| Version: | 1.0.6 |
| Title: | Phylogenetic Monte Carlo |
| Description: | Monte Carlo based model choice for applied phylogenetics of continuous traits. Method described in Carl Boettiger, Graham Coop, Peter Ralph (2012) Is your phylogeny informative? Measuring the power of comparative methods, Evolution 66 (7) 2240-51. <doi:10.1111/j.1558-5646.2011.01574.x>. |
| URL: | https://github.com/cboettig/pmc |
| BugReports: | https://github.com/cboettig/pmc/issues |
| License: | CC0 |
| LazyData: | true |
| VignetteBuilder: | knitr |
| Suggests: | covr, gridExtra, knitr, testthat, rmarkdown |
| Imports: | dplyr, geiger (≥ 2.0.11), ggplot2, parallel, ouch, tidyr, phytools (≥ 1.5-1) |
| RoxygenNote: | 7.2.3 |
| Encoding: | UTF-8 |
| NeedsCompilation: | no |
| Packaged: | 2023-10-02 22:38:10 UTC; cboettig |
| Author: | Carl Boettiger [aut, cre] |
| Maintainer: | Carl Boettiger <cboettig@gmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2023-10-03 01:00:02 UTC |
pmc: Phylogenetic Monte Carlo
Description
Monte Carlo based model choice for applied phylogenetics of continuous traits. Method described in Carl Boettiger, Graham Coop, Peter Ralph (2012) Is your phylogeny informative? Measuring the power of comparative methods, Evolution 66 (7) 2240-51. doi:10.1111/j.1558-5646.2011.01574.x.
Author(s)
Maintainer: Carl Boettiger cboettig@gmail.com
See Also
Useful links:
The anoles data set
Description
as from ouch with additional regimes added and minor formatting changes
pmc
Description
Performs a phylogenetic monte carlo between modelA and modelB
Usage
pmc(
tree,
data,
modelA,
modelB,
nboot = 500,
optionsA = list(),
optionsB = list(),
...,
mc.cores = parallel::detectCores()
)
Arguments
tree |
A phylogenetic tree. Can be phylo (ape) or ouch tree |
data |
The data matrix |
modelA |
a model from the list, or a custom model, see details |
modelB |
any other model from the list, or custom model, see details |
nboot |
number of bootstrap replicates to use |
optionsA |
additional arguments to modelA |
optionsB |
additional arguments to modelB |
... |
additional arguments to both fitting methods |
mc.cores |
number of parallel cores to use |
Details
Simulates data under each model and returns the distribution of likelihood ratio, L(B)/L(A), under for both simulated datasets.
Value
list with the nboot likelihood ratios obtained from fitting both models to data simulated by model A, and the nboot likelihood ratios obtained by fitting both models to simulations from model B, and the likelihood ratio between the original MLE estimated models from the data.
Examples
library("geiger")
geo=get(data(geospiza))
tmp=treedata(geo$phy, geo$dat)
phy=tmp$phy
dat=tmp$data[,1]
pmc(phy, dat, "BM", "lambda", nboot = 20, mc.cores=1)
Fit any model used in PMC
Description
The fitting function used by pmc to generalize fitting to both geiger and ouch models.
Usage
pmc_fit(tree, data, model, ...)
Arguments
tree |
a phylogenetic tree. can be ouch or ape format |
data |
trait data in ape or ouch format |
model |
the name of the model to fit, |
... |
whatever additional options would be provided to the model fit |
Value
the object returned by the model fitting routine (gfit for geiger, hansen/brown for ouch)
simulate gfit
Description
simulate method for gfit objects
Usage
simulate.gfit(object, nsim = 1, seed = NULL, ...)
Arguments
object |
a gfit object |
nsim |
number of sims |
seed |
an optional seed for the simulations (not implemented) |
... |
additional arguments, not implemented for gfit simulations |
Value
simulated dataset
The phylogeny for the anoles data set
Description
The bimaculus phylogeny, as from the ouch package
update gfit
Description
update method for gfit objects
Usage
update.gfit(object, ...)
Arguments
object |
a gfit object |
... |
additional arguments, such as the data to use to update |
Value
updated gfit object