Title: Tools for spatial data
Diff between fields versions 6.6.3 dated 2012-01-03 and 6.7 dated 2012-10-16
Description: Fields is for curve, surface and function fitting with an
emphasis on splines, spatial data and spatial statistics. The
major methods include cubic, robust, and thin plate splines,
and Kriging for large data sets. The splines and Kriging
methods are supporting by functions that can determine the
smoothing parameter (nugget and sill variance) by cross
validation and also by restricted maximum likelihood. A major
feature is that any covariance function implemented in R with
the fields interface can be used for spatial prediction. Some
tailored optimization functions are supplied for find the MLEs
for the Matern family of covariances. There are also many
useful functions for plotting and working with spatial data as
images. This package also contains an implementation of a
sparse matrix methods for large data sets and currently
requires the sparse matrix (spam) package for testing (but not
for the standard spatial functions.) Use help(fields) to get
started and for an overview. The fields source code is heavily
commented and should provide useful explanation of numerical
details in addition to the manual pages.
Author: Reinhard Furrer, Douglas Nychka and Stephen Sain
Maintainer: Doug Nychka
fields-6.6.3/fields/R/conjugate.gradient.R |only
fields-6.6.3/fields/R/describe.bplot.R |only
fields-6.6.3/fields/R/draw.bplot.R |only
fields-6.6.3/fields/R/draw.bplot.obj.R |only
fields-6.6.3/fields/R/grey.level.R |only
fields-6.6.3/fields/R/image.plot.info.R |only
fields-6.6.3/fields/R/image.plot.plt.R |only
fields-6.6.3/fields/R/image2lz.R |only
fields-6.6.3/fields/R/print.qsreg.R |only
fields-6.6.3/fields/R/qsreg.family.R |only
fields-6.6.3/fields/R/qsreg.trace.R |only
fields-6.6.3/fields/R/replace.args.function.R |only
fields-6.6.3/fields/R/stats.bplot.R |only
fields-6.6.3/fields/R/summary.qsreg.R |only
fields-6.6.3/fields/man/qsreg.Rd |only
fields-6.7/fields/DESCRIPTION | 45 +-
fields-6.7/fields/MD5 | 135 ++++----
fields-6.7/fields/R/BACK/conjugate.gradient.R |only
fields-6.7/fields/R/BACK/describe.bplot.R |only
fields-6.7/fields/R/BACK/draw.bplot.R |only
fields-6.7/fields/R/BACK/draw.bplot.obj.R |only
fields-6.7/fields/R/BACK/fields.diagonalize.R |only
fields-6.7/fields/R/BACK/grey.level.R |only
fields-6.7/fields/R/BACK/image.plot.R.NEW |only
fields-6.7/fields/R/BACK/image.plot.info.R.BACK |only
fields-6.7/fields/R/BACK/image.plot.plt.R.BACK |only
fields-6.7/fields/R/BACK/image2lz.R.BACK |only
fields-6.7/fields/R/BACK/predict.surface.R.NEW |only
fields-6.7/fields/R/BACK/print.qsreg.R |only
fields-6.7/fields/R/BACK/qsreg.family.BACK |only
fields-6.7/fields/R/BACK/qsreg.trace.BACK |only
fields-6.7/fields/R/BACK/replace.args.function.R |only
fields-6.7/fields/R/BACK/stats.bplot.R |only
fields-6.7/fields/R/BACK/summary.qsreg.R |only
fields-6.7/fields/R/Krig.R |only
fields-6.7/fields/R/Krig.family.R | 21 +
fields-6.7/fields/R/bplot.family.R | 247 ----------------
fields-6.7/fields/R/image.family.R |only
fields-6.7/fields/R/image.plot.R | 10
fields-6.7/fields/R/mKrig.MLE.R |only
fields-6.7/fields/R/mKrig.R |only
fields-6.7/fields/R/mKrig.family.R | 25 +
fields-6.7/fields/R/ozone.R | 4
fields-6.7/fields/R/predict.se.mKrig.R | 1
fields-6.7/fields/R/rdist.R | 6
