Title: Simulating trees under the birth-death model
Diff between TreeSim versions 1.5 dated 2011-11-02 and 1.6 dated 2012-08-05
Description: The package simulates phylogenetic trees where (i) all
tips are sampled at one time point or (ii) tips are sampled
sequentially through time. (i) For sampling at one time point,
simulations are performed under a constant-rate birth-death
process, conditioned on having a fixed number of final tips
(sim.bd.taxa), or a fixed age (sim.bd.age), or a fixed age and
number of tips (sim.bd.taxa.age). When conditioning on the
number of final tips, the method allows for shifts in rates and
mass extinction events during the birth-death process
(sim.rateshift.taxa).sim.bd.age (and sim.rateshift.taxa without
extinction) allow the speciation rate to change in a
density-dependent way. The LTT plots of the simulations can be
displayed using LTT.plot, LTT.plot.gen and LTT.average.root.
TreeSim further samples appropriately trees with n final tips
from a set of trees generated by the common sampling algorithm
stopping when a fixed number m>>n of leaves is first reached
(sim.gsa.taxa). This latter method is appropriate for m-tip
trees generated under a big class of models (details in the
sim.gsa.taxa man page). For incomplete phylogeny, the missing
speciation events can be added through simulations (corsim).
(ii) sim.rateshifts.taxa is generalized to sim.bdsky.stt for
serially sampled trees, where the trees are conditioned on
either the number of sampled tips or the age. Furthermore, for
a multitype-branching process with sequential sampling, trees
on a fixed number of tips can be simulated using
sim.bdtypes.stt.taxa.
Author: Tanja Stadler
Maintainer: Tanja Stadler
TreeSim-1.5/TreeSim/man/LTT.average.root.Rd |only
TreeSim-1.6/TreeSim/DESCRIPTION | 35 ++++++-
TreeSim-1.6/TreeSim/MD5 | 42 +++++---
TreeSim-1.6/TreeSim/NAMESPACE | 2
TreeSim-1.6/TreeSim/R/LTT.plot.R |only
TreeSim-1.6/TreeSim/R/LTT.plot.gen.R |only
TreeSim-1.6/TreeSim/R/branching.times.complete.R | 2
TreeSim-1.6/TreeSim/R/get.times.polytomy.R |only
TreeSim-1.6/TreeSim/R/getx.R |only
TreeSim-1.6/TreeSim/R/sim.bdsky.stt.R |only
TreeSim-1.6/TreeSim/R/sim.bdtypes.stt.taxa.R |only
TreeSim-1.6/TreeSim/R/sim.gsa.taxa.R | 2
TreeSim-1.6/TreeSim/R/sim.rateshift.taxa.R | 4
TreeSim-1.6/TreeSim/R/sim.rateshift.taxa.help.R | 4
TreeSim-1.6/TreeSim/R/sim.rateshift.taxa.loop.R | 4
TreeSim-1.6/TreeSim/R/sim2.bd.rateshift.R | 4
TreeSim-1.6/TreeSim/R/sim2.bd.rateshift.single.R | 40 ++++++--
TreeSim-1.6/TreeSim/R/sim2.gsa.R | 110 +++++++++++------------
TreeSim-1.6/TreeSim/man/LTT.plot.Rd |only
TreeSim-1.6/TreeSim/man/LTT.plot.gen.Rd |only
TreeSim-1.6/TreeSim/man/TreeSim-package.Rd | 10 +-
TreeSim-1.6/TreeSim/man/getx.Rd |only
TreeSim-1.6/TreeSim/man/sim.bd.age.Rd | 2
TreeSim-1.6/TreeSim/man/sim.bd.taxa.Rd | 2
TreeSim-1.6/TreeSim/man/sim.bdsky.stt.Rd |only
TreeSim-1.6/TreeSim/man/sim.bdtypes.stt.taxa.Rd |only
TreeSim-1.6/TreeSim/man/sim.gsa.taxa.Rd | 4
TreeSim-1.6/TreeSim/man/sim.rateshift.taxa.Rd | 6 -
28 files changed, 166 insertions(+), 107 deletions(-)
Title: Estimating birth and death rates based on phylogenies
Diff between TreePar versions 2.2 dated 2011-11-02 and 2.3 dated 2012-08-05
Description: (i) For a given species phylogeny on present day data
which is calibrated to calendar-time, a method for estimating
maximum likelihood speciation and extinction processes is
