mypd: Total phylogenetic distance of species in your eBird lists.

Description Usage Arguments Details Value Author(s) References Examples

View source: R/mypd.R

Description

mypd provides the evolutionary time encompassed by your eBird checklist based on Jetz et al. (2014).

Usage

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mypd(mydata, ntrees = 20)

Arguments

mydata

Data frame created with ebirdclean.

ntrees

Integer indicating the number of phylogenetic trees to use for calculating PD. Value must be between 1 and 20. Defaults to 20. Lower this number if computation of PD is taking too long.

Details

Phylogenetic distance (PD) is simply the sum of all branch lengths of a tree, and represents the total evolutionary time covered by the species in the tree. Values returned by mypd are in million years of evolution, and are based in a subset of 20 trees from Jetz et al. (2014) using the full taxonomy and Hackett "structure". See raw-data/load-bird-trees.R for more info on how the trees were extracted from the original source.#'

Value

A tibble containing the mean ("mean_pd"), median ("median_pd"), and standard deviation ("sd_pd") vaules; units are in million years.

Author(s)

Sebastian Pardo [email protected]

References

Jetz, W., Thomas, G. H., Joy, J. B., Redding, D. W., Hartmann, K. & Mooers, A. O. (2014) Global Distribution and Conservation of Evolutionary Distinctness in Birds. Current Biology 24, 919–930. http://www.cell.com/current-biology/fulltext/S0960-9822(14)00270-X

Examples

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## Not run: 
mylist <- ebirdclean("MyEBirdData.csv")
# Estimate PD for your whole eBird checklist:
mypd(mylist)

# Estimate PD by country (using dplyr):
mylist %>%
  group_by(Country) %>%
  do(mypd(.))
## End(Not run)

sebpardo/myebird documentation built on April 11, 2018, 5:30 a.m.