++-
110 files changed, 447 insertions(+), 280 deletions(-)
Title: Multinomial Processing Tree (MPT) Models
Diff between mpt versions 0.5-0 dated 2014-10-06 and 0.5-1 dated 2015-02-03
Description: Fitting and testing multinomial processing tree models, a class
of statistical models for categorical data. The parameters are the link
probabilities of a tree-like graph and represent the latent cognitive
processing steps executed to arrive at observable response categories
(Batchelder & Riefer, 1999; Erdfelder et al., 2009; Riefer &
Batchelder, 1988).
Author: Florian Wickelmaier [aut, cre],
Achim Zeileis [aut]
Maintainer: Florian Wickelmaier
ChangeLog | 14 +++++++++-----
DESCRIPTION | 8 ++++----
MD5 | 24 +++++++++++++-----------
R/mpt.R | 13 +++++++------
R/mptspec.R | 47 +++++++++++++++++++++++++++++++++++++----------
data/proact.rda |binary
data/prospecMemory.rda |only
data/recogROC.rda |binary
data/retroact.rda |binary
man/mpt.Rd | 5 +++--
man/mptEM.Rd | 18 +++++++++---------
man/mptspec.Rd | 8 ++++++++
man/prospecMemory.Rd |only
man/simulate.mpt.Rd | 2 +-
14 files changed, 91 insertions(+), 48 deletions(-)
Title: Metapopulation and Landscape Simulation
Diff between MetaLandSim versions 0.1 dated 2014-11-09 and 0.2 dated 2015-02-03
Description: Tools to generate random landscape graphs, evaluate species
occurrence in dynamic landscapes, simulate future landscape occupation and
evaluate range expansion when new empty patches are available (e.g. as a
result of climate change).
Author: Frederico Mestre, Fernando Canovas, Ricardo Pita, Antonio Mira, Pedro
Beja.
Maintainer: Frederico Mestre
MetaLandSim-0.1/MetaLandSim/R/manage.simulations.R |only
MetaLandSim-0.1/MetaLandSim/man/manage.simulations.Rd |only
MetaLandSim-0.2/MetaLandSim/DESCRIPTION | 8 -
MetaLandSim-0.2/MetaLandSim/MD5 | 43 +++++-----
MetaLandSim-0.2/MetaLandSim/NAMESPACE | 4
MetaLandSim-0.2/MetaLandSim/R/manage_expansion_sim.R |only
MetaLandSim-0.2/MetaLandSim/R/manage_landscape_sim.R |only
MetaLandSim-0.2/MetaLandSim/build/vignette.rds |binary
MetaLandSim-0.2/MetaLandSim/data/cabrera.rda |binary
MetaLandSim-0.2/MetaLandSim/data/datalist | 1
MetaLandSim-0.2/MetaLandSim/data/landscape_change.rda |binary
MetaLandSim-0.2/MetaLandSim/data/mc_df.rda |binary
MetaLandSim-0.2/MetaLandSim/data/occ.landscape.rda |binary
MetaLandSim-0.2/MetaLandSim/data/occ.landscape2.rda |binary
MetaLandSim-0.2/MetaLandSim/data/param1.rda |binary
MetaLandSim-0.2/MetaLandSim/data/param2.rda |only
MetaLandSim-0.2/MetaLandSim/data/rg_exp.rda |binary
MetaLandSim-0.2/MetaLandSim/data/rland.rda |binary
MetaLandSim-0.2/MetaLandSim/inst/CITATION |only
MetaLandSim-0.2/MetaLandSim/inst/doc/MetaLandSim.pdf |binary
MetaLandSim-0.2/MetaLandSim/inst/doc/landscape_simulation.pdf |binary
MetaLandSim-0.2/MetaLandSim/inst/doc/range_expansion.pdf |binary
MetaLandSim-0.2/MetaLandSim/man/MetaLandSim-package.Rd | 39 +++++++--
MetaLandSim-0.2/MetaLandSim/man/iterate.graph.Rd | 8 -
MetaLandSim-0.2/MetaLandSim/man/manage_expansion_sim.Rd |only
MetaLandSim-0.2/MetaLandSim/man/manage_landscape_sim.Rd |only
MetaLandSim-0.2/MetaLandSim/man/param2.Rd |only
27 files changed, 68 insertions(+), 35 deletions(-)
Title: Fitting an interval response variable using gamlss.family
distributions
Diff between gamlss.cens versions 4.2.7 dated 2014-01-11 and 4.3.1 dated 2015-02-03
Description: This is an add on package to GAMLSS. The purpose of this
package is to allow users to fit interval response variables in
GAMLSS models. The main function gen.cens() generates a
censored version of an existing GAMLSS family distribution.
