TreePar

Package: TreePar
Type: Package
Title: Estimating birth and death rates based on phylogenies
Version: 3.3
Date: 2015-01-02
Author: Tanja Stadler
Maintainer: Tanja Stadler <tanja.stadler@bsse.ethz.ch>
Depends: ape, Matrix, subplex, TreeSim (>= 2.1), deSolve
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 (likelihood implemented as LikShifts, optimization as bd.shifts.optim and visualized as bd.shifts.plot) or (2) as a function of the number of species, i.e. density-dependence (likelihood implemented as LikDD and optimization as bd.densdep.optim) or (3) extinction rate may be a function of species age (likelihood implemented as LikAge and optimization as bd.age.optim.matlab). Note that the methods take into account the whole phylogeny, in particular it accounts for the "pull of the present" effect. (1-3) 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 missing), where the number of species is known within each higher taxa, speciation and extinction rates can be estimated under model (1) (implemented within LikShifts and 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 based on likelihood LikShiftsSTT (extending LikShifts and bd.shifts.optim). Furthermore, rates may vary as a function of host types using LikTypesSTT (multitype branching process extending functions in R package diversitree). This function can furthermore calculate the likelihood under an epidemiological model where infected individuals are first exposed and then infectious.
License: GPL-2
LazyLoad: yes
Packaged: 2015-01-02 16:26:29 UTC; tstadler
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-02 17:48:44

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'TreePar' ...
** package 'TreePar' successfully unpacked and MD5 sums checked
** R
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'TreePar'
    finding HTML links ... done
    LikAge                                  html  
    LikConstant                             html  
    LikConstantn                            html  
    LikDD                                   html  
    LikShifts                               html  
    LikShiftsPP                             html  
    LikShiftsSTT                            html  
    LikTypesSTT                             html  
    TreePar-package                         html  
    addroot                                 html  
    bd.age.optim.matlab                     html  
    bd.densdep.optim                        html  
    bd.shifts.optim                         html  
    bd.shifts.plot                          html  
    bdsky.stt.optim                         html  
    create.mat                              html  
    get.groups                              html  
** building package indices
** testing if installed package can be loaded
* DONE (TreePar)
Making 'packages.html' ... done