cal.SRI: Calculate Species Richness Index (SRI)

In Nematode: Ecological Indices Calculator for Nematode Communities

Calculate Species Richness Index (SRI)

Description

This function calculates the Species Richness Index (SRI) for ecological communities.

Usage

cal.SRI(data, total.abundance, method = "Margalef", ...)

## S3 method for class 'data.frame'
cal.SRI(data, total.abundance, method = "Margalef", ...)

## S3 method for class 'matrix'
cal.SRI(data, total.abundance, method = "Margalef", ...)

## Default S3 method:
cal.SRI(data, total.abundance, method = "Margalef", ...)

Arguments

data	data.frame or matrix. The nematode abundance table where rows represent samples and columns represent nematode genera. Each element indicates the count of a specific nematode genus in the corresponding sample. Row names must be sample names, and column names must be nematode genus names.
total.abundance	data.frame. A data frame with sample names as row names and a single column containing the total nematode abundance for each sample.
method	The method used to calculate the Species Richness Index. Default is "Margalef". Supported methods are "Margalef" and "Menhinick". Only one method can be specified. "Margalef": Margalef's Richness Index, calculated as (S - 1) / \ln(N). "Menhinick": Menhinick's Richness Index, calculated as S / \sqrt{N}.
...	Additional arguments (currently unused).

Value

A data frame with two columns:

Sample.ID	Character vector of sample identifiers (from row names of data)
SRI	Species Richness Index for each sample

Examples

# Example with a data frame
df <- data.frame(
  Cephalobus = c(10, NA, 15),
  Caenorhabditis = c(5, 10, NA),
  Pratylenchus = c(8, 12, 10),
  row.names = c("A", "B", "C")
)
abundance <- data.frame(
  abundance = c(100, 150, 120),
  row.names = c("A", "B", "C")
)
cal.SRI(data = df, total.abundance = abundance, method = "Margalef")

Nematode documentation built on Aug. 21, 2025, 5:58 p.m.