Author: Mikis Stasinopoulos
Maintainer: Mikis Stasinopoulos
DESCRIPTION | 10 +++++-----
MD5 | 6 +++---
NAMESPACE | 42 +++++++++++++++++++++---------------------
data/lip.rda |binary
4 files changed, 29 insertions(+), 29 deletions(-)
Title: GAMLSS Extra Additive terms
Diff between gamlss.add versions 4.3-0 dated 2014-06-03 and 4.3-3 dated 2015-02-03
Description: Extra additive terms for GAMLSS models.
Author: Mikis Stasinopoulos
Maintainer: Mikis Stasinopoulos
DESCRIPTION | 13 ++---
MD5 | 16 +++---
NAMESPACE | 13 +++--
R/freeKnots-18-06-13.R | 2
R/gam_gamlss.R | 13 +++--
R/nnet_gamlss.R | 28 +++++++----
R/plotNN.R |only
R/tree_gamlss.R | 23 ++++++---
man/gamlss.ga.Rd | 118 ++++++++++++++++++++++++-------------------------
man/plotNN.Rd |only
10 files changed, 128 insertions(+), 98 deletions(-)
Title: DetMCD Algorithm (Robust and Deterministic Estimation of
Location and Scatter)
Diff between DetMCD versions 0.0.1 dated 2014-10-21 and 0.0.2 dated 2015-02-03
Description: DetMCD is a new algorithm for robust and deterministic estimation of location and scatter. The benefits of robust and deterministic estimation are explained in Hubert, M., Rousseeuw, P.J. and Verdonck, T. (2012),"A deterministic algorithm for robust location and scatter", Journal of Computational and Graphical Statistics, Volume 21, Number 3, Pages 618--637.
Author: Vakili Kaveh [aut, cre],
Mia Hubert [ths]
Maintainer: Vakili Kaveh
DESCRIPTION | 10 +++++-----
MD5 | 6 +++---
NAMESPACE | 4 +---
R/DetMCD.R | 3 ++-
4 files changed, 11 insertions(+), 12 deletions(-)
Title: N-Gram Analysis of Biological Sequences
Diff between biogram versions 1.0 dated 2014-12-19 and 1.1 dated 2015-02-03
Description: Tools for extraction and analysis of various
n-grams (sequences of n items) derived from biological sequences (proteins
or nucleic acids). To deal with the dimensionality of the n-gram data,
biogram uses QuiPT (quick permutation test) for fast feature-filtering.
Author: Michal Burdukiewicz [cre, aut],
Piotr Sobczyk [aut],
Chris Lauber [aut]
Maintainer: Michal Burdukiewicz
biogram-1.0/biogram/man/data_sample.Rd |only
biogram-1.0/biogram/man/prepare_data.Rd |only
biogram-1.0/biogram/tests/testthat/test_quit_consistency.R |only
biogram-1.1/biogram/CHANGELOG |only
biogram-1.1/biogram/DESCRIPTION | 7
biogram-1.1/biogram/MD5 | 80 ++++----
biogram-1.1/biogram/NAMESPACE | 10 -
biogram-1.1/biogram/R/biogram.R | 89 +++++----
biogram-1.1/biogram/R/check_criterion.R | 2
biogram-1.1/biogram/R/check_ngrams.R |only
biogram-1.1/biogram/R/count_multigrams.R | 36 ++-
biogram-1.1/biogram/R/count_ngrams.R | 61 ++++--
biogram-1.1/biogram/R/criterion_distribution.R | 32 +--
biogram-1.1/biogram/R/data_manipulation.R | 112 ++++++------
biogram-1.1/biogram/R/decode_ngrams.R |only
biogram-1.1/biogram/R/feature_test_class.R |only
biogram-1.1/biogram/R/information_gain.R | 24 +-
biogram-1.1/biogram/R/ngrams.R | 11 -