fields-6.7/fields/R/spam_2lz.R | 30 +
fields-6.7/fields/R/splint.R | 5
fields-6.7/fields/R/sreg.family.R | 2
fields-6.7/fields/data/NorthAmericanRainfall.rda |only
fields-6.7/fields/man/Krig.Rd | 66 ++--
fields-6.7/fields/man/NorthAmericanRainfall.Rd |only
fields-6.7/fields/man/REML.test.Rd | 12
fields-6.7/fields/man/Tps.Rd | 20 -
fields-6.7/fields/man/bplot.Rd | 4
fields-6.7/fields/man/fields-internal.Rd | 50 ---
fields-6.7/fields/man/fields-stuff.Rd | 10
fields-6.7/fields/man/fields.Rd | 17 -
fields-6.7/fields/man/image.plot.Rd | 19 -
fields-6.7/fields/man/lennon.Rd | 2
fields-6.7/fields/man/mKrig.MLE.Rd |only
fields-6.7/fields/man/mKrig.Rd | 11
fields-6.7/fields/man/spam2lz.Rd | 3
fields-6.7/fields/man/world.Rd | 3
fields-6.7/fields/tests/Krig.Z.test.Rout.save | 19 -
fields-6.7/fields/tests/Krig.se.W.Rout.save | 19 -
fields-6.7/fields/tests/Krig.se.grid.test.Rout.save | 19 -
fields-6.7/fields/tests/Krig.se.test.Rout.save | 19 -
fields-6.7/fields/tests/Krig.test.Rout.save | 19 -
fields-6.7/fields/tests/Krig.test.W.Rout.save | 19 -
fields-6.7/fields/tests/Likelihood.test.Rout.save | 19 -
fields-6.7/fields/tests/REMLest.test.Rout.save | 19 -
fields-6.7/fields/tests/Tps.test.Rout.save | 19 -
fields-6.7/fields/tests/Wend.test.Rout.save | 19 -
fields-6.7/fields/tests/cov.test.Rout.save | 19 -
fields-6.7/fields/tests/derivative.test.Rout.save | 19 -
fields-6.7/fields/tests/diag.multiply.test.Rout.save | 19 -
fields-6.7/fields/tests/diagonal2.test.Rout.save | 19 -
fields-6.7/fields/tests/evlpoly.test.Rout.save | 19 -
fields-6.7/fields/tests/mKrig.parameters.test.R | 18 +
fields-6.7/fields/tests/mKrig.parameters.test.Rout.save | 22 -
fields-6.7/fields/tests/mKrig.se.test.R | 1
fields-6.7/fields/tests/mKrig.se.test.Rout.save | 19 -
fields-6.7/fields/tests/mKrig.test.R | 6
fields-6.7/fields/tests/mKrig.test.Rout.save | 22 -
fields-6.7/fields/tests/misc.test.Rout.save | 19 -
fields-6.7/fields/tests/spam.test.Rout.save | 19 -
fields-6.7/fields/tests/sreg.test.Rout.save | 19 -
fields-6.7/fields/tests/vgram.test.Rout.save | 19 -
88 files changed, 521 insertions(+), 676 deletions(-)
Title: Variational Bayes Latent Position Cluster Model for networks.
Diff between VBLPCM versions 2.2 dated 2012-08-20 and 2.3 dated 2012-10-16
Description: A package to fit and simulate latent position and cluster
models for statistical networks using a Variational Bayes
approximation.
Author: Michael Salter-Townshend
Maintainer: Michael Salter-Townshend
CHANGELOG | 5 +-
DESCRIPTION | 8 ++--
MD5 | 33 +++++++++---------
R/KL.R | 10 ++---
R/VBLPCM.R | 15 ++++++--
R/covs.R | 36 ++++++++++++++++----
R/plot_network.R | 8 +---
R/start.R | 90 +++++++++++++++++++++++++++++++++++---------------
R/summary.vblpcm.R | 2 -
inst |only
man/VBLPCM-package.Rd | 32 ++++++++++-------
man/vblpcmcovs.Rd | 9 +++--
man/vblpcmfit.Rd | 6 +--
man/vblpcmstart.Rd | 10 ++++-
src/KL_funcs.c | 54 +++++++++++++++---------------
src/VBLPCM.c | 4 +-
src/headers.h | 6 +--
src/likelihoods.c | 23 ++++++------
18 files changed, 218 insertions(+), 133 deletions(-)
Title: Inference for Phase-type Distributions
Diff between PhaseType versions 0.1.2 dated 2012-09-07 and 0.1.3 dated 2012-10-16
Description: Functions to perform Bayesian inference on absorption time
data for Phase-type distributions. Plans to expand this to
include frequentist inference and simulation tools.
