divDyn (version 0.8.0)

modeltab: Origination/extinction response table for statistical modelling.

Description

This function takes an occurrence dataset and reformats it to a table that can be used as input for logistic models.

Usage

modeltab(x, tax, bin, taxvars = NULL, rt = FALSE, singletons = FALSE)

Arguments

x

(data.frame) Fossil occurrence table.

tax

(character) Variable name of the occurring taxa (variable type: factor or character - such as "genus")

bin

(character) Variable name of the bin numbers of the occurrences. This variable should be numeric and should increase as time passes by (use negative values for age estimates). The current version only supports discreet, non-negative integer interval numbers.

taxvars

(character) Taxon-specific column names of the variables that should be included in the output table. Only one entry/taxon is used, make sure that the data are clean.

rt

(logical) Should the range-through assumption be applied within the function? If set to TRUE then missing occurrences will be interpolated with FALSE values in both the ext and ori variables. .

singletons

(logical) Should single-interval taxa be removed from the final table? This is recommended, as it is impossible to get a FALSE response for these taxa.

Details

Every entry in the output table corresponds to one cell in the bin/tax matrix. This function omits duplicates and concatenates two logical vectors (response variables) to the occurrence dataset: The ori vector is TRUE in the interval when the taxon first appeared, and FALSE in all others. The ext vector is TRUE in the interval the taxon appeared for the last time, and FALSE in the rest.

Examples

# NOT RUN {
# load necessary data
data(corals)
# simple table
modTab<-modeltab(corals, bin="stg", tax="genus", taxvars=c("ecology", "family"))

# }