Title: Phylogenetic Tools for comparative biology (and other things)
Diff between phytools versions 0.2-1 dated 2012-11-13 and 0.2-20 dated 2013-02-17
Description: phytools provides various functions for phylogenetic
analysis, mostly relevant to comparative biology.
Author: Liam J. Revell
Maintainer: Liam J. Revell
DESCRIPTION | 13 +-
MD5 | 101 ++++++++++--------
NAMESPACE | 32 +++--
R/add.everywhere.R | 2
R/add.random.R |only
R/allFurcTrees.R | 2
R/anc.Bayes.R | 5
R/anc.ML.R | 10 -
R/anc.trend.R | 25 ++--
R/ancThresh.R | 263 ++++++++++++++++++++++++++++++------------------
R/bind.tip.R |only
R/brownie.lite.R | 35 ------
R/densityMap.R | 2
R/estDiversity.R | 27 ----
R/evol.rate.mcmc.R | 24 ----
R/evol.vcv.R | 123 ++++++++++++++--------
R/evolvcv.lite.R | 17 ---
R/exhaustiveMP.R | 38 ++----
R/fancyTree.R | 30 ++---
R/fastAnc.R | 29 ++++-
R/make.simmap.R | 22 ----
R/mcmcLambda.R | 9 -
R/mrp.supertree.R | 94 ++++++++++++-----
R/optim.phylo.ls.R | 2
R/paintSubTree.R | 15 --
R/pgls.Ives.R | 48 ++++++++
R/phyl.RMA.R | 32 +----
R/phyl.pairedttest.R | 2
R/phylANOVA.R | 2
R/phylomorphospace.R | 4
R/plotSimmap.R | 13 --
R/reroot.R | 2
R/rescaleSimmap.R | 2
R/sim.corrs.R | 10 -
R/sim.history.R | 22 ----
R/sim.rates.R | 4
R/splitplotTree.R |only
R/utilities.R | 248 +++++++++++++++++++++++++++++++++++++++++----
R/write.simmap.R | 12 --
man/add.random.Rd |only
man/anc.trend.Rd | 4
man/ancThresh.Rd | 14 +-
man/applyEdgeLengths.Rd |only
man/ave.rates.Rd |only
man/bind.tip.Rd |only
man/evol.vcv.Rd | 2
man/fancyTree.Rd | 20 ++-
man/fastAnc.Rd | 14 +-
man/getSisters.Rd |only
man/matchNodes.Rd | 13 +-
man/mrp.supertree.Rd | 21 ++-
man/orderMappedEdge.Rd |only
man/pgls.Ives.Rd | 12 +-
man/plotThresh.Rd |only
man/roundBranches.Rd |only
man/splitplotTree.Rd |only
man/threshDIC.Rd | 10 +
man/threshState.Rd |only
58 files changed, 846 insertions(+), 585 deletions(-)
Title: Fits a catenary to given points
Diff between catenary versions 1.0 dated 2013-02-15 and 1.1 dated 2013-02-17
Description: Gives methods to create a catenary object and then plot it
and get properties of it. Can construct from parameters or
endpoints. Also can get catenary fitted to data.
