Title: Diagnostic test summary measures for three ordinal groups
Diff between DiagTest3Grp versions 1.4 dated 2012-03-31 and 1.5 dated 2012-10-08
Description: The R package provides utilities to estimate and make
inference on two summary measures for diagnostic tests when
there are three ordinal groups ----volume under ROC surface
(VUS) and the extended Youden index, assuming that diagnostic
markers increase monotonically and stochastically with disease
severity. Point estimates, variance, confidence interval and
optimal cut-points both under the normal assumption and also
the non-parametric method(s) will be provided for the summary
measures. Statistical tests are implemented to compare multiple
diagnostic tests and two diagnostic test. Sample size is
calculated to estimate the summary measures within a
user-specified margin of error for future study planning.
Author: Jingqin Luo, Chengjie Xiong
Maintainer: Jingqin Luo
DESCRIPTION | 10 ++++----
MD5 | 27 ++++++++++++----------
inst |only
man/DiagTest3Grp-package.Rd | 15 ++++++------
man/DiagTest3Grp.Test.Rd | 20 +++++++++-------
man/NonParametric.VUS.var.Rd | 2 -
man/Pairwise.DiagTest3Grp.Test.Rd | 19 ++++++++-------
man/Youden3Grp.OptimalCutoff.Normal.trueMeanSD.Rd | 6 ++--
man/Youden3Grp.PointEst.Rd | 4 +--
man/Youden3Grp.Rd | 4 +--
man/Youden3Grp.Variance.Bootstrap.Rd | 4 +--
man/Youden3Grp.Variance.Normal.Rd | 4 +--
man/var.mu.Rd | 4 +--
man/var.sigma.Rd | 4 +--
14 files changed, 66 insertions(+), 57 deletions(-)
Title: Shape constrained additive models
Diff between scam versions 1.1-3 dated 2012-09-23 and 1.1-4 dated 2012-10-08
Description: Routines for generalized additive modelling under shape
constraints on the component functions of the linear predictor.
Models can contain multiple shape constrained (univariate
and/or bivariate) and unconstrained terms. The routines of
mgcv(gam) package are used for setting up the model matrix,
printing and plotting the results. Penalized likelihood
maximization based on Newton-Raphson method is used to fit a
model with multiple smoothing parameter selection by GCV or
UBRE/AIC.
Author: Natalya Pya
Maintainer: Natalya Pya
DESCRIPTION | 8
MD5 | 34 -
R/bfgs.R | 778 +++++++++++++++------------------
R/bivar.smooth.const.R | 309 ++++---------
R/check.analytical.R | 2
R/estimate.scam.R | 481 ++++----------------
R/plot.scam.R | 23
R/predict.scam.R | 19
R/print.scam.R | 15
R/residuals.scam.R | 2
R/scam.R | 1137 +++++++++++++++++++++++--------------------------
R/summary.scam.R | 10
R/uni.smooth.const.R | 116 +---
man/bfgs_gcv.ubre.Rd | 5
man/gcv.ubre_grad.Rd | 6
man/scam-package.Rd | 6
man/scam.Rd | 18
man/scam.fit.Rd | 9
18 files changed, 1216 insertions(+), 1762 deletions(-)
Title: Gaussian Graphical Model selection based on birth-death MCMC
methodology
Diff between BDgraph versions 1.0 dated 2012-09-26 and 1.1 dated 2012-10-08
Description: BDgraph is a statistical tool for Bayessian model
determination in Gaussian graphical models based on birth-death
MCMC algorithm. This package includes several functions. The
main function is 'bdmcmc' which is a brith-death MCMC algorithm
for Bayesian model selection in Gaussian graphical models.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi
BDgraph-1.0/BDgraph/data/datalist |only
BDgraph-1.0/BDgraph/data/output.high.RData |only
BDgraph-1.0/BDgraph/data/output.low.RData |only
BDgraph-1.0/BDgraph/man/BDMCMC.Rd |only
BDgraph-1.0/BDgraph/man/BDMCMC.high.Rd |only
BDgraph-1.0/BDgraph/man/BDMCMC.low.Rd |only
BDgraph-1.0/BDgraph/man/CellSignal.Rd |only
BDgraph-1.0/BDgraph/man/FIV.Rd |only
BDgraph-1.0/BDgraph/man/I_G.Rd |only
BDgraph-1.0/BDgraph/man/Phat.Rd |only
BDgraph-1.0/BDgraph/man/output.Rd |only
BDgraph-1.0/BDgraph/man/plot_cumulative.Rd |only
BDgraph-1.0/BDgraph/man/plot_links.Rd |only
BDgraph-1.0/BDgraph/man/prob.allgraphs.Rd |only
BDgraph-1.0/BDgraph/man/prob.graph.Rd |only
BDgraph-1.0/BDgraph/man/sample.G.Wishart.Rd |only
BDgraph-1.0/BDgraph/man/selection.result.Rd |only
BDgraph-1.1/BDgraph/DESCRIPTION | 14 +-
BDgraph-1.1/BDgraph/MD5 | 38 ++---
BDgraph-1.1/BDgraph/R/BDgraph.R | 183 ++++++++++++++++++----------
BDgraph-1.1/BDgraph/data/CellSignal.RData |binary
BDgraph-1.1/BDgraph/man/BDgraph-internal.Rd | 5
BDgraph-1.1/BDgraph/man/BDgraph-package.Rd | 23 ---
BDgraph-1.1/BDgraph/man/I.g.Rd |only
BDgraph-1.1/BDgraph/man/bdmcmc.Rd |only
BDgraph-1.1/BDgraph/man/bdmcmc.high.Rd |only
BDgraph-1.1/BDgraph/man/bdmcmc.low.Rd |only
BDgraph-1.1/BDgraph/man/phat.Rd |only
BDgraph-1.1/BDgraph/man/plotConvergency.Rd |only
BDgraph-1.1/BDgraph/man/plotLinks.Rd |only
BDgraph-1.1/BDgraph/man/prob.allg.Rd |only
BDgraph-1.1/BDgraph/man/prob.g.Rd |only
BDgraph-1.1/BDgraph/man/sample.gwishart.Rd |only
BDgraph-1.1/BDgraph/man/select.g.Rd |only
34 files changed, 152 insertions(+), 111 deletions(-)
Title: Community Ecology Package
Diff between vegan versions 2.0-4 dated 2012-06-19 and 2.0-5 dated 2012-10-08
Description: Ordination methods, diversity analysis and other functions
for community and vegetation ecologists.
