myedge: EDGE scores of species in your eBird lists.

Description Usage Arguments Details Value Author(s) Source References Examples

View source: R/myedge.R

Description

myedge provides Evolutionarily Distinct (ED) and Globally Endangered (EDGE) species scores and rankings based on Jetz et al. (2014).

Usage

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myedge(mydata, edge.cutoff = 9999)

Arguments

mydata

Data frame created with ebirdclean.

edge.cutoff

Cutoff for EDGE rankings to be returned. Defaults to 9999, which returns all species in the EDGE list.

Details

EDGE scores are calculated from a species evolutionary distinctiveness (ED) and Global IUCN Red List status (GE) using the following equation:

EDGE = ln(ED + 1) + GE * ln(2)

Where ED is defined as species-level measure representing the weighted sum of the branch lengths along the path from the root of a tree to a given tip/species, and GE is a rank scalar ranging from 0 (IUCN Red List designation “Least Concern”) to 4 (IUCN Red List designation “Critically Endangered”). See Jetz et al. (2014) for more details.

It's important to note a few issues with the EDGE metric and the values provided by this function. The EDGE score can be strongly influenced by the taxonomy being used. This is particularly important if species with relatively high ED values are considered multiple species by other authors; this can considerably change evolutionary distinctiveness estimates. Furthermore, the EDGE taxonomy is considerably different to that in eBird (the latter includes many recent splits and other revisions), and thus the matching of species between EDGE species and eBird species is imperfect, thus EDGE scores and rankings based on eBird might not be accurate.

Value

A data frame containing the following six columns:

"sciName": Scientific name. Most of these have been updated using eBird's taxonomy (see raw-data/edge-data-clean.R for more info).

"comName": Common name.

"ED.Score": Evolutionary distinctiveness as it appears in http://www.edgeofexistence.org/birds/default.php.

"EDGE.Score": EDGE score calculated using the equation above, as it appears in http://www.edgeofexistence.org/birds/default.php.

"EDGE.Rank": Ranking based on EDGE score, as it appears in http://www.edgeofexistence.org/birds/default.php.

"sciName.edge": Scientific name as they appear in the Jetz et al. (2014) phylogeny.

Author(s)

Sebastian Pardo [email protected]

Source

http://www.edgeofexistence.org/birds/default.php.

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")
myedge <- myedge(mylist, edge.cutoff = 500)
## End(Not run)

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