spp.est {fossil}R Documentation

Estimating Species Diversity

Description

Estimate the diversity of a sample(s) using a number of species diversity estimators.

Usage

spp.est(x, rand = 10, abund = TRUE, counter = TRUE)

Arguments

x A vector, matrix or data frame with species as rows and locations/samples as columns
rand The number of times to run the internal randomizations; default is set to 10
abund If the data is abundance or presence/absence; default is set to TRUE for abundance
counter Whether or not to provide a running total of progress of randomizations

Details

This function will accept a vector, matrix or data frame of species by samples and return a large matrix with various species estimation values.

Value

Returns a table with the following column names if abund=TRUE:

N.obs Total sample size
S.obs Number of observed species
S.obs(+95%) 95% upper confidence interval
S.obs(-95%) 95% lower confidence interval
Chao1 Chao Species Estimation
Chao1(upper) 95% upper confidence interval
Chao1(lower) 95% lower confidence interval
ACE Abundance-based Coverage Estimator
ACE(upper) 95% upper confidence interval
ACE(lower) 95% lower confidence interval
Jack1 First Order Jacknife Estimator
Jack1(upper) 95% upper confidence interval
Jack1(lower) 95% lower confidence interval
N.obs Total sample size
S.obs Number of observed species
S.obs(+95%) 95% upper confidence interval
S.obs(-95%) 95% lower confidence interval
Chao2 Chao Species Estimation
Chao2(upper) 95% upper confidence interval
Chao2(lower) 95% lower confidence interval
ICE Incidence-based Coverage Estimator
ICE(upper) 95% upper confidence interval
ICE(lower) 95% lower confidence interval
Jack1 First Order Jacknife Estimator
Jack1(upper) 95% upper confidence interval
Jack1(lower) 95% lower confidence interval

Note

This function can be very long to run due to its iterative nature. The randomizations are initially set to 10 so the process will run relatively quickly, but a low value for randomizations will not give nicely smoothed curves.

Author(s)

Matthew Vavrek

References

The original idea for a program similar to this came from the extremely useful EstimateS program by Robert K. Colwell: newline Colwell, R. K. 2005. EstimateS: Statistical estimation of species richness and shared species from samples. Version 7.5. User's Guide and application published at: http://purl.oclc.org/estimates.

See Also

chao1, jack1, bootstrap

Examples

##add examples

[Package fossil version 0.2.0 Index]