Author: Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre
Legendre, Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson,
Peter Solymos, M. Henry H. Stevens, Helene Wagner
Maintainer: Jari Oksanen
vegan-2.0-4/vegan/R/print.adipart.R |only
vegan-2.0-4/vegan/R/print.hiersimu.R |only
vegan-2.0-4/vegan/R/print.multipart.R |only
vegan-2.0-5/vegan/DESCRIPTION | 8
vegan-2.0-5/vegan/MD5 | 190 ++++++++++---------
vegan-2.0-5/vegan/NAMESPACE | 27 ++
vegan-2.0-5/vegan/R/AIC.radfit.R | 41 +++-
vegan-2.0-5/vegan/R/adipart.default.R | 12 -
vegan-2.0-5/vegan/R/adipart.formula.R | 118 +-----------
vegan-2.0-5/vegan/R/adonis.R | 14 -
vegan-2.0-5/vegan/R/anova.ccabyaxis.R | 6
vegan-2.0-5/vegan/R/anova.ccabyterm.R | 2
vegan-2.0-5/vegan/R/betadisper.R | 12 +
vegan-2.0-5/vegan/R/biplot.rda.R | 16 -
vegan-2.0-5/vegan/R/cIndexKM.R | 106 -----------
vegan-2.0-5/vegan/R/coef.radfit.R | 8
vegan-2.0-5/vegan/R/density.anosim.R |only
vegan-2.0-5/vegan/R/density.oecosimu.R | 10 -
vegan-2.0-5/vegan/R/densityplot.oecosimu.R | 2
vegan-2.0-5/vegan/R/fitted.radfit.R | 8
vegan-2.0-5/vegan/R/hierParseFormula.R |only
vegan-2.0-5/vegan/R/hiersimu.default.R | 8
vegan-2.0-5/vegan/R/hiersimu.formula.R | 105 +---------
vegan-2.0-5/vegan/R/labels.envfit.R |only
vegan-2.0-5/vegan/R/lines.radline.R | 8
vegan-2.0-5/vegan/R/mantel.R | 44 +++-
vegan-2.0-5/vegan/R/mantel.partial.R | 25 +-
vegan-2.0-5/vegan/R/multipart.default.R | 20 +-
vegan-2.0-5/vegan/R/multipart.formula.R | 147 +--------------
vegan-2.0-5/vegan/R/oecosimu.R | 1
vegan-2.0-5/vegan/R/permutest.betadisper.R | 9
vegan-2.0-5/vegan/R/plot.envfit.R | 51 +++--
vegan-2.0-5/vegan/R/plot.radfit.R | 9
vegan-2.0-5/vegan/R/points.radline.R | 8
vegan-2.0-5/vegan/R/predict.radline.R |only
vegan-2.0-5/vegan/R/print.oecosimu.R | 21 +-
vegan-2.0-5/vegan/R/protest.R | 4
vegan-2.0-5/vegan/R/rad.null.R | 1
vegan-2.0-5/vegan/R/rad.preempt.R | 1
vegan-2.0-5/vegan/R/radfit.R | 4
vegan-2.0-5/vegan/R/radfit.data.frame.R | 16 +
vegan-2.0-5/vegan/R/radlattice.R | 8
vegan-2.0-5/vegan/inst/ChangeLog | 36 +++
vegan-2.0-5/vegan/inst/NEWS.Rd | 92 +++++++++
vegan-2.0-5/vegan/inst/doc/FAQ-vegan.pdf |binary
vegan-2.0-5/vegan/inst/doc/Makefile | 8
vegan-2.0-5/vegan/inst/doc/NEWS.html | 109 +++++++++++
vegan-2.0-5/vegan/inst/doc/decision-vegan.pdf |binary
vegan-2.0-5/vegan/inst/doc/decision-vegan.tex | 16 -
vegan-2.0-5/vegan/inst/doc/diversity-vegan.Rnw | 7
vegan-2.0-5/vegan/inst/doc/diversity-vegan.pdf |binary
vegan-2.0-5/vegan/inst/doc/diversity-vegan.tex | 71 +++----
