codyn (version 2.0.6)

community_diversity: Community Diversity

Description

Calculates Shannon's or Inverse Simpson's diversity of a community, but only one measure of diversity can be calculated at a time and must be specified.

Usage

community_diversity(
  df,
  time.var = NULL,
  abundance.var,
  replicate.var = NULL,
  metric = c("Shannon", "InverseSimpson")
)

Value

The `community_diversity()` function returns a data frame with the following attributes: - **time.var**: A column that has the same name and type as the `time.var` column, if `time.var` is specified. - **replicate.var**: A column that has same name and type as the `replicate.var` column, if `replicate.var` is specified. - **Shannon**: A numeric column of Shannon's diversity if `metric = "Shannon"`. - **InverseSimpson**: A numeric column of the inverse of Simpson's diversity if `metric = "InverseSimpson"`.#' @references Magurran, A.E. 2004. Measuring Biological Diversity. Blackwell Publishing, Malden MA, USA.

Arguments

df

A data frame containing species and abundance columns and optional columns of time and/or replicate.

time.var

The name of the optional time column

abundance.var

The name of the abundance column

replicate.var

The name of the optional replicate column. If specified, replicate must be unique within the dataset and cannot be nested within treatments or blocks.

metric

The diversity measure to return: - `"Shannon"`: The default measure, calculates Shannon's diversity. - `"InverseSimpson"`: Calculates inverse of Simpson's diversity.

Examples

data(pplots)
#Example with both time and replicates
df <- subset(pplots, plot == 25 | plot == 6)
community_diversity(df,
                    time.var="year", 
                    replicate.var = "plot", 
                    abundance.var = "relative_cover") # for Shannon's diversity measure

df <- subset(pplots, plot == 25 | plot == 6)
community_diversity(df, 
                    time.var="year", 
                    replicate.var = "plot", 
                    abundance.var = "relative_cover", 
                    metric = "InverseSimpson") # for Inverse of Simpson's diversity measure

#Example with no replicates
df <- subset(pplots, plot == 25)
community_diversity(df,
                    time.var="year", 
                    abundance.var = "relative_cover") # for Shannon's diversity measure
                    
#Example with no time or replicate
df <- subset(pplots, plot == 25 & year == 2002)
community_diversity(df,
                    abundance.var = "relative_cover") # for Shannon's diversity measure