Author: Louis Aslett
Maintainer: Louis Aslett
DESCRIPTION | 6 -
MD5 | 20 ++--
NEWS | 8 +
R/phtMCMC.R | 6 +
R/phtMCMC2.R | 14 ++-
man/phtMCMC.Rd | 2
man/phtMCMC2.Rd | 17 +++
src/PHT_MCMC_Aslett.c | 56 ++++++++-----
src/Simulate_AbsCTMC_eq_Aslett_ECS.c | 149 ++++++++++++++++++++++++++++-------
src/utility.c | 2
tests/phtMCMC2.R | 2
11 files changed, 214 insertions(+), 68 deletions(-)
Title: Linear Latent Variable Models
Diff between lava versions 1.1-3 dated 2012-08-14 and 1.1-8 dated 2012-10-16
Description: Estimation and simulation of latent variable models
Author: Klaus K. Holst
Maintainer: Klaus K. Holst
DESCRIPTION | 8 -
MD5 | 94 ++++++++++----------
NAMESPACE | 6 +
R/addvar.R | 99 +++++++++++++++------
R/cluster.hook.R | 13 ++
R/coef.R | 58 ++++++------
R/confint.R | 6 -
R/constrain.R | 9 +
R/covariance.R | 4
R/deriv.R | 88 +++++++++---------
R/estimate.R | 143 +++++++++++++++++++++++++-----
R/estimate.multigroup.R | 134 ++++++++++++++++++++++++----
R/eventTime.R | 69 +++++++++++++-
R/exogenous.R | 10 +-
R/finalize.R | 33 +++++--
R/fix.R | 8 -
R/glmest.R | 145 ++++++++++++++++++++++++++++++-
R/gof.R | 160 +++++++++++++++++++++++-----------
R/hooks.R | 37 +++----
R/index.sem.R | 2
R/labels.R | 1
R/latent.R | 2
R/lava-package.R | 42 +++++++--
R/logLik.R | 79 +++++++++++++++--
R/matrices.R | 14 +--
R/missingMLE.R | 60 +++++++++---
R/multigroup.R | 32 +++---
R/plot.R | 15 +++
R/print.R | 48 ++++++++--
R/profile.R | 11 +-
R/regression.R | 65 ++++++++-----
R/reorder.R | 2
R/score.R | 5 -
R/sim.R | 223 ++++++++++++++++++++++++++++++++----------------
R/utils.R | 25 ++++-
R/vars.R | 4
data/serotonin.rda |binary
data/serotonin2.rda |only
inst/CITATION | 2
man/confint.lvmfit.Rd | 8 +
man/constrain-set.Rd | 2
man/estimate.lvm.Rd | 7 -
man/gof.Rd | 15 +++
man/internal.Rd | 3
man/regression-set.Rd | 5 +
man/serotonin.Rd | 18 +++
man/serotonin2.Rd |only
man/sim.Rd | 3
man/vars.Rd | 4
49 files changed, 1327 insertions(+), 494 deletions(-)
Title: Calculate the predictive squared correlation coefficient.
Diff between cvq2 versions 1.0 dated 2012-09-26 and 1.0.1 dated 2012-10-16
Description: The external prediction capability of quantitative
structure-activity relationship (QSAR) models is often
quantified using the predictive squared correlation
coefficient. This value indicates the actual prediction
capability of a model, calculated with an external data set or
by cross validation, if no external data set is available.
Author: Torsten Thalheim
Maintainer: Torsten Thalheim
DESCRIPTION | 19 +
MD5 | 29 +-
R/cvq2.R | 242 ++++++++++++++--------
R/func.constructRegressionFormula.R |only
R/func.extendDataframeForRegValues.R | 2
R/func.leaveOneOut.R | 12 -
R/func.output.PerformanceValues.R | 36 ++-
R/func.output.coefficients.R | 7
R/func.output.linearFormula.R | 13 -
R/func.output.regressionFormulaWithCoefficients.R |only
R/func.predValue.R | 4
R/func.sortDataColumns.R | 8
R/increment.R |only
data/cvq2.setA.rda |binary
man/cvq2-package.Rd | 59 ++++-
man/cvq2.Rd | 181 +++++++++-------
man/cvq2.setA.Rd | 15 -
17 files changed, 404 insertions(+), 223 deletions(-)
Title: SIMulated Structural Equation Modeling.
