curve_change: Curve Change

In codyn: Community Dynamics Metrics

Description

Calculates the area difference between two rank abundance curves between two time periods. If replicate is specified, it must be measured in both time points, otherwise it will be dropped for that time period comparison.

Usage

curve_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 curve_change function returns a data frame with the following attributes:

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

• curve_change: A numeric column of the change in curves between time points.

• replicate.var: A column that has same name and type as the replicate.var column, if specified.

References

Avolio et al. Submitted

Examples

data(pplots)
# Without replicates
df <- subset(pplots, plot == 25)
curve_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))
curve_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))
curve_change(df = df,
           species.var = "species",
           abundance.var = "relative_cover",
           replicate.var = "plot",
           time.var = "year",
           reference.time = 2002)

Example output

   year year2 curve_change
5  2002  2003   0.03259107
10 2003  2004   0.04098240
15 2004  2005   0.07383364
  year year2 plot curve_change
1 2002  2003    6   0.04780344
2 2002  2003   25   0.03259107
3 2002  2003   32   0.03634063
  year year2 plot curve_change
1 2002  2003    6   0.04780344
2 2002  2004    6   0.01845279
3 2002  2003   25   0.03259107
4 2002  2004   25   0.02217456
5 2002  2003   32   0.03634063
6 2002  2004   32   0.02264086

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