vegan-2.0-5/vegan/inst/doc/intro-vegan.Rnw | 7
vegan-2.0-5/vegan/inst/doc/intro-vegan.pdf |binary
vegan-2.0-5/vegan/inst/doc/intro-vegan.tex | 64 +++---
vegan-2.0-5/vegan/man/BCI.Rd | 2
vegan-2.0-5/vegan/man/RsquareAdj.Rd | 5
vegan-2.0-5/vegan/man/add1.cca.Rd | 26 +-
vegan-2.0-5/vegan/man/adipart.Rd | 188 +++++++++++--------
vegan-2.0-5/vegan/man/adonis.Rd | 26 +-
vegan-2.0-5/vegan/man/anosim.Rd | 14 -
vegan-2.0-5/vegan/man/anova.cca.Rd | 92 ++++-----
vegan-2.0-5/vegan/man/beals.Rd | 23 +-
vegan-2.0-5/vegan/man/betadisper.Rd | 27 +-
vegan-2.0-5/vegan/man/betadiver.Rd | 14 -
vegan-2.0-5/vegan/man/bgdispersal.Rd | 21 +-
vegan-2.0-5/vegan/man/bioenv.Rd | 2
vegan-2.0-5/vegan/man/capscale.Rd | 4
vegan-2.0-5/vegan/man/cascadeKM.Rd | 4
vegan-2.0-5/vegan/man/cca.Rd | 4
vegan-2.0-5/vegan/man/cca.object.Rd | 2
vegan-2.0-5/vegan/man/clamtest.Rd | 8
vegan-2.0-5/vegan/man/decostand.Rd | 10 -
vegan-2.0-5/vegan/man/density.adonis.Rd |only
vegan-2.0-5/vegan/man/designdist.Rd | 12 -
vegan-2.0-5/vegan/man/envfit.Rd | 17 +
vegan-2.0-5/vegan/man/fisherfit.Rd | 8
vegan-2.0-5/vegan/man/goodness.metaMDS.Rd | 4
vegan-2.0-5/vegan/man/humpfit.Rd | 6
vegan-2.0-5/vegan/man/isomap.Rd | 4
vegan-2.0-5/vegan/man/kendall.global.Rd | 17 -
vegan-2.0-5/vegan/man/make.cepnames.Rd | 4
vegan-2.0-5/vegan/man/mantel.Rd | 21 +-
vegan-2.0-5/vegan/man/mantel.correlog.Rd | 14 -
vegan-2.0-5/vegan/man/metaMDS.Rd | 3
vegan-2.0-5/vegan/man/mrpp.Rd | 3
vegan-2.0-5/vegan/man/multipart.Rd | 10 -
vegan-2.0-5/vegan/man/ordiplot3d.Rd | 3
vegan-2.0-5/vegan/man/ordisurf.Rd | 6
vegan-2.0-5/vegan/man/predict.cca.Rd | 10 -
vegan-2.0-5/vegan/man/procrustes.Rd | 5
vegan-2.0-5/vegan/man/radfit.Rd | 239 +++++++++++++------------
vegan-2.0-5/vegan/man/raupcrick.Rd | 4
vegan-2.0-5/vegan/man/screeplot.cca.Rd | 4
vegan-2.0-5/vegan/man/specaccum.Rd | 7
vegan-2.0-5/vegan/man/stepacross.Rd | 12 -
vegan-2.0-5/vegan/man/treedive.Rd | 6
vegan-2.0-5/vegan/man/varpart.Rd | 10 -
vegan-2.0-5/vegan/man/vegan-internal.Rd | 7
vegan-2.0-5/vegan/man/vegdist.Rd | 35 +--
100 files changed, 1268 insertions(+), 1155 deletions(-)
Title: sybil - Efficient Constrained Based Modelling in R
Diff between sybil versions 1.0.2 dated 2012-04-20 and 1.1.1 dated 2012-10-08
Description: The package sybil is a Systems Biology Library for R,
implementing algorithms for constraint based analyses of
metabolic networks (e.g. flux-balance analysis (FBA),
minimization of metabolic adjustment (MOMA), regulatory on/off
minimization (ROOM), robustness analysis and flux variability
analysis).