Diff between simsem versions 0.3-5 dated 2012-09-11 and 0.3-12 dated 2012-10-16
Description: This package can be used to generate data using the
structural equation modeling framework. This package is
tailored to use those simulated data for various purposes, such
as model fit evaluation, power analysis, or missing data
handling and planning.
Author: Sunthud Pornprasertmanit
Maintainer: Sunthud Pornprasertmanit
DESCRIPTION | 8
MD5 | 76 +--
NAMESPACE | 4
R/AllClass.R | 6
R/AllGenerics.R | 3
R/analyze.R | 34 +
R/anova-methods.R | 2
R/bind.R | 8
R/clean.R | 53 +-
R/createData.R | 4
R/drawParam.R | 18
R/exportData.R |only
R/generate.R | 278 +++++++++++++
R/getPowerFit-methods.R | 10
R/getPowerFitNested-methods.R | 10
R/imposeMissing.R | 149 +++++--
R/miss.R | 4
R/model.R | 166 +++-----
R/sim.R | 837 ++++++++++++++++++++++++------------------
R/summary-methods.R | 87 ++--
R/summaryShort-methods.R | 48 +-
R/summarySimResult.R | 168 +++++---
R/validate.R | 31 -
man/SimMissing-class.Rd | 1
man/SimResult-class.Rd | 6
man/estmodel.Rd | 11
man/exportData.Rd |only
man/getExtraOutput.Rd | 5
man/getPowerFit.Rd | 16
man/getPowerFitNested.Rd | 2
man/imposeMissing.Rd | 11
man/miss.Rd | 15
man/model.Rd | 11
man/modelLavaan.Rd | 5
man/sim.Rd | 5
man/summaryConverge.Rd | 5
man/summaryFit.Rd | 5
man/summaryMisspec.Rd | 5
man/summaryParam.Rd | 5
man/summaryPopulation.Rd | 5
40 files changed, 1352 insertions(+), 765 deletions(-)
Title: Useful tools for structural equation modeling.
Diff between semTools versions 0.2-6 dated 2012-09-11 and 0.2-7 dated 2012-10-16
Description: This package provide useful tools for structural equation
modeling analysis.
Author: Sunthud Pornprasertmanit
Maintainer: Sunthud Pornprasertmanit
DESCRIPTION | 21 ++++++++++++++++-----
MD5 | 6 +++---
man/monteCarloMed.Rd | 2 +-
man/runMI.Rd | 2 ++
4 files changed, 22 insertions(+), 9 deletions(-)
Title: Breiman and Cutler's random forests for classification and
regression
Diff between randomForest versions 4.6-6 dated 2012-01-06 and 4.6-7 dated 2012-10-16
Description: Classification and regression based on a forest of trees
using random inputs.
Author: Fortran original by Leo Breiman and Adele Cutler, R port by
Andy Liaw and Matthew Wiener.
