community_structure: Community Structure

In codyn: Community Dynamics Metrics

Description

Calculates species richness and evenness of a community. Evenness may be calculated as Simpson's (1/D/S), EQ, or Evar, but only one metric of evenness can be calculated at a time and must be specified.

Usage

community_structure(
  df,
  time.var = NULL,
  abundance.var,
  replicate.var = NULL,
  metric = c("Evar", "SimpsonEvenness", "EQ")
)

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 measure of evenness to return: "Evar": The default measure, calculates evenness as Evar from Smith and Wilson 1996 "SimpsonEvenness": Calculates Simpson's evenness "EQ": Calculates evenness as EQ from Smith and Wilson 1996

Value

The community_structure 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 specified.

• richness: A numeric column of species richness

• Evar: A numeric column of Evar if evenness = "Evar"

• EQ: A numeric column of EQ if evenness = "EQ"

• SimpsonEvenness: A numeric column of Simpson's evenness if evenness = "SimpsonEveness"

References

Smith, B. and Wilson, J. B. 1996. A consumer's guide to evenness indices. Oikos 76: 70-82.

Examples

data(pplots)
#Example with both time and replicates
df <- subset(pplots, plot == 25 | plot == 6)
community_structure(df, 
                    time.var="year", 
                    replicate.var = "plot", 
                    abundance.var = "relative_cover") # for Evar evenness measure

df <- subset(pplots, plot == 25 | plot == 6)
community_structure(df,
                    time.var="year", 
                    replicate.var = "plot", 
                    abundance.var = "relative_cover", 
                    metric = "SimpsonEvenness") # for Simpson's evenness measure

#Example with no replicates
df <- subset(pplots, plot == 25)
community_structure(df, 
                    time.var="year", 
                    abundance.var = "relative_cover",
                    metric = "EQ") # for EQ evenness measure

#Example with only a single time point and no replicates
df <- subset(pplots, plot == 25 & year == 2002)
community_structure(df, 
                    abundance.var = "relative_cover") # for Evar evenness measure

Example output

  year plot richness      Evar
1 2002    6       23 0.2816103
2 2003    6       18 0.2039001
3 2004    6       22 0.3091447
4 2005    6       15 0.2917799
5 2002   25       18 0.2598594
6 2003   25       15 0.2065058
7 2004   25       20 0.2441690
8 2005   25       16 0.1912342
  year plot richness SimpsonEvenness
1 2002    6       23       0.1761222
2 2003    6       18       0.2784896
3 2004    6       22       0.1327396
4 2005    6       15       0.2499747
5 2002   25       18       0.2262414
6 2003   25       15       0.2646880
7 2004   25       20       0.1463984
8 2005   25       16       0.3654740
  year richness        EQ
1 2002       18 0.1189180
2 2003       15 0.1057368
3 2004       20 0.1243605
4 2005       16 0.1033874
  richness      Evar
1       18 0.2598594

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