biogram-1.1/biogram/R/position_ngrams.R |only
biogram-1.1/biogram/R/test_features.R | 98 +++++++---
biogram-1.1/biogram/R/utilities.R | 1
biogram-1.1/biogram/README.md | 13 +
biogram-1.1/biogram/inst |only
biogram-1.1/biogram/man/biogram-package.Rd | 92 +++++----
biogram-1.1/biogram/man/calc_ig.Rd | 8
biogram-1.1/biogram/man/calc_ig_single.Rd | 5
biogram-1.1/biogram/man/count_multigrams.Rd | 43 ++--
biogram-1.1/biogram/man/count_ngrams.Rd | 61 ++++--
biogram-1.1/biogram/man/create_feature_target.Rd | 3
biogram-1.1/biogram/man/create_ngrams.Rd | 16 +
biogram-1.1/biogram/man/criterion_distribution.Rd | 9
biogram-1.1/biogram/man/criterions.Rd | 3
biogram-1.1/biogram/man/cut.feature_test.Rd |only
biogram-1.1/biogram/man/decode_ngrams.Rd |only
biogram-1.1/biogram/man/degenerate.Rd | 3
biogram-1.1/biogram/man/fast_crosstable.Rd | 3
biogram-1.1/biogram/man/feature_test.Rd |only
biogram-1.1/biogram/man/get_ngrams_ind.Rd | 3
biogram-1.1/biogram/man/human_cleave.Rd | 3
biogram-1.1/biogram/man/is_ngram.Rd |only
biogram-1.1/biogram/man/l2n.Rd | 3
biogram-1.1/biogram/man/n2l.Rd | 3
biogram-1.1/biogram/man/position_ngrams.Rd |only
biogram-1.1/biogram/man/print.feature_test.Rd |only
biogram-1.1/biogram/man/seq2ngrams.Rd | 6
biogram-1.1/biogram/man/summary.feature_test.Rd |only
biogram-1.1/biogram/man/test_features.Rd | 49 +++--
biogram-1.1/biogram/tests/testthat/test_count_ngrams.R | 76 ++++----
biogram-1.1/biogram/tests/testthat/test_position_ngrams.R |only
biogram-1.1/biogram/tests/testthat/test_quipt_consistency.R |only
50 files changed, 580 insertions(+), 385 deletions(-)
Title: Embedded JavaScript Engine
Diff between V8 versions 0.4 dated 2015-01-12 and 0.5 dated 2015-02-03
Description: V8 is Google's open source, high performance JavaScript engine. It
is written in C++ and implements ECMAScript as specified in ECMA-262, 5th
edition. In addition, this package implements typed arrays as specified in
ECMA 6 in order to support high performance computing and libraries compiled
with emscripten.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms
DESCRIPTION | 14
MD5 | 37 -
R/RcppExports.R | 12
R/V8.R | 7
configure | 6
inst/doc/npm.R | 2
inst/doc/npm.Rmd | 2
inst/doc/npm.html | 11
inst/doc/v8_intro.R | 22
inst/doc/v8_intro.Rmd | 20
inst/doc/v8_intro.html | 28
inst/js/crossfilter.js |only
inst/js/underscore.js | 1414 -------------------------------------------------
man/new_context.Rd | 5
src/RcppExports.cpp | 48 +
src/V8.cpp | 63 ++
src/v8_typed_array.cpp |only
src/v8_typed_array.h |only
tools/v8-3.14.5.rb | 5
vignettes/npm.Rmd | 2
vignettes/v8_intro.Rmd | 20
21 files changed, 238 insertions(+), 1480 deletions(-)
Title: Seawater Carbonate Chemistry
Diff between seacarb versions 3.0.5 dated 2015-01-12 and 3.0.6 dated 2015-02-03
Description: Calculates parameters of the seawater carbonate system and assists the design of ocean acidification perturbation experiments.
