CalcRange: Calculate the Extent of Occurrence

In speciesgeocodeR: Prepare Species Distributions for the Use in Phylogenetic Analyses

Description

Uses the areaPolygon function of the geosphere package to calculate the extent of occurrence (EOO) for each species in the list, which can be used for criterion B of the IUCN red list classification.

Usage

CalcRange(x, mode =  "EOO", value = c("area", "shape"))

Arguments

x	data.frame, with 3 columns: 1 = species name, 2 = longitude coordinates, y = latitude coordinates.
mode	character string, setting the mode of calculation, currently only “EOO” is supported.
value	character string, setting the output value. If value = “area”: A data.frame with the EOO for each species in square kilometers; if value = “shape”, a list of convex hull polygons.

Value

If value = “area”: A data.frame with the EOO for each species in square kilometers; if value = “shape”, a list of convex hull polygons.

Note

See the speciesgeocodeR documentation for further information and examples.

Examples

data(lemurs)
CalcRange(lemurs)

Example output

Loading required package: maps
                                EOO
Avahi laniger                 20663
Avahi occidentalis              123
Cheirogaleus major            48184
Cheirogaleus medius             120
Eulemur albifrons              1857
Eulemur coronatus              1396
Eulemur fulvus               136347
Eulemur mongoz                 2576
Eulemur rubriventer           25845
Hapalemur aureus                  5
Hapalemur griseus            114605
Hapalemur simus                 142
Indri indri                   43472
Lemur catta                   91678
Lepilemur edwardsi              168
Lepilemur microdon             3959
Lepilemur mustelinus         226069
Microcebus murinus           309021
Microcebus rufus              33647
Phaner furcifer                1190
Propithecus coquereli          2616
Propithecus diadema           77151
Propithecus edwardsi             66
Propithecus verreauxi        266380
Varecia rubra                   331
Varecia variegata             41417
Daubentonia madagascariensis     NA
Eulemur collaris                 NA
Eulemur rufifrons                NA
Eulemur rufus                    NA
Eulemur sanfordi                 NA
Lepilemur septentrionalis        NA
Microcebus griseorufus           NA
Microcebus lehilahytsara         NA
Microcebus ravelobensis          NA
Propithecus candidus             NA
Propithecus coronatus            NA
Propithecus deckenii             NA
Propithecus tattersalli          NA
Warning messages:
1: In CalcRange(lemurs) :
  177 points were excluded due to duplicated coordinate
2: In CalcRange(lemurs) :
  the following species have less than 3 occurrence, values set to NA:
 Daubentonia madagascariensis
 Eulemur collaris
 Eulemur rufifrons
 Eulemur rufus
 Eulemur sanfordi
 Lepilemur septentrionalis
 Microcebus griseorufus
 Microcebus lehilahytsara
 Microcebus ravelobensis
 Propithecus candidus
 Propithecus coronatus
 Propithecus deckenii
 Propithecus tattersalli
3: In if (value == "area") { :
  the condition has length > 1 and only the first element will be used

speciesgeocodeR documentation built on May 30, 2017, 12:34 a.m.