Calculate Species Diversity Index for Polygons

Given polygons representing zones of interest and points representing species occurrence observations, calculates a species diversity index for each polygon.

Command line syntax

SpeciesDiversityCalculateDiversityIndexForArcGISPolygons_GeoEco <zonesPolygons> <Hurlbert's expected species richness | Hurlbert's standard errors | Shannon index | Simpson's index of diversity | Simpson's reciprocal index | Species richness> <destField> <speciesPoints> <speciesIDField> {speciesCountField} {where} {hurlbertSampleSize}

Parameters

Expression	Explanation
<zonesPolygons>	Polygon features representing the zones of interest for which the species diversity index should be calculated.
<Hurlbert's expected species richness \| Hurlbert's standard errors \| Shannon index \| Simpson's index of diversity \| Simpson's reciprocal index \| Species richness>	Species diversity index to calculate, one of: Hurlbert's expected species richness - sometimes abbreviated ES(n) in the literature. Gives the expected species richness in random subsamples from the community. To use this index, you must also specify the sample size parameter (n). This parameter should be smaller than total community size, but the function will silently work for larger sizes as well. The calculation is based on Hurlbert (1971). Hurlbert's standard errors - Gives the standard errors for Hurlbert's expected species richness (see above). You must also specify the sample size parameter. The standard errors are based on Heck et al. (1975). Shannon index - abbreviated H in the literature. Also known as the Shannon-Wiener or Shannon-Weaver index. The calculation is performed using a natural logarithm. Simpson's index of diversity - abbreviated 1-D in the literature. Simpson's reciprocal index - abbreviated 1/D in the literature. Species richness - abbreviated S in the literature. The simplest measure of diversity: the count of distinct species present in the zone. Please consult the literature for exact definitions of the indices. The calculations are performed by the R vegan package.
<destField>	Field of the polygon features to receive the value of the species diversity index. The field must already exist.
<speciesPoints>	Point features representing species occurrence observations.
<speciesIDField>	Field of the point features that specifies the name or ID of the species that was observed. It does not matter how species names or IDs are coded in this field. The tool simply counts occurrences of the different values and does not care what they actually mean.
{speciesCountField}	Field of the point features that specifies the number of individuals observed. This field is optional. If not specified, the tool assumes that one individual was observed at each point.
{where}	SQL WHERE clause expression that specifies the subset of points to use when calculating the species diversity index. If this parameter is not provided, all of the points will be used. The exact syntax of this expression depends on the type of feature class that contains the point features. ESRI recommends you reference fields using the following syntax: If the points are stored in an ArcInfo coverage or a shapefile, enclose field names in double quotes in the SQL expression: "MY_FIELD". If the points are stored in personal a geodatabase (.mdb file), enclose field names in square brackets: [MY_FIELD]. If the point features are stored in an ArcSDE or ArcIMS feature class, don't enclose field names: MY_FIELD.
{hurlbertSampleSize}	Sample size parameter for the calculation of Hurlbert's expected species richness. You must provide this parameter when claculating Hurlbert's expected species richness. This parameter is ignored when calculating other indices.

Scripting syntax

SpeciesDiversityCalculateDiversityIndexForArcGISPolygons_GeoEco (zonesPolygons, index, destField, speciesPoints, speciesIDField, speciesCountField, where, hurlbertSampleSize)

Parameters

Expression	Explanation
Polygons representing zones of interest (Required)	Polygon features representing the zones of interest for which the species diversity index should be calculated.
Species diversity index (Required)	Species diversity index to calculate, one of: Hurlbert's expected species richness - sometimes abbreviated ES(n) in the literature. Gives the expected species richness in random subsamples from the community. To use this index, you must also specify the sample size parameter (n). This parameter should be smaller than total community size, but the function will silently work for larger sizes as well. The calculation is based on Hurlbert (1971). Hurlbert's standard errors - Gives the standard errors for Hurlbert's expected species richness (see above). You must also specify the sample size parameter. The standard errors are based on Heck et al. (1975). Shannon index - abbreviated H in the literature. Also known as the Shannon-Wiener or Shannon-Weaver index. The calculation is performed using a natural logarithm. Simpson's index of diversity - abbreviated 1-D in the literature. Simpson's reciprocal index - abbreviated 1/D in the literature. Species richness - abbreviated S in the literature. The simplest measure of diversity: the count of distinct species present in the zone. Please consult the literature for exact definitions of the indices. The calculations are performed by the R vegan package.
Destination field (Required)	Field of the polygon features to receive the value of the species diversity index. The field must already exist.
Points representing species occurrence observations (Required)	Point features representing species occurrence observations.
Species ID field (Required)	Field of the point features that specifies the name or ID of the species that was observed. It does not matter how species names or IDs are coded in this field. The tool simply counts occurrences of the different values and does not care what they actually mean.
Species count field (Optional)	Field of the point features that specifies the number of individuals observed. This field is optional. If not specified, the tool assumes that one individual was observed at each point.
Where clause (Optional)	SQL WHERE clause expression that specifies the subset of points to use when calculating the species diversity index. If this parameter is not provided, all of the points will be used. The exact syntax of this expression depends on the type of feature class that contains the point features. ESRI recommends you reference fields using the following syntax: If the points are stored in an ArcInfo coverage or a shapefile, enclose field names in double quotes in the SQL expression: "MY_FIELD". If the points are stored in personal a geodatabase (.mdb file), enclose field names in square brackets: [MY_FIELD]. If the point features are stored in an ArcSDE or ArcIMS feature class, don't enclose field names: MY_FIELD.
Hurlbert's sample size (Optional)	Sample size parameter for the calculation of Hurlbert's expected species richness. You must provide this parameter when claculating Hurlbert's expected species richness. This parameter is ignored when calculating other indices.