Author: Jean-Pierre Gattuso [aut, cre, cph],
Jean-Marie Epitalon [aut],
Heloise Lavigne [aut],
James Orr [ctb],
Bernard Gentili [ctb],
Andreas Hofmann [ctb],
Aurélien Proye [ctb],
Karline Soetaert [ctb],
James Rae [ctb]
Maintainer: Jean-Pierre Gattuso
ChangeLog | 6 ++-
DESCRIPTION | 8 ++--
MD5 | 26 ++++++-------
R/buffer.R | 19 ++++-----
R/carb.R | 112 ++++++++++++++++++++++++++++++++++++++-------------------
man/Om.Rd | 4 +-
man/buffer.Rd | 2 -
man/buffesm.Rd | 2 -
man/carb.Rd | 16 +++++---
man/oa.Rd | 2 -
man/pCa.Rd | 2 -
man/pTA.Rd | 2 -
man/pgas.Rd | 2 -
man/pmix.Rd | 2 -
14 files changed, 125 insertions(+), 80 deletions(-)
Title: Whole Genome Average Interval Mapping for QTL Detection using
Mixed Models
Diff between wgaim versions 1.4-5 dated 2015-01-31 and 1.4-6 dated 2015-02-03
Description: This package integrates sophisticated mixed modelling methods with a whole genome approach to detecting significant QTL in linkage maps.
Author: Julian Taylor
Maintainer: Julian Taylor
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/wgaim8.R | 9 +++++----
inst/doc/wgaim.pdf |binary
4 files changed, 12 insertions(+), 11 deletions(-)
Title: Simulation and Analysis of Random Fields
Diff between RandomFields versions 3.0.60 dated 2015-01-28 and 3.0.62 dated 2015-02-03
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 [ctr], Ulrike Ober [ctb], Katharina Burmeister [ctb], Juliane Manitz [ctb], Paulo Ribeiro [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather
DESCRIPTION | 6
MD5 | 79 +++++-----
NAMESPACE | 8 +
R/Methods-RFsp.R | 18 ++
R/RC_GLOBALS.R | 3
R/RFempvario-Methods-plots.R | 2
R/RFgui.R | 4
R/RMmodels-Methods-plots.R | 11 -
R/RMmodelsSpecial.R | 4
R/convert.R | 21 +-
R/getNset.R | 37 +++++
R/rf-plots.R | 6
man/CoordinateSystems.Rd | 50 +++++-
man/RFgridDataFrame-class.Rd | 6
man/RFpar.Rd |only
man/RFpointsDataFrame-class.Rd | 6
man/RFspatialGridDataFrame-class.Rd | 6
man/RFspatialPointsDataFrame-class.Rd | 6
man/RandomFields.Rd | 1
man/plot-method.Rd | 4
src/Coordinate_systems.cc | 67 ++-------
src/Coordinate_systems.h | 13 -
src/Huetchen.cc | 2
src/InternalCov.cc | 17 +-
src/KeyInfo.cc | 245 ++++++++++++++++------------------
src/Makevars.in | 2
src/Primitive.cc | 97 ++++++++-----
src/RF.h | 150 ++++++++++++--------
src/auxiliary.cc | 2
src/basic.h | 3
src/circulant.cc | 2
src/extremes.cc | 4
src/families.cc | 7
src/getNset.cc | 7
src/initNerror.cc | 16 +-
src/operator.cc | 2
src/plusmalS.cc | 193 +++++++++++++++++++-------
src/primitive.h | 10 -
src/rf_interfaces.cc | 22 +--
src/startGetNset.cc | 16 +-
src/variogramAndCo.cc | 16 +-
41 files changed, 690 insertions(+), 481 deletions(-)
Title: Analyzing RNA Sequence Count Tables Using Quasi-likelihood
Diff between QuasiSeq versions 1.0-5 dated 2015-01-05 and 1.0-6 dated 2015-02-03
Description: Identify differentially expressed genes in RNA-seq count data using quasi-Poisson or quasi-negative binomial models with QL, QLShrink and QLSpline methods (Lund, Nettleton, McCarthy, and Smyth, 2012).
Author: Steve Lund
Maintainer: Steve Lund
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
R/QL.results.R | 2 +-
3 files changed, 7 insertions(+), 7 deletions(-)
Title: Evaluation of Diversity in Nucleotide Libraries
Diff between peptider versions 0.1.6 dated 2014-12-03 and 0.1.7 dated 2015-02-03
Description: Functions for evaluating diversity in peptide libraries, including
NNN, NNB, NNK/S, and 20/20 schemes. This includes expected coverage,
relative efficiency, and functional diversity of the library.
