gamStat.batch {laser} | R Documentation |
Takes a matrix or dataframe of branching times obtained from a
set of phylogenies using getBtimes.batch
and performs the
MCCR test of Pybus and Harvey (2000). Can also be used to generate the posterior
distribution of the gamma statistic for Bayesian inference.
gamStat.batch(x, stat = NULL)
x |
a matrix or dataframe containing branching times for phylogenies |
stat |
value of the gamma statistic for the test phylogeny |
'x' is obtained through use of getBtimes.batch
.
'stat' is the calculated value of the gamma statistic you wish to compare to the null distribution for a given level of sampling and number of tips. If stat = NULL (the default), the function returns a list with calculated gamma statistics for each set of branching times, as well as the critical value of the distribution (alpha = 0.05). Observed gamma statistic values less than the critical value have probability < 0.05 under the null hypothesis that rates have not decreased over time. If stat is specified, the function will determine the p-value of the observed value under the null hypothesis by tabulating the number of simulated values above and below the observed value.
a list with the following components:
gamstat |
a vector of calculated gamma statistics for the matrix of branching times |
gamcrit |
the critical value of the distribution specified by the simulated trees (alpha = 0.05) |
pval |
the Type I error probability of the observed value under the null distribution specified by the input data x |
This performs the MCCR test of Pybus and Harvey (2000). However, you must generate phylogenies under a rate-constant pure-birth (Yule) model using either Phyl-O-Gen (http://evolve.zoo.ox.ac.uk/software/PhyloGen/main.html) or another program.
This function can also be used for Bayesian inference. For example, you can tabulate the distribution of the gamma statistic from the posterior distribution of phylogenetic trees sampled using MCMC or MCMCMC.
Dan Rabosky DLR32@cornell.edu
Pybus, O. G., and P. H. Harvey. 2000. Testing macro-evolutionary models using incomplete molecular phylogenies. Proc. R. Soc. Lond. Biol. B 267:2267-2272.
gamStat
, getBtimes.batch
, fitdAICrc.batch
data("rtrees50") write.table(rtrees50, file = 'temp.txt', quote=FALSE, row.names = FALSE, col.names = FALSE) #generates file 'temp.txt' with data formatted appropriately intrees <- getBtimes.batch(file = 'temp.txt') result <- gamStat.batch(intrees) hist(result$gamstat) result$gamcrit unlink('temp.txt') #delete temp file