Maintainer: Andy Liaw
DESCRIPTION | 14 ++++++++------
MD5 | 22 +++++++++++-----------
R/predict.randomForest.R | 2 +-
R/print.randomForest.R | 10 +++++-----
R/randomForest.default.R | 12 ++++++------
R/randomForest.formula.R | 2 +-
R/rfImpute.R | 4 ++--
R/rfcv.R | 3 ++-
inst/NEWS | 19 +++++++++++++++++++
src/regrf.c | 2 +-
src/rf.c | 23 ++++++++++-------------
src/rfutils.c | 6 +++---
12 files changed, 69 insertions(+), 50 deletions(-)
Title: Iterative Bias Reduction
Diff between ibr versions 1.4.1 dated 2012-03-05 and 1.4.2 dated 2012-10-16
Description: an R package for multivariate smoothing
Author: Pierre-Andre Cornillon, Nicolas Hengartner, Eric Matzner-Lober
Maintainer: Pierre-Andre Cornillon
DESCRIPTION | 8 +++----
MD5 | 48 +++++++++++++++++++++++------------------------
man/betaA.Rd | 7 +++---
man/cvobs.Rd | 6 +++--
man/fittedA.Rd | 6 +++--
man/fittedS1.Rd | 6 +++--
man/forward.Rd | 7 +++---
man/ibr-package.Rd | 3 +-
man/ibr.Rd | 6 +++--
man/iterchoiceA.Rd | 7 +++---
man/iterchoiceAcv.Rd | 7 +++---
man/iterchoiceAcve.Rd | 7 +++---
man/iterchoiceAe.Rd | 7 +++---
man/iterchoiceS1.Rd | 6 +++--
man/iterchoiceS1cv.Rd | 5 ++--
man/iterchoiceS1cve.Rd | 7 +++---
man/iterchoiceS1e.Rd | 6 +++--
man/plot.forwardibr.Rd | 5 ++--
man/plot.ibr.Rd | 5 ++--
man/predict.ibr.Rd | 6 ++---
man/print.summary.ibr.Rd | 5 ++--
man/summary.ibr.Rd | 5 ++--
man/sumvalpr.Rd | 6 +++--
src/dssplines.c | 6 ++---
src/ibr.c | 2 -
25 files changed, 108 insertions(+), 81 deletions(-)
Title: Searching for optimal clustering procedure for a data set
Diff between clusterSim versions 0.41-5 dated 2012-03-01 and 0.41-7 dated 2012-10-16
Description: GDM Distance, Sokal-Michener Distance, Bray-Curtis
Distance, Calinski-Harabasz Index, G2 Index, G3 Index,
Silhouette Index, Krzanowski-Lai Index, Hartigan Index, Gap
Index, DB Index, Data Normalization, HINoV method, Replication
analysis for cluster validation, Clustering with several
algorithms, distances, Symbolic interval distances, Plot
functions, Random cluster generation, Linear ordering methods,
Comparing partitions, Spectral clustering.
Author: Marek Walesiak
Maintainer: Andrzej Dudek
clusterSim-0.41-5/clusterSim/inst/pdf |only
clusterSim-0.41-7/clusterSim/DESCRIPTION | 8 -
clusterSim-0.41-7/clusterSim/MD5 | 112 +++++++-------
clusterSim-0.41-7/clusterSim/R/Last.Lib.r | 4
clusterSim-0.41-7/clusterSim/R/cluster.Gen.r | 3
clusterSim-0.41-7/clusterSim/R/comparing.Partitions.r | 2
clusterSim-0.41-7/clusterSim/R/dist.BC.r | 3
clusterSim-0.41-7/clusterSim/R/dist.SM.r | 2
clusterSim-0.41-7/clusterSim/R/index.G2.r | 2
clusterSim-0.41-7/clusterSim/R/index.GAP.r | 2
clusterSim-0.41-7/clusterSim/R/index.KL.r | 2
clusterSim-0.41-7/clusterSim/R/reszta.r | 2
clusterSim-0.41-7/clusterSim/R/speccl.r | 49 +++---
clusterSim-0.41-7/clusterSim/clusterSim-Ex.R | 117 ++++++---------
clusterSim-0.41-7/clusterSim/inst/doc |only
clusterSim-0.41-7/clusterSim/man/HINoV.Mod.rd | 4
clusterSim-0.41-7/clusterSim/man/HINoV.Symbolic.rd | 2
clusterSim-0.41-7/clusterSim/man/cluster.Gen.rd | 4
clusterSim-0.41-7/clusterSim/man/cluster.Sim.rd | 23 +-