Author: Heike Hofmann, Eric Hare, ggobi Foundation
Maintainer: Eric Hare
DESCRIPTION | 10 +++----
MD5 | 56 ++++++++++++++++++++++----------------------
NAMESPACE | 2 -
R/peptider.r | 45 +++++++++++++++++++----------------
R/tabulate.r | 8 +++---
data/schemes.rda |binary
man/BLOSUM80.Rd | 3 +-
man/codons.Rd | 3 +-
man/coverage.Rd | 5 ++-
man/detect.Rd | 3 +-
man/diversity.Rd | 3 +-
man/efficiency.Rd | 5 ++-
man/encodingReduce.Rd | 3 +-
man/genNeighbors.Rd | 5 ++-
man/genNeighbors_reduced.Rd | 5 ++-
man/generateCustom.Rd | 5 ++-
man/generateCustomLib.Rd | 5 ++-
man/generateCustomNei.Rd | 5 ++-
man/generateCustomProbs.Rd | 5 ++-
man/getChoices.Rd | 3 +-
man/getCounts.Rd | 3 +-
man/getNeighbors.Rd | 3 +-
man/getNofNeighbors.Rd | 3 +-
man/libBuild.Rd | 3 +-
man/libscheme.Rd | 5 ++-
man/makowski.Rd | 5 ++-
man/ppeptide.Rd | 3 +-
man/scheme.Rd | 3 +-
man/schemes.Rd | 11 ++++----
29 files changed, 123 insertions(+), 95 deletions(-)
Title: Unified interface to Some Popular Parallelization Back-ends for
Interactive Usage and Package Development
Diff between parallelMap versions 1.1 dated 2014-07-03 and 1.2 dated 2015-02-03
Description: Map over lists in parallel. Supports local, multicore, mpi
and BatchJobs mode. Allows "tagging" of the parallel operation
with a level name that can be later selected by the user to
switch on parallel execution for exactly this operation.
Author: Bernd Bischl
Maintainer: Bernd Bischl
parallelMap-1.1/parallelMap/man/parallelShowRegisteredLevels.Rd |only
parallelMap-1.2/parallelMap/DESCRIPTION | 16 -
parallelMap-1.2/parallelMap/MD5 | 71 ++++---
parallelMap-1.2/parallelMap/NAMESPACE | 6
parallelMap-1.2/parallelMap/NEWS | 8
parallelMap-1.2/parallelMap/R/autodetectCpus.R | 20 +-
parallelMap-1.2/parallelMap/R/batchjobs.R | 36 ----
parallelMap-1.2/parallelMap/R/displayErrorMessages.R | 15 -
parallelMap-1.2/parallelMap/R/getExtraPackages.R | 15 -
parallelMap-1.2/parallelMap/R/getOption.R | 4
parallelMap-1.2/parallelMap/R/logging.R | 2
parallelMap-1.2/parallelMap/R/makeMulticoreCluster.R |only
parallelMap-1.2/parallelMap/R/mclapply_fixed.R | 70 ++++---
parallelMap-1.2/parallelMap/R/parallelApply.R | 6
parallelMap-1.2/parallelMap/R/parallelExport.R | 15 -
parallelMap-1.2/parallelMap/R/parallelLibrary.R | 35 ++-
parallelMap-1.2/parallelMap/R/parallelMap.R | 89 ++++------
parallelMap-1.2/parallelMap/R/parallelRegisterLevels.R | 62 +++++-
parallelMap-1.2/parallelMap/R/parallelSource.R | 35 ++-
parallelMap-1.2/parallelMap/R/parallelStart.R | 59 ++++--
parallelMap-1.2/parallelMap/R/parallelStop.R | 13 -
parallelMap-1.2/parallelMap/R/utils.R | 10 -
parallelMap-1.2/parallelMap/R/zzz.R | 5
parallelMap-1.2/parallelMap/man/parallelExport.Rd | 15 -
parallelMap-1.2/parallelMap/man/parallelGetRegisteredLevels.Rd |only
parallelMap-1.2/parallelMap/man/parallelLapply.Rd | 15 -
parallelMap-1.2/parallelMap/man/parallelLibrary.Rd | 5
parallelMap-1.2/parallelMap/man/parallelMap.Rd | 5
parallelMap-1.2/parallelMap/man/parallelRegisterLevels.Rd | 27 ++-
parallelMap-1.2/parallelMap/man/parallelShowOptions.Rd | 3
parallelMap-1.2/parallelMap/man/parallelSource.Rd | 5
