This R package is for leveraging taxonomic information to impute the values of a binary trait for species with missing data. The approach is described in FitzJohn et al. 2014 (Journal of Ecology) and originally implemented here.
The easiest way to install the package is with
## install.packages("devtools") devtools::install_github("richfitz/traitfill")
The primary function of the package is also called
traitfill. To demonstrate how it works, we will use the data from our woodiness study
library(traitfill) wood <- load_wood() res <- traitfill(wood, nrep=50, with_replacement=FALSE, names=c("H", "W")) res
As described in FitzJohn et al. 2014, we consider two different sampling distributions for the traits:
Sampling with replacement (
with_replacement = TRUEin the
traitfillfunction) in which trait values for missing taxa are drawn from a binomial distribution. If all the records in a genus are of one type, then this implies that the rest of the unsampled species also share this trait.
Sampling without replacement (
with_replacement = FALSEin the
traitfillfunction) in which trait values for missing taxa are drawn from a hypergeometric distribution. Even if all trait records for a genus are of one type, we consider the possibility that there may be a species of the other type that we simply have not sampled. The probablility of this descreases as the proportion of taxa that are sampled increases.