clusterSim-0.41-7/clusterSim/man/comparing.Partitions.rd | 2
clusterSim-0.41-7/clusterSim/man/data.Normalization.rd | 2
clusterSim-0.41-7/clusterSim/man/dist.BC.rd | 2
clusterSim-0.41-7/clusterSim/man/dist.GDM.rd | 2
clusterSim-0.41-7/clusterSim/man/dist.SM.rd | 2
clusterSim-0.41-7/clusterSim/man/dist.Symbolic.rd | 2
clusterSim-0.41-7/clusterSim/man/index.DB.rd | 2
clusterSim-0.41-7/clusterSim/man/index.G1.rd | 27 ---
clusterSim-0.41-7/clusterSim/man/index.G2.rd | 2
clusterSim-0.41-7/clusterSim/man/index.G3.rd | 2
clusterSim-0.41-7/clusterSim/man/index.GAP.rd | 2
clusterSim-0.41-7/clusterSim/man/index.H.rd | 2
clusterSim-0.41-7/clusterSim/man/index.KL.rd | 2
clusterSim-0.41-7/clusterSim/man/index.S.rd | 2
clusterSim-0.41-7/clusterSim/man/pattern.GDM1.rd | 6
clusterSim-0.41-7/clusterSim/man/pattern.GDM2.rd | 4
clusterSim-0.41-7/clusterSim/man/replication.Mod.rd | 2
clusterSim-0.41-7/clusterSim/man/speccl.rd | 82 +++++-----
37 files changed, 231 insertions(+), 257 deletions(-)
Title: Cluster ensembles
Diff between clue versions 0.3-44 dated 2012-03-05 and 0.3-45 dated 2012-10-16
Description: CLUster Ensembles
Author: Kurt Hornik, with contributions from Walter Boehm
Maintainer: Kurt Hornik
DESCRIPTION | 8 +--
MD5 | 45 ++++++++++----------
NAMESPACE | 3 -
R/addtree.R | 24 ++++------
R/agreement.R | 18 +++++++-
R/dissimilarity.R | 8 ++-
R/lsap.R | 6 +-
R/registration.R | 3 +
R/ultrametric.R | 21 ++++-----
data/CKME.rda |binary
data/Cassini.rda |binary
data/GVME.rda |binary
data/GVME_Consensus.rda |binary
data/Kinship82.rda |binary
data/Kinship82_Consensus.rda |binary
data/Phonemes.rda |binary
inst/doc/clue.pdf |binary
man/addtree.Rd | 94 ++++++++-----------------------------------
man/cl_agreement.Rd | 27 +++++++++---
man/cl_consensus.Rd | 2
man/cl_medoid.Rd | 2
man/cl_validity.Rd | 2
man/ls_fit_addtree.Rd |only
man/ls_fit_ultrametric.Rd | 2
24 files changed, 120 insertions(+), 145 deletions(-)
Title: Weighted Likelihood Estimation
Diff between wle versions 0.9-4 dated 2010-06-05 and 0.9-7 dated 2012-10-16
Description: Approach to the robustness via Weighted Likelihood.
Author: Claudio Agostinelli
Maintainer: Claudio Agostinelli
wle-0.9-4/wle/data/artificial.R |only
wle-0.9-4/wle/data/cavendish.R |only
wle-0.9-4/wle/data/hald.R |only
wle-0.9-4/wle/data/rocky.R |only
wle-0.9-4/wle/data/selection.R |only
wle-0.9-4/wle/src/bd0.c |only
wle-0.9-4/wle/src/d9lgmc.f |only
wle-0.9-4/wle/src/dcsevl.f |only
wle-0.9-4/wle/src/dgamlm.f |only
wle-0.9-4/wle/src/dgamma.f |only
wle-0.9-4/wle/src/dpois.c |only
wle-0.9-4/wle/src/dpoisrawF77.c |only
wle-0.9-4/wle/src/dpq.h |only
wle-0.9-4/wle/src/getcgn.f |only
wle-0.9-4/wle/src/ignlgi.f |only
wle-0.9-4/wle/src/ignuin.f |only
wle-0.9-4/wle/src/initgn.f |only
wle-0.9-4/wle/src/inrgcm.f |only
wle-0.9-4/wle/src/mltmod.f |only
wle-0.9-4/wle/src/nmath.h |only
wle-0.9-4/wle/src/qrgnin.f |only
wle-0.9-4/wle/src/setall.f |only
wle-0.9-4/wle/src/stirlerr.c |only
wle-0.9-4/wle/src/wlenmath.h |only
wle-0.9-7/wle/CREDITS | 58 +------------
wle-0.9-7/wle/DESCRIPTION | 11 +-
wle-0.9-7/wle/MD5 |only