Author: Gabriel Gelius-Dietrich [aut, cre], C. Jonathan Fritzemeier
[ctb], Rajen Piernikarczyk [ctb], Marc Andre Daxer [ctb],
Benjamin Braasch [ctb], Abdelmoneim Desouki [ctb]
Maintainer: Gabriel Gelius-Dietrich
sybil-1.0.2/sybil/R/optObj_clpClass.R |only
sybil-1.0.2/sybil/R/optObj_cplexClass.R |only
sybil-1.0.2/sybil/R/optObj_glpkClass.R |only
sybil-1.0.2/sybil/R/optsol_doublefluxdelClass.R |only
sybil-1.0.2/sybil/R/optsol_doublegenedelClass.R |only
sybil-1.0.2/sybil/R/optsol_simpleFBAClass.R |only
sybil-1.0.2/sybil/inst/doc/optsol.Rnw |only
sybil-1.0.2/sybil/inst/doc/optsol.pdf |only
sybil-1.0.2/sybil/inst/doc/simpleFBA.Rnw |only
sybil-1.0.2/sybil/inst/doc/simpleFBA.pdf |only
sybil-1.0.2/sybil/man/optObj_clp-class.Rd |only
sybil-1.0.2/sybil/man/optObj_cplex-class.Rd |only
sybil-1.0.2/sybil/man/optObj_glpk-class.Rd |only
sybil-1.0.2/sybil/man/optsol_doublefluxdel-class.Rd |only
sybil-1.0.2/sybil/man/optsol_doublegenedel-class.Rd |only
sybil-1.0.2/sybil/man/optsol_simpleFBA-class.Rd |only
sybil-1.0.2/sybil/vignettes/optsol.Rnw |only
sybil-1.0.2/sybil/vignettes/simpleFBA.Rnw |only
sybil-1.1.1/sybil/DESCRIPTION | 80
sybil-1.1.1/sybil/MD5 | 324 +-
sybil-1.1.1/sybil/NAMESPACE | 14
sybil-1.1.1/sybil/R/addAlgorithm.R |only
sybil-1.1.1/sybil/R/addExchReact.R | 8
sybil-1.1.1/sybil/R/addReact.R | 8
sybil-1.1.1/sybil/R/addSolver.R |only
sybil-1.1.1/sybil/R/blockedReact.R | 74
sybil-1.1.1/sybil/R/bracket_pairs.R | 8
sybil-1.1.1/sybil/R/ceilValues.R | 8
sybil-1.1.1/sybil/R/changeBounds.R | 8
sybil-1.1.1/sybil/R/changeGPR.R | 8
sybil-1.1.1/sybil/R/changeObjFunc.R | 8
sybil-1.1.1/sybil/R/checkAlgorithm.R |only
sybil-1.1.1/sybil/R/checkDefaultMethod.R | 105
sybil-1.1.1/sybil/R/checkOptSol.R | 14
sybil-1.1.1/sybil/R/checkReactId.R | 8
sybil-1.1.1/sybil/R/check_brackets.R | 8
sybil-1.1.1/sybil/R/checksolClass.R | 8
sybil-1.1.1/sybil/R/createReactionString.R | 8
sybil-1.1.1/sybil/R/deadEndMetabolite.R | 8
sybil-1.1.1/sybil/R/doInRound.R | 8
sybil-1.1.1/sybil/R/doubleFluxDel.R | 73
sybil-1.1.1/sybil/R/doubleGeneDel.R | 90
sybil-1.1.1/sybil/R/doubleReact.R | 8
sybil-1.1.1/sybil/R/findExchReact.R | 8
sybil-1.1.1/sybil/R/floorValues.R | 8
sybil-1.1.1/sybil/R/fluxDistributionClass.R | 9
sybil-1.1.1/sybil/R/fluxVar.R | 195 -
sybil-1.1.1/sybil/R/geneDel.R | 8
sybil-1.1.1/sybil/R/geneDeletion.R | 36
sybil-1.1.1/sybil/R/generateWT.R |only
sybil-1.1.1/sybil/R/generics.R | 122
sybil-1.1.1/sybil/R/getsybilenv.R |only
sybil-1.1.1/sybil/R/mod2irrev.R | 8
sybil-1.1.1/sybil/R/modelorg2ExPA.R |only
sybil-1.1.1/sybil/R/modelorg2text.R | 8
sybil-1.1.1/sybil/R/modelorg2tsv.R | 11
sybil-1.1.1/sybil/R/modelorgClass.R | 182 +
sybil-1.1.1/sybil/R/modelorg_irrevClass.R | 8
sybil-1.1.1/sybil/R/multiDel.R | 8
sybil-1.1.1/sybil/R/oneFluxDel.R | 47
sybil-1.1.1/sybil/R/oneGeneDel.R | 37
sybil-1.1.1/sybil/R/onlyChangeGPR.R | 8
sybil-1.1.1/sybil/R/onlyCheckGPR.R | 8
sybil-1.1.1/sybil/R/optObjClass.R | 2429 ++--------------
sybil-1.1.1/sybil/R/optObj_basicfunc.R | 42
sybil-1.1.1/sybil/R/optObj_clpAPIClass.R |only
sybil-1.1.1/sybil/R/optObj_cplexAPIClass.R |only
sybil-1.1.1/sybil/R/optObj_glpkAPIClass.R |only
sybil-1.1.1/sybil/R/optObj_lpSolveAPIClass.R | 629 ++++
sybil-1.1.1/sybil/R/optObj_lpSolveAPIcompat.R | 20
sybil-1.1.1/sybil/R/optObj_pointer.R |only
sybil-1.1.1/sybil/R/optimizer.R | 573 +--
sybil-1.1.1/sybil/R/optsolClass.R | 90
sybil-1.1.1/sybil/R/optsol_blockedReactClass.R | 46
sybil-1.1.1/sybil/R/optsol_fluxVarClass.R | 99
sybil-1.1.1/sybil/R/optsol_fluxdelClass.R | 256 -
sybil-1.1.1/sybil/R/optsol_genedelClass.R | 123
sybil-1.1.1/sybil/R/optsol_optimizeProbClass.R |only