provided. The method allows for non-constant rates. Rates may
change (1) as a function of time, i.e. rate shifts at specified
times or mass extinction events (implemented as bd.shifts.optim
and visualized as bd.shifts.plot) or (2) as a function of the
number of species, i.e. density-dependence (implemented as
bd.densdep.optim). Note that the method takes into account the
whole phylogeny, in particular it accounts for the "pull of the
present" effect. Both models can take into account incomplete
species sampling, as long as each species has the same
probability of being sampled. For a given phylogeny on higher
taxa (i.e. all but one species per taxa are mission), but where
the number of species is known within each higher taxa,
speciation and extinction rates can be estimated under model
(1) (implemented as bd.shifts.optim with groups !=0). (ii) For
a given phylogeny with sequentially sampled tips, e.g. a virus
phylogeny, rates can be estimated under a model where rates
vary across time using bdsky.stt.optim (extending
bd.shifts.optim). Furthermore rates may vary as a function of
host types using bdtypes.stt.lik (multitype branching process
extending functions in R package diversitree).
Author: Tanja Stadler
Maintainer: Tanja Stadler
TreePar-2.2/TreePar/R/getx.R |only
TreePar-2.2/TreePar/man/bd.groups.optim.Rd |only
TreePar-2.2/TreePar/man/getx.Rd |only
TreePar-2.3/TreePar/DESCRIPTION | 36 ++++++++++++++----
TreePar-2.3/TreePar/MD5 | 55 +++++++++++++++++++---------
TreePar-2.3/TreePar/NAMESPACE | 2 -
TreePar-2.3/TreePar/R/BDSSanal.R |only
TreePar-2.3/TreePar/R/BDSSnum.help.R |only
TreePar-2.3/TreePar/R/BDSSsky.R |only
TreePar-2.3/TreePar/R/Ffuncshift.R |only
TreePar-2.3/TreePar/R/Ffuncshifth.R |only
TreePar-2.3/TreePar/R/R0types.R |only
TreePar-2.3/TreePar/R/ai.R |only
TreePar-2.3/TreePar/R/bd.ME.optim.R | 12 ++++--
TreePar-2.3/TreePar/R/bd.ME.optim.rho.R | 4 +-
TreePar-2.3/TreePar/R/bd.ME.optim.rho.all.R | 4 +-
TreePar-2.3/TreePar/R/bd.MEyule.optim.R | 4 +-
TreePar-2.3/TreePar/R/bd.densdep.optim.R | 3 +
TreePar-2.3/TreePar/R/bd.groups.optim.R | 11 +++--
TreePar-2.3/TreePar/R/bd.shifts.optim.R | 14 ++++---
TreePar-2.3/TreePar/R/bd.shifts.plot.R |only
TreePar-2.3/TreePar/R/bdsky.stt.optim.R |only
TreePar-2.3/TreePar/R/bdtypes.stt.lik.R |only
TreePar-2.3/TreePar/R/bi.R |only
TreePar-2.3/TreePar/R/get.groups.R |only
TreePar-2.3/TreePar/R/get.times2.R |only
TreePar-2.3/TreePar/R/integrator.R |only
TreePar-2.3/TreePar/R/integrator2.R |only
TreePar-2.3/TreePar/R/interstt.R |only
TreePar-2.3/TreePar/R/p.R |only
TreePar-2.3/TreePar/R/pnshift.R |only
TreePar-2.3/TreePar/R/qfuncsky.R |only
TreePar-2.3/TreePar/R/qfuncskylog.R |only
TreePar-2.3/TreePar/R/treemrcashifts.R | 14 ++++++-
TreePar-2.3/TreePar/man/TreePar-package.Rd | 14 ++++---
TreePar-2.3/TreePar/man/bd.densdep.optim.Rd | 8 ++--
TreePar-2.3/TreePar/man/bd.shifts.optim.Rd | 28 +++++++++++---
TreePar-2.3/TreePar/man/bd.shifts.plot.Rd |only
TreePar-2.3/TreePar/man/bdsky.stt.optim.Rd |only
TreePar-2.3/TreePar/man/bdtypes.stt.lik.Rd |only
TreePar-2.3/TreePar/man/get.groups.Rd |only
TreePar-2.3/TreePar/man/treemrcashifts.Rd | 6 ++-
42 files changed, 150 insertions(+), 65 deletions(-)
Title: HIBAG -- HLA Genotype Imputation with Attribute Bagging
Diff between HIBAG versions 0.9.1 dated 2012-06-21 and 0.9.2 dated 2012-08-05
Description: To impute HLA types from unphased SNP data using an
attribute bagging method.