Author: Jonathan Tuke, Matthew Roughan
Maintainer: Jonathan Tuke
catenary-1.0/catenary/R/ctestiphon.R |only
catenary-1.0/catenary/data/ctestiphon.rda |only
catenary-1.0/catenary/man/ctestiphon.Rd |only
catenary-1.1/catenary/DESCRIPTION | 14 +++++++-------
catenary-1.1/catenary/MD5 | 14 +++++++-------
catenary-1.1/catenary/NEWS | 7 +++++++
catenary-1.1/catenary/R/ctesiphon.R |only
catenary-1.1/catenary/data/ctesiphon.rda |only
catenary-1.1/catenary/inst/shiny/calcCat/server.R | 11 +++++++++++
catenary-1.1/catenary/inst/shiny/calcCat/ui.R | 4 +---
catenary-1.1/catenary/man/ctesiphon.Rd |only
11 files changed, 33 insertions(+), 17 deletions(-)
Title: Miscellaneous Functions from M. Kohl
Diff between MKmisc versions 0.92 dated 2012-09-12 and 0.93 dated 2013-02-17
Description: Miscellaneous Functions from M. Kohl
Author: Matthias Kohl
Maintainer: Matthias Kohl
DESCRIPTION | 9 +++++----
MD5 | 10 ++++++----
NAMESPACE | 3 ++-
NEWS | 8 ++++++++
R/powerDiagnosticTest.R |only
man/0MKmisc-package.Rd | 4 ++--
man/power.diagnostic.test.Rd |only
7 files changed, 23 insertions(+), 11 deletions(-)
Title: Routines for fitting kinetic models with one or more state
variables to chemical degradation data
Diff between mkin versions 0.9-06 dated 2012-07-12 and 0.9-10 dated 2013-02-17
Description: Calculation routines based on the FOCUS Kinetics Report
(2006). Includes a function for conveniently defining
differential equation models, model solution based on
eigenvalues if possible or using numerical solvers and a choice
of the optimisation methods made available by the FME package
(default is a Levenberg-Marquardt variant). Please note that
no warranty is implied for correctness of results or fitness
for a particular purpose.
Author: Johannes Ranke, Katrin Lindenberger, René Lehmann
Maintainer: Johannes Ranke
mkin-0.9-06/mkin/inst/GUI/.RData |only
mkin-0.9-06/mkin/inst/GUI/.Rhistory |only
mkin-0.9-10/mkin/DESCRIPTION | 11 -
mkin-0.9-10/mkin/MD5 | 50 +++---
mkin-0.9-10/mkin/R/mkinfit.R | 17 +-
mkin-0.9-10/mkin/R/mkinmod.R | 15 +
mkin-0.9-10/mkin/R/mkinplot.R | 38 -----
mkin-0.9-10/mkin/R/mkinresplot.R | 2
mkin-0.9-10/mkin/R/plot.mkinfit.R |only
mkin-0.9-10/mkin/TODO | 5
mkin-0.9-10/mkin/data/FOCUS_2006_DFOP_ref_A_to_B.rda |binary
mkin-0.9-10/mkin/data/FOCUS_2006_FOMC_ref_A_to_F.rda |binary
mkin-0.9-10/mkin/data/FOCUS_2006_HS_ref_A_to_F.rda |binary
mkin-0.9-10/mkin/data/FOCUS_2006_SFO_ref_A_to_F.rda |binary
mkin-0.9-10/mkin/data/FOCUS_2006_datasets.RData |binary
mkin-0.9-10/mkin/data/schaefer07_complex_case.RData |binary
mkin-0.9-10/mkin/inst/doc/examples.Rnw |only
mkin-0.9-10/mkin/inst/doc/examples.pdf |only
mkin-0.9-10/mkin/inst/doc/mkin.Rnw | 12 -
mkin-0.9-10/mkin/inst/doc/mkin.pdf |binary
mkin-0.9-10/mkin/man/mkin_long_to_wide.Rd | 5
mkin-0.9-10/mkin/man/mkinfit.Rd | 2
mkin-0.9-10/mkin/man/mkinplot.Rd | 34 ----
mkin-0.9-10/mkin/man/mkinresplot.Rd | 2
mkin-0.9-10/mkin/man/plot.mkinfit.Rd |only
mkin-0.9-10/mkin/mkin-Ex.R |only
mkin-0.9-10/mkin/test.R |only
mkin-0.9-10/mkin/vignettes/examples-L1_SFO_plots.pdf |only
mkin-0.9-10/mkin/vignettes/examples.Rnw |only
mkin-0.9-10/mkin/vignettes/examples.bbl |only
mkin-0.9-10/mkin/vignettes/examples.blg |only
mkin-0.9-10/mkin/vignettes/mkin.Rnw | 12 -
mkin-0.9-10/mkin/vignettes/references.bib | 144 ++++++++++---------
33 files changed, 161 insertions(+), 188 deletions(-)