| Name : R-TreePar
| |
| Version : 3.3
| Vendor : obs://build_opensuse_org/devel:languages:R
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| Release : lp153.5.11
| Date : 2024-06-14 12:06:26
|
| Group : Development/Libraries/Other
| Source RPM : R-TreePar-3.3-lp153.5.11.src.rpm
|
| Size : 0.18 MB
| |
| Packager : (none)
| |
| Summary : Estimating birth and death rates based on phylogenies
|
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.
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RPM found in directory: /packages/linux-pbone/ftp5.gwdg.de/pub/opensuse/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Leap_15.3/x86_64 |
