CoordinateCleaner (version 1.0-7)

WritePyRate: Create Input Files for PyRate

Description

Creates the input necessary to run Pyrate, based on a data.frame with fossil ages (as derived e.g. from CleanCoordinatesFOS) and a vector of the extinction status for each sample. Creates files in the working directory!

Usage

WritePyRate(x, taxon = "accepted_name", min.age = "min_ma", max.age = "max_ma", 
            status = NULL, trait = NULL, fname = NULL, path = getwd(), 
            replicates = 1, cutoff = NULL, random = TRUE)

Arguments

x

a data.frame. Containing geographical coordinates and species names.

taxon

a character string. The column with the taxon name. If “”, searches for outliers over the entire dataset, otherwise per specified taxon. Default = “identified_name”.

min.age

a character string. The column with the minimum age. Default = “min_ma”.

max.age

a character string. The column with the maximum age. Default = “max_ma”.

status

a vector of character strings of length nrow(x). Indicating for each record “extinct” or “extant”.

trait

a numeric vector of length nrow(x). Indicating trait values for each record. Optional. Default = NULL.

fname

a character string. The prefix to use for the output files.

path

a character string. giving the absolute path to write the output files. Default is the working directory.

replicates

a numerical. The number of replicates for the randomized age generation. See details. Default = 1.

cutoff

a numerical. Specify a threshold to exclude fossil occurrences with a high temporal uncertainty, i.e. with a wide temporal range between min.age and max.age. Examples: cutoff=NULL (default; all occurrences are kept in the data set) cutoff=5 (all occurrences with a temporal range of 5 Myr or higher are excluded from the data set)

random

logical. Specify whether to take a random age (between MinT and MaxT) for each occurrence or the midpoint age. Note that this option defaults to TRUE if several replicates are generated (i.e. replicates > 1). Examples: random = TRUE (default) random = FALSE (use midpoint ages)

Value

PyRate input files in the working directory.

Details

The replicate option allows the user to generate several replicates of the data set in a single input file, each time re-drawing the ages of the occurrences at random from uniform distributions with boundaries MinT and MaxT. The replicates can be analyzed in different runs (see PyRate command -j) and combining the results of these replicates is a way to account for the uncertainty of the true ages of the fossil occurrences. Examples: replicates=1 (default, generates 1 data set), replicates=10 (generates 10 random replicates of the data set).

Examples

# NOT RUN {
minages <- runif(250, 0, 65)
exmpl <- data.frame(identified_name = sample(letters, size = 250, replace = TRUE),
                    lng = runif(250, min = 42, max = 51),
                    lat = runif(250, min = -26, max = -11),
                    min_ma = minages,
                    max_ma = minages + runif(250, 0.1, 65))

#a vector with the status for each record, 
#make sure species are only classified as either extinct or extant, 
#otherwise the function will drop an error

status <- sample(c("extinct", "extant"), size = nrow(exmpl), replace = TRUE)

#or from a list of species
status <- sample(c("extinct", "extant"), size = length(letters), replace = TRUE)
names(status) <- letters
status <- status[exmpl$identified_name]

# }
# NOT RUN {
WritePyRate(x = exmpl,fname = "test", status = status)
# }