community_stability {codyn}

Community Stability

Description

Calculates the stability of the overall community over time as the temporal mean / temporal standard deviation of aggregate species abundances (Tilman 1999).

Usage

community_stability(df, time.var, abundance.var, replicate.var = NA)

Arguments

df

A data frame containing time, species and abundance columns and an optional column of replicates

time.var

The name of the time column

abundance.var

The name of the abundance column

replicate.var

The name of the optional replicate column

Details

The input data frame needs to contain columns for time, species and abundance; time.var, species.var and abundance.var are used to indicate which columns contain those variables. If multiple replicates are included in the data frame, that column should be specified with replicate.var. Each replicate should reflect a single experimental unit - there should be a single community represented within each time point and replicate.

Value

The community_stability function returns a numeric stability value unless a replication column is specified in the input data frame. If replication is specified, the function returns a data frame with the following columns:

• stability: A numeric column with the stability values.

• replicate.var: A column that shares the same name and type as the replicate.var column in the input data frame.

References

Tilman, D. "The Ecological Consequences of Changes in Biodiversity: A Search for General Principles." Ecology 80, no. 5 (July 1999): 1455-74. doi:10.1890/0012-9658(1999)080[1455:TECOCI]2.0.CO;2.

Examples

data(knz_001d)
community_stability(knz_001d[knz_001d$subplot=="A_1",], 
                     time.var = "year", 
                     abundance.var = "abundance") # for one subplot
community_stability(knz_001d,
                     time.var = "year", 
                     abundance.var = "abundance",
                     replicate.var = "subplot") # across all subplots