sybil-1.1.1/sybil/R/optsol_robAnaClass.R | 58
sybil-1.1.1/sybil/R/parseBoolean.R | 13
sybil-1.1.1/sybil/R/ppProcClass.R | 8
sybil-1.1.1/sybil/R/ppProcessing.R | 8
sybil-1.1.1/sybil/R/prepProbObj.R | 10
sybil-1.1.1/sybil/R/prepareSubSysMatrix.R | 8
sybil-1.1.1/sybil/R/printLogComment.R | 8
sybil-1.1.1/sybil/R/printNamedList.R | 8
sybil-1.1.1/sybil/R/printObjFunc.R | 8
sybil-1.1.1/sybil/R/progress.R | 8
sybil-1.1.1/sybil/R/promptSysBiolAlg.R |only
sybil-1.1.1/sybil/R/reactIdClass.R | 8
sybil-1.1.1/sybil/R/readTEXTmod.R | 8
sybil-1.1.1/sybil/R/readTSVmod.R | 26
sybil-1.1.1/sybil/R/reassignFwBwMatch.R | 8
sybil-1.1.1/sybil/R/rmReact.R | 8
sybil-1.1.1/sybil/R/robAna.R | 104
sybil-1.1.1/sybil/R/settings.R | 62
sybil-1.1.1/sybil/R/simpleFBA.R | 78
sybil-1.1.1/sybil/R/singletonMetabolite.R | 8
sybil-1.1.1/sybil/R/sybilErrorClass.R | 8
sybil-1.1.1/sybil/R/sybilLogClass.R | 8
sybil-1.1.1/sybil/R/sybilStack.R | 56
sybil-1.1.1/sybil/R/sysBiolAlgClass.R |only
sybil-1.1.1/sybil/R/sysBiolAlg_fbaClass.R |only
sybil-1.1.1/sybil/R/sysBiolAlg_fvClass.R |only
sybil-1.1.1/sybil/R/sysBiolAlg_lmomaClass.R |only
sybil-1.1.1/sybil/R/sysBiolAlg_momaClass.R |only
sybil-1.1.1/sybil/R/sysBiolAlg_mtfClass.R |only
sybil-1.1.1/sybil/R/sysBiolAlg_roomClass.R |only
sybil-1.1.1/sybil/R/validmodelorg.R | 8
sybil-1.1.1/sybil/R/validoptsol.R | 54
sybil-1.1.1/sybil/R/validreactId.R | 8
sybil-1.1.1/sybil/R/validsysBiolAlg.R |only
sybil-1.1.1/sybil/R/ypd.R | 8
sybil-1.1.1/sybil/R/zzz.R | 105
sybil-1.1.1/sybil/inst/NEWS.Rd | 92
sybil-1.1.1/sybil/inst/doc/sybil.Rnw | 440 +-
sybil-1.1.1/sybil/inst/doc/sybil.pdf |binary
sybil-1.1.1/sybil/man/SYBIL_SETTINGS.Rd | 39
sybil-1.1.1/sybil/man/addAlgorithm.Rd |only
sybil-1.1.1/sybil/man/addCols-methods.Rd |only
sybil-1.1.1/sybil/man/addColsToProb-methods.Rd |only
sybil-1.1.1/sybil/man/addRows-methods.Rd |only
sybil-1.1.1/sybil/man/addRowsCols-methods.Rd |only
sybil-1.1.1/sybil/man/addRowsToProb-methods.Rd |only
sybil-1.1.1/sybil/man/addSolver.Rd |only
sybil-1.1.1/sybil/man/backupProb-methods.Rd |only
sybil-1.1.1/sybil/man/blockedReact.Rd | 23
sybil-1.1.1/sybil/man/changeColsBnds-methods.Rd |only
sybil-1.1.1/sybil/man/changeColsBndsObjCoefs-methods.Rd |only
sybil-1.1.1/sybil/man/changeMatrixRow-methods.Rd |only
sybil-1.1.1/sybil/man/changeObjCoefs-methods.Rd |only
sybil-1.1.1/sybil/man/changeRowsBnds-methods.Rd |only
sybil-1.1.1/sybil/man/checkAlgorithm.Rd |only
sybil-1.1.1/sybil/man/checkDefaultMethod.Rd | 42
sybil-1.1.1/sybil/man/checkOptSol.Rd | 10
sybil-1.1.1/sybil/man/delProb-methods.Rd |only
sybil-1.1.1/sybil/man/deprecated.Rd |only
sybil-1.1.1/sybil/man/doubleFluxDel.Rd | 27
sybil-1.1.1/sybil/man/doubleGeneDel.Rd | 27
sybil-1.1.1/sybil/man/fluxVar.Rd | 73
sybil-1.1.1/sybil/man/geneDel.Rd | 3
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sybil-1.1.1/sybil/man/oneFluxDel.Rd | 45
sybil-1.1.1/sybil/man/oneGeneDel.Rd | 39
sybil-1.1.1/sybil/man/optObj-class.Rd | 499 +--
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sybil-1.1.1/sybil/man/optimizer.Rd | 68
sybil-1.1.1/sybil/man/optsol-class.Rd | 102
sybil-1.1.1/sybil/man/optsol_blockedReact-class.Rd | 41
sybil-1.1.1/sybil/man/optsol_fluxVar-class.Rd | 60
sybil-1.1.1/sybil/man/optsol_fluxdel-class.Rd | 108
sybil-1.1.1/sybil/man/optsol_genedel-class.Rd | 96
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sybil-1.1.1/sybil/man/optsol_robAna-class.Rd | 61
sybil-1.1.1/sybil/man/ppProc-class.Rd | 7
sybil-1.1.1/sybil/man/prepProbObj.Rd | 12
sybil-1.1.1/sybil/man/promptSysBiolAlg.Rd |only
sybil-1.1.1/sybil/man/readTSVmod.Rd | 15
sybil-1.1.1/sybil/man/robAna.Rd | 37