parallelMap-1.2/parallelMap/man/parallelStart.Rd | 11 -
parallelMap-1.2/parallelMap/man/parallelStop.Rd | 3
parallelMap-1.2/parallelMap/tests/testthat/helpers.R | 4
parallelMap-1.2/parallelMap/tests/testthat/test_autodetectCpus.R |only
parallelMap-1.2/parallelMap/tests/testthat/test_batchjobs.R | 20 --
parallelMap-1.2/parallelMap/tests/testthat/test_multicore.R | 2
parallelMap-1.2/parallelMap/tests/testthat/test_registerLevels.R | 32 ++-
parallelMap-1.2/parallelMap/tests/testthat/test_stopWithJobErrorMessages.R |only
39 files changed, 403 insertions(+), 336 deletions(-)
Title: Matrix eQTL: Ultra fast eQTL analysis via large matrix
operations
Diff between MatrixEQTL versions 2.1.0 dated 2014-02-25 and 2.1.1 dated 2015-02-03
Description: Matrix eQTL is designed for fast eQTL analysis on large datasets.
Matrix eQTL can test for association between genotype and gene expression using linear regression
with either additive or ANOVA genotype effects.
The models can include covariates to account for factors
as population stratification, gender, and clinical variables.
It also supports models with heteroscedastic and/or correlated errors,
false discovery rate estimation and separate treatment of local (cis) and distant (trans) eQTLs.
Author: Andrey Shabalin
Maintainer: Andrey Shabalin
MatrixEQTL-2.1.0/MatrixEQTL/demo/a.nocvrt.R |only
MatrixEQTL-2.1.0/MatrixEQTL/demo/b.cvrt.R |only
MatrixEQTL-2.1.0/MatrixEQTL/demo/c.weights.R |only
MatrixEQTL-2.1.0/MatrixEQTL/demo/d.ANOVA.R |only
MatrixEQTL-2.1.0/MatrixEQTL/demo/d.ANOVA5.R |only
MatrixEQTL-2.1.0/MatrixEQTL/demo/e.interaction.R |only
MatrixEQTL-2.1.1/MatrixEQTL/DESCRIPTION | 9
MatrixEQTL-2.1.1/MatrixEQTL/MD5 | 38 ++-
MatrixEQTL-2.1.1/MatrixEQTL/R/Matrix_eQTL_engine.R | 170 +++++++----------
MatrixEQTL-2.1.1/MatrixEQTL/demo/00Index | 6
MatrixEQTL-2.1.1/MatrixEQTL/demo/a.nocvrt.r |only
MatrixEQTL-2.1.1/MatrixEQTL/demo/b.cvrt.r |only
MatrixEQTL-2.1.1/MatrixEQTL/demo/c.weights.r |only
MatrixEQTL-2.1.1/MatrixEQTL/demo/d.ANOVA.r |only
MatrixEQTL-2.1.1/MatrixEQTL/demo/d.ANOVA5.r |only
MatrixEQTL-2.1.1/MatrixEQTL/demo/e.interaction.r |only
MatrixEQTL-2.1.1/MatrixEQTL/demo/p.hist.r |only
MatrixEQTL-2.1.1/MatrixEQTL/demo/q.qqplot.r |only
MatrixEQTL-2.1.1/MatrixEQTL/demo/sample.cis.r | 6
MatrixEQTL-2.1.1/MatrixEQTL/inst/CITATION | 2
MatrixEQTL-2.1.1/MatrixEQTL/man/MatrixEQTL-package.Rd | 2
MatrixEQTL-2.1.1/MatrixEQTL/man/MatrixEQTL_cis_code.Rd | 4
MatrixEQTL-2.1.1/MatrixEQTL/man/Matrix_eQTL_main.Rd | 2
MatrixEQTL-2.1.1/MatrixEQTL/man/modelANOVA.Rd | 15 +
MatrixEQTL-2.1.1/MatrixEQTL/man/modelLINEAR.Rd | 6
MatrixEQTL-2.1.1/MatrixEQTL/man/modelLINEAR_CROSS.Rd | 5
MatrixEQTL-2.1.1/MatrixEQTL/man/plot.MatrixEQTL.Rd | 5
27 files changed, 131 insertions(+), 139 deletions(-)
Title: Functions to Create and Manipulate Discrete Random Variables
Diff between discreteRV versions 1.1.3 dated 2014-12-03 and 1.1.4 dated 2015-02-03
Description: discreteRV implements a set of functions that allow computations
involving discrete random variables. It uses a syntax which is familiar to
that which is used in mathematical statistics and probability courses.
