Description Usage Arguments Details Value Author(s) References Examples
mypd
provides the evolutionary time encompassed by your eBird checklist
based on Jetz et al. (2014).
1 | mypd(mydata, ntrees = 20)
|
mydata |
Data frame created with |
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. |
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.#'
A tibble containing the mean ("mean_pd"), median ("median_pd"), and standard deviation ("sd_pd") vaules; units are in million years.
Sebastian Pardo sebpardo@gmail.com
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
1 2 3 4 5 6 7 8 9 10 | ## 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)
|
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