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sybil-1.1.1/sybil/man/sybil-internal.Rd | 9
sybil-1.1.1/sybil/man/sybil-package.Rd | 12
sybil-1.1.1/sybil/man/sybilError-class.Rd | 2
sybil-1.1.1/sybil/man/sybilStack.Rd | 8
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sybil-1.1.1/sybil/vignettes/net-crop.pdf |binary
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sybil-1.1.1/sybil/vignettes/optObj-const.pdf |only
sybil-1.1.1/sybil/vignettes/optsol-class.pdf |only
sybil-1.1.1/sybil/vignettes/sybil.Rnw | 440 +-
sybil-1.1.1/sybil/vignettes/sybil.bib | 22
sybil-1.1.1/sybil/vignettes/sysBiolAlg-class.pdf |only
sybil-1.1.1/sybil/vignettes/sysBiolAlg-const.pdf |only
sybil-1.1.1/sybil/vignettes/sysBiolAlg-init.pdf |only
214 files changed, 4112 insertions(+), 5110 deletions(-)
More information about coalescentMCMC at CRAN
Permanent link
Title: Analyses of Phylogenetics and Evolution
Diff between ape versions 3.0-5 dated 2012-08-01 and 3.0-6 dated 2012-10-08
Description: ape provides functions for reading, writing, plotting, and
manipulating phylogenetic trees, analyses of comparative data
in a phylogenetic framework, ancestral character analyses,
analyses of diversification and macroevolution, computing
distances from allelic and nucleotide data, reading and writing
nucleotide sequences, and several tools such as Mantel's test,
minimum spanning tree, generalized skyline plots, graphical
exploration of phylogenetic data (alex, trex, kronoviz),
estimation of absolute evolutionary rates and clock-like trees
using mean path lengths and penalized likelihood. Phylogeny
estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and
triangle methods, and several methods handling incomplete
distance matrices (NJ*, BIONJ*, MVR*, and the corresponding
triangle method). Some functions call external applications
(PhyML, Clustal, T-Coffee, Muscle) whose results are returned
into R.
Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong,
Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel,
Christoph Heibl, Daniel Lawson, Vincent Lefort, Pierre
Legendre, Jim Lemon, Yvonnick Noel, Johan Nylander, Rainer
Opgen-Rhein, Andrei-Alin Popescu, Klaus Schliep, Korbinian
Strimmer, Damien de Vienne
Maintainer: Emmanuel Paradis
DESCRIPTION | 8 +--
MD5 | 73 ++++++++++++++--------------
NEWS | 42 ++++++++++++++++
R/CDF.birth.death.R | 11 ++--
R/DNA.R | 16 +++---
R/cophenetic.phylo.R | 77 +++++-------------------------
R/dbd.R | 6 --
R/drop.tip.R | 14 ++---
R/evonet.R | 6 +-
R/ladderize.R | 4 -
R/me.R | 22 +++++---
R/pic.R | 6 +-
R/plot.phylo.R | 53 ++++++++++++++++++++
R/read.nexus.R | 4 +
R/read.tree.R | 5 +
R/reorder.phylo.R | 33 +++++++-----
R/rtree.R | 3 -
inst/doc/MoranI.pdf |binary
man/ace.Rd | 44 ++++++++---------
man/ape-internal.Rd | 2
man/collapse.singles.Rd | 2
man/dbd.Rd | 9 +--
man/dist.dna.Rd | 17 +++---
man/mantel.test.Rd | 3 -
man/node.depth.Rd | 22 ++++++--
man/nodelabels.Rd | 3 -
man/plot.phylo.Rd | 6 +-
man/print.phylo.Rd | 2
man/rTraitCont.Rd | 2
man/rTraitMult.Rd | 19 +++----
man/read.caic.Rd | 7 --
man/read.nexus.Rd | 28 +----------
man/reorder.phylo.Rd | 37 +++++++++-----
man/woodmouse.Rd | 6 +-
man/yule.Rd | 2
src/dist_nodes.c |only
src/plot_phylo.c | 21 +-------
src/reorder_phylo.c | 122 +++++++++++++++++++++++++++++++-----------------
38 files changed, 408 insertions(+), 329 deletions(-)
Title: Linear and Nonlinear Mixed Effects Models
Diff between nlme versions 3.1-104 dated 2012-05-23 and 3.1-105 dated 2012-10-08
Description: Fit and compare Gaussian linear and nonlinear
mixed-effects models.