wle-0.9-7/wle/NAMESPACE | 74 ++++++++++++++++-
wle-0.9-7/wle/R/anova.wle.glm.R |only
wle-0.9-7/wle/R/extractRoot.R |only
wle-0.9-7/wle/R/mle.cv.one.R | 17 +---
wle-0.9-7/wle/R/mle.cv.robust.bootstrap.R |only
wle-0.9-7/wle/R/mle.inversegaussian.R |only
wle-0.9-7/wle/R/residualsAnscombe.R |only
wle-0.9-7/wle/R/weights.negbin.R |only
wle-0.9-7/wle/R/wle.aic.R | 27 ++++--
wle-0.9-7/wle/R/wle.aicfast.R |only
wle-0.9-7/wle/R/wle.control.R |only
wle-0.9-7/wle/R/wle.cp.R | 56 +++++++------
wle-0.9-7/wle/R/wle.cv.R | 38 ++++++++-
wle-0.9-7/wle/R/wle.cv.one.R | 17 +---
wle-0.9-7/wle/R/wle.cv.robust.bootstrap.R |only
wle-0.9-7/wle/R/wle.cv.robust.bootstrap.m.R |only
wle-0.9-7/wle/R/wle.cv.robust.bootstrap.mc.R |only
wle-0.9-7/wle/R/wle.fracdiff.R | 16 +--
wle-0.9-7/wle/R/wle.gamma.R | 14 +--
wle-0.9-7/wle/R/wle.gamma.shape.R | 5 -
wle-0.9-7/wle/R/wle.glm.R |only
wle-0.9-7/wle/R/wle.inversegaussian.R |only
wle-0.9-7/wle/R/wle.inversegaussian.lambda.R |only
wle-0.9-7/wle/R/wle.normal.high.R |only
wle-0.9-7/wle/R/wle.normal.high.r.R |only
wle-0.9-7/wle/R/wle.normal.multi.R | 2
wle-0.9-7/wle/R/wle.t.test.R | 2
wle-0.9-7/wle/R/wmme.gamma.R | 43 ++++++----
wle-0.9-7/wle/README | 6 -
wle-0.9-7/wle/STATUS | 18 +++-
wle-0.9-7/wle/data/artificial.rda |only
wle-0.9-7/wle/data/cavendish.rda |only
wle-0.9-7/wle/data/hald.rda |only
wle-0.9-7/wle/data/rocky.rda |only
wle-0.9-7/wle/data/selection.rda |only
wle-0.9-7/wle/man/anova.wle.glm.root.Rd |only
wle-0.9-7/wle/man/extractRoot.Rd |only
wle-0.9-7/wle/man/residualsAnscombe.Rd |only
wle-0.9-7/wle/man/summary.wle.glm.Rd |only
wle-0.9-7/wle/man/wle.cv.Rd | 7 +
wle-0.9-7/wle/man/wle.fracdiff.Rd | 36 +++-----
wle-0.9-7/wle/man/wle.glm.Rd |only
wle-0.9-7/wle/man/wle.glm.control.Rd |only
wle-0.9-7/wle/man/wle.glm.summaries.Rd |only
wle-0.9-7/wle/man/wle.glm.weights.Rd |only
wle-0.9-7/wle/man/wle.lm.control.Rd |only
wle-0.9-7/wle/src/dgammaF77.c |only
wle-0.9-7/wle/src/genprm.f | 71 +++++++----------
wle-0.9-7/wle/src/mlecv.f | 22 ++---
wle-0.9-7/wle/src/mlecvone.f | 45 +---------
wle-0.9-7/wle/src/random.c |only
wle-0.9-7/wle/src/wleaicfast.f |only
wle-0.9-7/wle/src/wleaicls.f |only
wle-0.9-7/wle/src/wlechisq.f |only
wle-0.9-7/wle/src/wlecv.f | 112 ++-------------------------
wle-0.9-7/wle/src/wlecvone.f | 45 +---------
wle-0.9-7/wle/src/wlecvonem.f |only
wle-0.9-7/wle/src/wlecvonemc.f |only
wle-0.9-7/wle/src/wlegamma.f | 80 ++++---------------
wle-0.9-7/wle/src/wleinvga.f |only
wle-0.9-7/wle/src/wlenorm.f | 46 +----------
wle-0.9-7/wle/src/wlenormalhigh.f |only
wle-0.9-7/wle/src/wwlecv.f |only
wle-0.9-7/wle/src/xerhlt.f | 3
wle-0.9-7/wle/src/xermsg.f | 36 ++++----
wle-0.9-7/wle/src/xerprn.f | 10 +-
wle-0.9-7/wle/src/xersve.f | 12 +-
94 files changed, 392 insertions(+), 537 deletions(-)
Title: Tools for Polyploid Microsatellite Analysis
Diff between polysat versions 1.2-1 dated 2011-06-17 and 1.3-1 dated 2012-10-16
Description: polysat is a collection of tools to handle microsatellite
data of any ploidy (and samples of mixed ploidy) where allele
copy number is not known in partially heterozygous genotypes.
