traitfill: Fill missing trait values

In traitecoevo/traitfill: Generalises the approach in the woodiness paper

Description

Fill missing binary trait data values based on taxonomic structure.

Usage

traitfill(dat, nrep, with_replacement = TRUE, names = c("n0", "n1"))

Arguments

dat	A data set (see Details)
nrep	Number of simulation runs to do.
with_replacement	Do the sampling with or without replacement (default is TRUE)
names	Names for columns in dat corresponding to state 0 and state1.

Details

This is a direct port from richfitz/wood with nothing other than stylistic changes.

It assumes that the taxonomy is structured into order / family / genus. Trait data are assumed in columns called "n0" and "n1", unless alternative names are passed through in names. A column called "N" must be present that has the estimate of the number of species within the genus.

So dat must have columns:

• order

• family

• genus

• n1 (unless renamed by names)

• n0 (unless renamed by names)

• N (must be at least n0 + n1)

The function returns a big list with elements:

• genus: estimates at the level of genus

• family: estimates at the level of family

• order: estimates at the level of order

• overall: overall estimates

each element is a data.frame with columns

• n0, n1: observed numbers of species in each state, possibly renamed

• N: number of species at that taxonomic level

• K: number of species with known states

• mean, lower, upper: mean and lower/upper bounds on the estimated number of species in state 1

• p_mean, p_lower, p_upper: mean and lower/upper bounds on the estimated fraction of species in state 1

Examples

## Data from "How much of the world is woody?"
wood <- load_wood()
## Fill in missing woodiness data; this says that the "H" column
## is state 0 and the "W" column is state 1, so that the generated
## percentages are "percentage woody" and not "percentage herbacious.
res <- traitfill(wood, 50, names=c("H", "W"))

traitecoevo/traitfill documentation built on May 31, 2019, 7:44 p.m.