Author: Jose Pinheiro (S version), Douglas Bates (up to 2007), Saikat
DebRoy (up to 2002), Deepayan Sarkar (up to 2005), the R Core
team.
Maintainer: R-core
nlme-3.1-104/nlme/po/R-en@quot.po |only
nlme-3.1-104/nlme/po/en@quot.po |only
nlme-3.1-105/nlme/ChangeLog | 15
nlme-3.1-105/nlme/DESCRIPTION | 8
nlme-3.1-105/nlme/MD5 | 66
nlme-3.1-105/nlme/R/VarCov.R | 10
nlme-3.1-105/nlme/R/corStruct.R | 118
nlme-3.1-105/nlme/R/gls.R | 65
nlme-3.1-105/nlme/R/gnls.R | 36
nlme-3.1-105/nlme/R/groupedData.R | 43
nlme-3.1-105/nlme/R/lmList.R | 99
nlme-3.1-105/nlme/R/lme.R | 202 -
nlme-3.1-105/nlme/R/newFunc.R | 36
nlme-3.1-105/nlme/R/newMethods.R | 64
nlme-3.1-105/nlme/R/nlme.R | 96
nlme-3.1-105/nlme/R/nlsList.R | 12
nlme-3.1-105/nlme/R/pdMat.R | 194 -
nlme-3.1-105/nlme/R/reStruct.R | 27
nlme-3.1-105/nlme/R/simulate.R | 25
nlme-3.1-105/nlme/R/varFunc.R | 127 -
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nlme-3.1-105/nlme/src/init.c | 4
36 files changed, 3304 insertions(+), 2404 deletions(-)
Title: Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, dBase,
...
Diff between foreign versions 0.8-50 dated 2012-05-23 and 0.8-51 dated 2012-10-08
Description: Functions for reading and writing data stored by
statistical packages such as Minitab, S, SAS, SPSS, Stata,
Systat, ..., and for reading and writing dBase files.
Author: R Core Team [aut, cph, cre], Roger Bivand [ctb, cph], Vincent
J. Carey [ctb, cph], Saikat DebRoy [ctb, cph], Stephen Eglen
[ctb, cph], Rajarshi Guha [ctb, cph], Nicholas Lewin-Koh [ctb,
cph], Mark Myatt [ctb, cph], Ben Pfaff [ctb], Frank Warmerdam
[ctb, cph], Stephen Weigand [ctb, cph], Free Software
Foundation, Inc. [cph]. See the COPYRIGHTS file in the sources
for details on contributions and copyrights.
Maintainer: R Core Team
foreign-0.8-50/foreign/po/R-en@quot.po |only
foreign-0.8-50/foreign/po/en@quot.po |only
foreign-0.8-51/foreign/ChangeLog | 14
foreign-0.8-51/foreign/DESCRIPTION | 8
foreign-0.8-51/foreign/MD5 | 54 -
foreign-0.8-51/foreign/R/R_systat.R | 2
foreign-0.8-51/foreign/R/Sread.R | 4
foreign-0.8-51/foreign/R/dbf.R | 11
foreign-0.8-51/foreign/R/octave.R | 3
foreign-0.8-51/foreign/R/read.dta.R | 5
foreign-0.8-51/foreign/R/read.ssd.R | 6
foreign-0.8-51/foreign/R/spss.R | 2
foreign-0.8-51/foreign/R/writeForeignSAS.R | 3
foreign-0.8-51/foreign/R/zzz.R | 6
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foreign-0.8-51/foreign/po/R-fr.po | 152 +--
foreign-0.8-51/foreign/po/R-pl.po |only
foreign-0.8-51/foreign/po/de.po | 153 +--
foreign-0.8-51/foreign/po/foreign.pot | 145 +--
foreign-0.8-51/foreign/po/fr.po | 435 +++++-----
foreign-0.8-51/foreign/po/pl.po |only
foreign-0.8-51/foreign/src/init.c | 4
30 files changed, 604 insertions(+), 558 deletions(-)
Title: Bootstrap Functions (originally by Angelo Canty for S)
