codyn (version 2.0.0)

community_diversity: Community Diversity

Description

Calculates Shannon's or Inverse Simpson's diversity of a community, but only one metric 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"))

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 metric to return:

• "Shannon": The default metric, calculates Shannon's diversity.

• "InverseSimpson": Calculates inverse of Simpson's diversity.

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.

Examples

# NOT RUN {
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 metric

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 metric

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