It can import and export data in ABI GeneMapper, Structure,
ATetra, Tetrasat/Tetra, GenoDive, SPAGeDi, POPDIST, STRand, and
binary presence/absence formats. It can calculate pairwise
distances between individuals using a stepwise mutation model
or infinite alleles model, with or without taking ploidies and
allele frequencies into account. These distances can be used
for the calculation of clonal diversity statistics or used for
further analysis in R. Allelic diversity statistics are also
available. polysat can assist the user in estimating the
ploidy of samples, and lastly it can estimate allele
frequencies in populations, calculate pairwise Fst values based
on those frequencies, and export allele frequencies to SPAGeDi
and adegenet.
Author: Lindsay V. Clark
Maintainer: Lindsay V. Clark
DESCRIPTION | 29 +-
MD5 |only
NAMESPACE | 8
NEWS | 48 +++
R/class_conversion.R | 60 +++-
R/classes_generics_methods.R | 585 ++++++++++++++++++++++++++++++++++++++-----
R/dataexport.R | 83 ++++--
R/dataimport.R | 77 ++++-
R/individual_distance.R | 21 +
R/population_stats.R | 223 +++++++++++-----
data/FCRinfo.txt.gz |binary
data/simgen.RData |binary
data/testgenotypes.RData |binary
inst/doc/STRandExample.txt |only
inst/doc/polysattutorial.Rnw | 169 ++++++++++--
inst/doc/polysattutorial.pdf |binary
inst/extdata/simgen.R | 1
man/Lynch.distance.Rd | 5
man/Samples.Rd | 35 +-
man/alleleDiversity.Rd |only
man/assignClones.Rd | 4
man/calcFst.Rd | 10
man/deSilvaFreq.Rd | 16 -
man/deleteSamples.Rd | 8
man/editGenotypes.Rd | 12
man/estimatePloidy.Rd | 16 -
man/find.missing.gen.Rd | 12
man/freq.to.genpop.Rd | 11
man/genambig-class.Rd | 8
man/genambig.to.genbinary.Rd | 8
man/genbinary-class.Rd | 8
man/gendata-class.Rd | 64 ++--
man/gendata.to.genind.Rd |only
man/genotypeDiversity.Rd | 17 -
man/genotypeProbs.Rd | 7
man/isMissing.Rd | 11
man/meandist.from.array.Rd | 8
man/meandistance.matrix.Rd | 11
man/merge-methods.Rd | 3
man/pld.Rd |only
man/ploidysuper-class.Rd |only
man/polysat-internal.Rd | 24 +
man/read.ATetra.Rd | 14 -
man/read.GeneMapper.Rd | 5
man/read.GenoDive.Rd | 8
man/read.POPDIST.Rd | 13
man/read.SPAGeDi.Rd | 10
man/read.STRand.Rd |only
man/read.Structure.Rd | 20 -
man/read.Tetrasat.Rd | 13
man/reformatPloidies.Rd |only
man/simpleFreq.Rd | 37 +-
man/viewGenotypes.Rd | 9
man/write.ATetra.Rd | 10
man/write.GeneMapper.Rd | 21 -
man/write.GenoDive.Rd | 8
man/write.POPDIST.Rd | 8
man/write.SPAGeDi.Rd | 11
man/write.Structure.Rd | 22 -
man/write.Tetrasat.Rd | 12
man/write.freq.SPAGeDi.Rd | 11
61 files changed, 1309 insertions(+), 525 deletions(-)