Usage
PLD_interface(fileTREES, fileDATA, num_step = 1e+05, freq = 100,
burnin = 0, ess_lim = 100, sigma = NA, lambda = NA, tau = NA,
num_step_sigma = 1, num_step_lambda = 1, num_step_tau = 1,
id_filena = NA, pattern_trees_likelihood = "treeLikelihood",
names_locations = NA)
Arguments
fileTREES
a character string that specifies the name of the file containing the phylogenetic trees.
A Nexus file (e.g. BEAST output) with tips names (no space characters allowed), the phylogenetic trees and the trees likelihood.
If only one tree is contained in th
fileDATA
a character string that specifies the name of the file containing the tips locations : a text file with 3 columns (separated by tabs).
The first one with the tips names (the same as in fileTrees), the second one with the location latitudes an
num_step
a strictly positive integer specifying the length of the Markov Chain (the number of MCMC steps).
Suggested values : 50 000 - 100 000.
freq
a strictly positive integer specifying how often the sampled model parameters and the locations are saved.
Suggested values : 50 - 100.
burnin
a strictly positive integer specifying the number of trees dropped from the file fileTREES.
Suggested value : 10% of the total number of trees, 0 in case of only one tree.
ess_lim
a strictly positive integer specifying the Effective Sample Size.
The MCMC stops when the ess of all parameters reach this value.
sigma
a vector of two elements, strictly positive values specifying the standard deviation of the normal distribution for dispersal steps in each dimension.
Default is NA: the 2 sigma parameters are estimated in the MCMC.
Alternatively, if values are specified
lambda
a strictly positive value specifying the probability of migrating to an occupied location.
Default is NA: the lambda parameter is estimated in the MCMC.
Alternatively, if a value is specified the lambda parameter is not estimated by the MCMC.
A lambda val
tau
a strictly positive value specifying the overall dispersal rate.
Default is NA: the tau parameter is estimated in the MCMC.
Alternatively, if a value specified the tau parameter is not estimated by the MCMC.
num_step_sigma
a strictly positive integer specifying how many times the sigma parameters are sampled at each MCMC step.
num_step_lambda
a strictly positive integer specifying how many times the lambda parameter is sampled at each MCMC step.
num_step_tau
a strictly positive integer specifying how many times the tau parameter is sampled at each MCMC step.
id_filena
an optional character string specifying the ID for the output files.
pattern_trees_likelihood
a character string specifying the text pattern to retrieve the trees likelihood in fileTREES.
names_locations
a vector of character strings that specifies the location names, in the same order as in fileDATA.