Author: Xiuwen Zheng
Maintainer: Xiuwen Zheng
HIBAG-0.9.1/HIBAG/man/hlaClusterAttrBagging.Rd |only
HIBAG-0.9.2/HIBAG/DESCRIPTION | 10 ++--
HIBAG-0.9.2/HIBAG/MD5 | 21 +++++-----
HIBAG-0.9.2/HIBAG/NEWS |only
HIBAG-0.9.2/HIBAG/R/main.r | 50 +++++++++++++++++++-----
HIBAG-0.9.2/HIBAG/man/HIBAG-package.Rd | 29 +++++++------
HIBAG-0.9.2/HIBAG/man/hlaAlleleDigit.Rd | 20 ++-------
HIBAG-0.9.2/HIBAG/man/hlaAttrBagging.Rd | 18 +++++---
HIBAG-0.9.2/HIBAG/man/hlaCombineModelObj.Rd | 2
HIBAG-0.9.2/HIBAG/man/hlaCompareAllele.Rd | 15 +++++--
HIBAG-0.9.2/HIBAG/man/hlaGenoSwitchStrand.Rd | 8 +--
HIBAG-0.9.2/HIBAG/man/hlaParallelAttrBagging.Rd |only
HIBAG-0.9.2/HIBAG/src/LibHLA.h | 2
13 files changed, 107 insertions(+), 68 deletions(-)
Title: Shape constrained additive models
Diff between scam versions 1.1-1 dated 2012-01-28 and 1.1-2 dated 2012-08-05
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
scam-1.1-1/scam/man/monotonic.smooth.terms.Rd |only
scam-1.1-2/scam/DESCRIPTION | 8
scam-1.1-2/scam/MD5 | 42 +-
scam-1.1-2/scam/NAMESPACE | 10
scam-1.1-2/scam/R/bfgs.R | 2
scam-1.1-2/scam/R/extrapolate.uni.scam.R |only
scam-1.1-2/scam/R/plot.scam.R | 12
scam-1.1-2/scam/R/predict.scam.R | 9
scam-1.1-2/scam/R/scam.R | 12
scam-1.1-2/scam/R/uni.smooth.const.R | 183 +++++++++++++
scam-1.1-2/scam/man/Predict.matrix.mpi.smooth.Rd | 4
scam-1.1-2/scam/man/extrapolate.uni.scam.Rd |only
scam-1.1-2/scam/man/predict.scam.Rd | 12
scam-1.1-2/scam/man/scam-package.Rd | 10
scam-1.1-2/scam/man/scam.Rd | 18 -
scam-1.1-2/scam/man/shape.constrained.smooth.terms.Rd |only
scam-1.1-2/scam/man/smooth.construct.cv.smooth.spec.rd |only
scam-1.1-2/scam/man/smooth.construct.cx.smooth.spec.Rd |only
scam-1.1-2/scam/man/smooth.construct.mdcv.smooth.spec.Rd | 2
scam-1.1-2/scam/man/smooth.construct.mdcx.smooth.spec.Rd | 2
scam-1.1-2/scam/man/smooth.construct.micv.smooth.spec.Rd | 5
scam-1.1-2/scam/man/smooth.construct.micx.smooth.spec.Rd | 5
scam-1.1-2/scam/man/smooth.construct.mpd.smooth.spec.Rd | 5
scam-1.1-2/scam/man/smooth.construct.mpi.smooth.spec.Rd | 5
scam-1.1-2/scam/man/smooth.construct.tesmi1.smooth.spec.Rd | 2
25 files changed, 290 insertions(+), 58 deletions(-)
Title: Converting Odds Ratio to Relative Risk in Cohort Studies with
Partial Data Information
Diff between orsk versions 0.1-3 dated 2012-03-14 and 0.1-4 dated 2012-08-05
Description: Converting the Odds Ratio to the Relative Risk in Cohort
