community_diversity: Community Diversity

In codyn: Community Dynamics Metrics

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")
)

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.

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

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

Example output

  year plot  Shannon
1 2002    6 1.964799
2 2003    6 2.013032
3 2004    6 1.805089
4 2005    6 1.708760
5 2002   25 1.842618
6 2003   25 1.651746
7 2004   25 1.616162
8 2005   25 2.012171
  year plot InverseSimpson
1 2002    6       4.050810
2 2003    6       5.012813
3 2004    6       2.920272
4 2005    6       3.749621
5 2002   25       4.072345
6 2003   25       3.970320
7 2004   25       2.927968
8 2005   25       5.847584
  year  Shannon
1 2002 1.842618
2 2003 1.651746
3 2004 1.616162
4 2005 2.012171
   Shannon
1 1.842618

codyn documentation built on Dec. 1, 2020, 9:09 a.m.