modeltab {divDyn} | R Documentation |
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,
probs = NULL
)
Arguments
x |
|
tax |
|
bin |
|
taxvars |
|
rt |
|
singletons |
|
probs |
|
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.
The true date of extinction and origination is unknown, therefore these events can only be expressed as probabilities. The argument probs
allows the replacement of a binary response with two probability values, which are based on the apparent sampling patterns. For extinctions, when probs
is set to "samp3t"
, the response parameter for extinctions in the last bin of appearance is set to the three-timer sampling compelteness of the following bin. Assuming that the taxon'as range offset is not larger than a whole bin, if the taxon did not go extinct in the bin in which it appeared the last time, it is assumed to be going extinct in the following bin, and the remainder (1 - sampling completeness) is assigned to that bin. The pattern is reversed for originations. For probs="sampRange"
, the range-based completeness measures are applied in a similar fashion. For Phanerozoic-scale analyses, a whole bin difference between apparent event and the actual event is reasonable. See more in Reddin et al. 2021. Note that the response probabilities are set to missing values (NA
s) when the probabilities cannot be calculated. The variable ext
is also set to NaN
for the early virtual extension of the range, and ori
is treated the same for the late-extension.
References:
Reddin, C. J., Kocsis, Á. T., Aberhan, M., & Kiessling, W. (2021). Victims of ancient hyperthermal events herald the fates of marine clades and traits under global warming. Global Change Biology, 27(4), 868–878. https://doi.org/10.1111/gcb.15434
Value
A data.frame with binary response variables.
Examples
# load necessary data
data(corals)
# simple table
modTab<-modeltab(corals, bin="stg", tax="genus", taxvars=c("ecology", "family"))
# probabilities for extinction modeling
modTab2 <- modeltab(corals, bin="stg", tax="genus", probs="samp3t")
# only extinction response (omit virtual origination extensions)
extTab <- modTab2[!is.nan(modTab2$ext), ]
# only extinction response (omit virtual extinction extensions)
oriTab <- modTab2[!is.nan(modTab2$ori), ]