Studies with Partial Data Information
Author: Zhu Wang
Maintainer: Zhu Wang
DESCRIPTION | 16 ++--
MD5 | 20 ++---
NEWS | 2
R/multiStartNew.R | 4 -
R/orsk.R | 12 ---
inst/doc/orsk_demo.Rnw | 176 ++++++++++++++++++++++++++++---------------------
inst/doc/orsk_demo.bib | 23 +++++-
inst/doc/orsk_demo.pdf |binary
man/orsk-package.Rd | 9 +-
man/orsk.Rd | 44 ++++++------
man/zy.Rd | 10 +-
11 files changed, 179 insertions(+), 137 deletions(-)
Title: Copula based cluster analysis
Diff between CoClust versions 0.2-0 dated 2012-02-27 and 0.2-7 dated 2012-08-05
Description: Copula based cluster analysis.
Author: Francesca Marta Lilja Di Lascio, Simone Giannerini
Maintainer: Simone Giannerini
CoClust-0.2-0/CoClust/ChangeLog.tex |only
CoClust-0.2-7/CoClust/ChangeLog.txt |only
CoClust-0.2-7/CoClust/DESCRIPTION | 10
CoClust-0.2-7/CoClust/MD5 | 13
CoClust-0.2-7/CoClust/R/CoClust.R | 355 +++++++++++++++------------
CoClust-0.2-7/CoClust/R/Internal_functions.R | 48 ++-
CoClust-0.2-7/CoClust/inst |only
CoClust-0.2-7/CoClust/man/CoClust-class.Rd | 8
CoClust-0.2-7/CoClust/man/CoClust.Rd | 53 ++--
9 files changed, 276 insertions(+), 211 deletions(-)
Title: Centrality-based pathway enrichment
Diff between CePa versions 0.3 dated 2012-06-29 and 0.4 dated 2012-08-05
Description: Use pathway topology information to assign weight to
pathway nodes.
Author: Zuguang Gu
Maintainer: Zuguang Gu
CePa-0.3/CePa/man/eccentricity.Rd |only
CePa-0.3/CePa/vignettes/CePa.tex |only
CePa-0.4/CePa/CHANGES | 12
CePa-0.4/CePa/DESCRIPTION | 10
CePa-0.4/CePa/MD5 | 99 ++++----
CePa-0.4/CePa/NAMESPACE | 2
CePa-0.4/CePa/R/centrality.R | 15 -
CePa-0.4/CePa/R/cepa.all.parallel.R |only
CePa-0.4/CePa/R/pathway.nodes.R | 2
CePa-0.4/CePa/R/plot_print.R | 47 ++-
CePa-0.4/CePa/R/report.R | 14 -
CePa-0.4/CePa/data/PID.db.rda |binary
CePa-0.4/CePa/inst/doc/CePa.Rnw | 355 +++++++++++++----------------
CePa-0.4/CePa/inst/doc/CePa.pdf |binary
CePa-0.4/CePa/inst/extdata/cepa.template | 99 --------
CePa-0.4/CePa/inst/extdata/js |only
CePa-0.4/CePa/inst/extdata/swf |only
CePa-0.4/CePa/man/CePa-package.Rd | 8
CePa-0.4/CePa/man/PID.db.Rd | 29 +-
CePa-0.4/CePa/man/cepa.Rd | 10
CePa-0.4/CePa/man/cepa.all.Rd | 15 -
CePa-0.4/CePa/man/cepa.all.parallel.Rd |only
CePa-0.4/CePa/man/cepa.ora.Rd | 4
CePa-0.4/CePa/man/cepa.ora.all.Rd | 10
CePa-0.4/CePa/man/cepa.univariate.Rd | 11
