abundance_change {codyn}

Species Abundance Changes

Description

Calculates the abundance change for species in a replicate between two time points. Changes are on abundance values provided, if relative data is used, then changes in relative abundance will be calculated.

Usage

abundance_change(
  df,
  time.var,
  species.var,
  abundance.var,
  replicate.var = NULL,
  reference.time = NULL
)

Arguments

df

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

time.var

The name of the time column.

species.var

The name of the species 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.

reference.time

The name of the optional time point that all other time points should be compared to (e.g. the first year of data). If not specified, each comparison is between consecutive time points (the first and second year, second and third year, etc.)

Value

The abundance_change function returns a data frame with a subset of the following columns:

• replicate.var: A column with the specified replicate.var, if it is specified.

• time.var: A column with the specified time.var and a second column, with '2' appended to the name. Time is subtracted from time2

• species.var: A column with the specified species.var.

• change: A numeric column of the change in abundance between time points. A positive value occurs when a species increases in abundance over time, and a negative value when a species decreases in abundance over time.

References

Avolio et al. Submitted

Examples

data(pplots)
# Without replicates
df <- subset(pplots, plot == 25)
abundance_change(df = df,
                 species.var = "species",
                 abundance.var = "relative_cover",
                 time.var = "year")

# With replicates
df <- subset(pplots, year < 2004 & plot %in% c(6, 25, 32))
abundance_change(df = df,
                 species.var = "species",
                 abundance.var = "relative_cover",
                 replicate.var = "plot",
                 time.var = "year")
                 
# With reference year
df <- subset(pplots, year < 2005 & plot %in% c(6, 25, 32))
abundance_change(df = df,
                 species.var = "species",
                 abundance.var = "relative_cover",
                 replicate.var = "plot",
                 time.var = "year",
                 reference.time = 2002)