Author: Andreas Buja
Maintainer: Eric Hare
DESCRIPTION | 12 ++++----
MD5 | 60 +++++++++++++++++++++----------------------
NAMESPACE | 3 +-
R/discreteRV-Probabilities.r | 31 ++++++++++++----------
man/Conditional.Rd | 3 +-
man/E.Rd | 3 +-
man/KURT.Rd | 3 +-
man/P.Rd | 3 +-
man/Prop.Rd | 3 +-
man/SD.Rd | 3 +-
man/SKEW.Rd | 3 +-
man/SofI.Rd | 3 +-
man/SofIID.Rd | 3 +-
man/V.Rd | 3 +-
man/as.RV.Rd | 3 +-
man/grapes-AND-grapes.Rd | 3 +-
man/grapes-OR-grapes.Rd | 3 +-
man/grapes-in-grapes.Rd | 3 +-
man/make.RV.Rd | 17 +++++++-----
man/margins.Rd | 3 +-
man/mult.Rd | 3 +-
man/multN.Rd | 3 +-
man/outcomes.Rd | 3 +-
man/plot.RV.Rd | 3 +-
man/plot.RVsim.Rd | 3 +-
man/print.RV.Rd | 3 +-
man/probs.Rd | 3 +-
man/props.Rd | 3 +-
man/qqnorm.RV.Rd | 3 +-
man/rsim.Rd | 3 +-
man/skewSim.Rd | 3 +-
31 files changed, 117 insertions(+), 84 deletions(-)
Title: Cross-Entropy Clustering
Diff between CEC versions 0.9.2 dated 2014-11-15 and 0.9.3 dated 2015-02-03
Description: Cross-Entropy Clustering (CEC) divides the data into Gaussian type clusters. It performs the automatic reduction of unnecessary clusters, while at the same time allows the simultaneous use of various type Gaussian mixture models.
Author: Konrad Kamieniecki [aut, cre], Przemyslaw Spurek [ctb]
Maintainer: Konrad Kamieniecki
CEC-0.9.2/CEC/R/initcenters.R |only
CEC-0.9.2/CEC/README.md |only
CEC-0.9.2/CEC/man/initcenters.Rd |only
CEC-0.9.3/CEC/DESCRIPTION | 8
CEC-0.9.3/CEC/MD5 | 31
CEC-0.9.3/CEC/NAMESPACE | 2
CEC-0.9.3/CEC/R/cec.R | 82
CEC-0.9.3/CEC/R/cec.plot.cost.function.R |only
CEC-0.9.3/CEC/R/init.centers.R |only
CEC-0.9.3/CEC/R/model.covariance.R |only
CEC-0.9.3/CEC/data/fourGaussians.rda |only
CEC-0.9.3/CEC/data/mixShapes.rda |only
CEC-0.9.3/CEC/inst/cec_tests/cec1.dp | 2481 --
CEC-0.9.3/CEC/inst/cec_tests/clustering.test.R | 9
CEC-0.9.3/CEC/inst/cec_tests/energy.calculation.test.mouseset3d.R | 22
CEC-0.9.3/CEC/inst/cec_tests/mouse3d.data |11330 +++-------
CEC-0.9.3/CEC/man/cec.Rd | 38
CEC-0.9.3/CEC/man/fourGaussians.Rd |only
CEC-0.9.3/CEC/man/init.centers.Rd |only
CEC-0.9.3/CEC/man/mixShapes.Rd |only
CEC-0.9.3/CEC/src/Makevars | 2
CEC-0.9.3/CEC/src/cec.c | 13
22 files changed, 4765 insertions(+), 9253 deletions(-)