Diff between boot versions 1.3-5 dated 2012-06-27 and 1.3-6 dated 2012-10-08
Description: functions and datasets for bootstrapping from the book
"Bootstrap Methods and Their Applications" by A. C. Davison and
D. V. Hinkley (1997, CUP).
Author: S original
Maintainer: Brian Ripley
boot-1.3-5/boot/po/R-en@quot.po |only
boot-1.3-6/boot/ChangeLog | 5
boot-1.3-6/boot/DESCRIPTION | 8
boot-1.3-6/boot/MD5 | 29 -
boot-1.3-6/boot/R/bootfuns.q | 138 ++---
boot-1.3-6/boot/R/bootpracs.q | 6
boot-1.3-6/boot/inst/po/de/LC_MESSAGES/R-boot.mo |binary
boot-1.3-6/boot/inst/po/en@quot/LC_MESSAGES/R-boot.mo |binary
boot-1.3-6/boot/inst/po/fr/LC_MESSAGES/R-boot.mo |binary
boot-1.3-6/boot/inst/po/pl/LC_MESSAGES/R-boot.mo |binary
boot-1.3-6/boot/inst/po/ru/LC_MESSAGES/R-boot.mo |binary
boot-1.3-6/boot/po/R-boot.pot | 128 ++---
boot-1.3-6/boot/po/R-de.po | 260 +++++-----
boot-1.3-6/boot/po/R-fr.po | 201 +++----
boot-1.3-6/boot/po/R-pl.po | 455 ++++++++++++------
boot-1.3-6/boot/po/R-ru.po | 241 +++++----
16 files changed, 836 insertions(+), 635 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-08-29 1.0
Title: Conventional Tukey Test
Diff between TukeyC versions 1.0-7 dated 2012-06-26 and 1.1-0 dated 2012-10-08
Description: Perform the conventional Tukey test from aov and aov.list
objects
Author: Jose Claudio Faria, Enio Jelihovschi and Ivan Bezerra Allaman
Maintainer: Jose Claudio Faria
ChangeLog | 20 +-
DESCRIPTION | 10 -
MD5 | 28 +--
R/TukeyC.nest.aov.R | 355 +++++++++++++++++++++++++++++++++++++++------
R/TukeyC.nest.aovlist.R | 373 +++++++++++++++++++++++++++++++++++++++++-------
R/TukeyC.nest.default.R | 10 -
demo/CRD.R | 16 +-
demo/FE.R | 94 ++++++------
demo/SPE.r | 34 ++--
demo/SSPE.r | 62 +++----
man/TukeyC-package.Rd | 82 +++++-----
man/TukeyC.Rd | 4
man/TukeyC.nest.Rd | 48 +++---
man/plot.TukeyC.Rd | 20 +-
man/summary.Rd | 71 ++++-----
15 files changed, 897 insertions(+), 330 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-09-11 0.1-07
2012-02-06 0.1-05
2011-10-20 0.1-01
2011-08-17 0.0-7
2011-08-09 0.0-6
2011-08-08 0.0-5
Title: Protein (identification and) quantification based on peptide
evidence
Diff between protiq versions 1.0 dated 2012-10-02 and 1.0-1 dated 2012-10-08
Description: Method for protein quantification based on identified and
quantified peptides. protiq can be used for absolute and
relative protein quantification. Input peptide abundance scores
can come from various sources, including SRM transition areas
and intentisites or spectral counts derived from shotgun
experiments. The package is still being extended to also
include the model for protein identification, MIPGEM, presented
in Gerster, S., Qeli, E., Ahrens, C.H. and Buehlmann, P.
(2010). Protein and gene model inference based on statistical
modeling in k-partite graphs. Proceedings of the National
Academy of Sciences 107(27):12101-12106.
Author: Sarah Gerster and Peter Buehlmann
Maintainer: Sarah Gerster
DESCRIPTION | 11 +++++++----
MD5 | 32 ++++++++++++++++----------------
NAMESPACE | 3 +++
R/protiq.R | 5 ++---
R/scampi_classes.R | 8 ++++++++
man/checkInputData.Rd | 6 +++---
man/checkInputData.scampi.Rd | 6 +++---
man/estimateModelParameters.Rd | 6 +++---
man/getCovU.Rd | 7 ++++---
man/preprocessInputData.Rd | 6 +++---
man/preprocessInputData.scampi.Rd | 6 +++---
man/protiq-package.Rd | 2 +-
man/quantifyPeptide.Rd | 7 +++----
man/quantifyProtein.Rd | 7 +++----
man/quantifyProteins.Rd | 7 +++----
man/scampi-class.Rd | 32 ++++++++++++++++++--------------
man/scampiVal-class.Rd | 1 +
17 files changed, 84 insertions(+), 68 deletions(-)
Title: Optimal distance-based clustering for one-dimensional data
Diff between Ckmeans.1d.dp versions 2.4 dated 2012-09-03 and 2.5 dated 2012-10-08
Description: This package implements a dynamic programming algorithm to
cluster one-dimensional data optimally, by minimizing the sum
of squares of within-cluster distances. As an alternative to
the heuristic k-means algorithm, the algorithm guarantees
optimality and repeatability of clustering.
Author: Joe Song
Maintainer: Haizhou Wang
DESCRIPTION | 18 +++++++++---------
MD5 | 3 ++-
inst |only
3 files changed, 11 insertions(+), 10 deletions(-)