CePa-0.4/CePa/man/cepa.univariate.all.Rd | 14 -
CePa-0.4/CePa/man/get.cepa.Rd | 6
CePa-0.4/CePa/man/p.table.Rd | 6
CePa-0.4/CePa/man/pathway.nodes.Rd | 2
CePa-0.4/CePa/man/plot.cepa.Rd | 8
CePa-0.4/CePa/man/plot.cepa.all.Rd | 35 ++
CePa-0.4/CePa/man/plotGraph.Rd | 7
CePa-0.4/CePa/man/plotNull.Rd | 11
CePa-0.4/CePa/man/radiality.Rd | 2
CePa-0.4/CePa/man/reach.Rd | 2
CePa-0.4/CePa/man/read.cls.Rd | 4
CePa-0.4/CePa/man/read.gct.Rd | 12
CePa-0.4/CePa/man/report.Rd | 21 +
CePa-0.4/CePa/man/sampleLabel.Rd | 4
CePa-0.4/CePa/man/set.pathway.catalogue.Rd | 19 +
CePa-0.4/CePa/man/spread.Rd | 2
CePa-0.4/CePa/vignettes/CePa.Rnw | 355 +++++++++++++----------------
CePa-0.4/CePa/vignettes/bibliography.bib | 14 +
CePa-0.4/CePa/vignettes/f1.pdf |binary
CePa-0.4/CePa/vignettes/f11.pdf |only
CePa-0.4/CePa/vignettes/f2.pdf |binary
CePa-0.4/CePa/vignettes/f3.pdf |binary
CePa-0.4/CePa/vignettes/f4.pdf |binary
CePa-0.4/CePa/vignettes/f5.pdf |binary
CePa-0.4/CePa/vignettes/f6.pdf |binary
CePa-0.4/CePa/vignettes/f8.pdf |binary
CePa-0.4/CePa/vignettes/f9.pdf |binary
52 files changed, 639 insertions(+), 627 deletions(-)
Title: Seasonal analysis of health data
Diff between season versions 0.3-1 dated 2012-01-23 and 0.3-2 dated 2012-08-05
Description: Routines for the seasonal analysis of health data,
including regression models, time-stratified case-crossover,
plotting functions and residual checks. Thanks to Yuming Guo
for checking the case-crossover code.
Author: Adrian Barnett
Maintainer: Adrian Barnett
DESCRIPTION | 11 +++++------
MD5 | 6 +++---
R/plot.Monthmean.R | 3 ++-
R/plot.nsCosinor.R | 2 +-
4 files changed, 11 insertions(+), 11 deletions(-)
Title: A simple interface to the PROJ.4 cartographic projections
library
Diff between proj4 versions 1.0-7 dated 2011-12-11 and 1.0-8 dated 2012-08-05
Description: A simple interface to lat/long projection and datum
transformation of the PROJ.4 cartographic projections library.
It allows transformation of geographic coordinates from one
projection and/or datum to another.
Author: Simon Urbanek
Maintainer: Simon Urbanek
proj4-1.0-7/proj4/src/win32 |only
proj4-1.0-7/proj4/src/win64 |only
proj4-1.0-8/proj4/DESCRIPTION | 12 ++++++------
proj4-1.0-8/proj4/MD5 | 11 ++++-------
proj4-1.0-8/proj4/NEWS | 5 +++++
proj4-1.0-8/proj4/configure.win |only
proj4-1.0-8/proj4/src/Makevars.win | 7 ++++++-
7 files changed, 21 insertions(+), 14 deletions(-)