getFuncsMaxed: getFuncsMaxed

In jebyrnes/multifunc: Analysis of Ecological Drivers on Ecosystem Multifunctionality

getFuncsMaxed

Description

getFuncsMaxed the number of functions greater than or equal to a wide variety of thresholds in each experimental unit

Usage

getFuncsMaxed(
  adf,
  vars = NA,
  threshmin = 0.05,
  threshmax = 0.99,
  threshstep = 0.01,
  proportion = FALSE,
  prepend = "Diversity",
  maxN = 1
)

Arguments

adf	A data frame with functions.
vars	The column names of the functions to be assessed.
threshmin	The lowest threshold value to assess.
threshmax	The highest threshold value to assess
threshstep	The incremental steps between lowest and highest thresholds to be assessed. See seq.
proportion	Whether the output will be returned as a porportion of all functions. Defaults to FALSE.
prepend	Additional columns that will be imported from the data for the returned data frame.
maxN	As a 'maximum' value can be subject to outliers, etc., what number of the highest data points for a function will be used to calculate the value against which thresholds will be judged. E.g., if maxN=1 then all thresholds are porportions of the largest value measured for a function. If maxN=8, then it's the porportion of the mean of the highest 8 measurements.

Details

Create a data frame that has the value of number or proportion of functions greater than a threshold for several different thresholds at the plot.

Value

Returns a data frame of number or fraction of functions greater than or equal to the selected thresholds in each plot over all thresholds within the relevant range.

Author(s)

Jarrett Byrnes.

Examples

data(all_biodepth)
allVars <- qw(biomassY3, root3, N.g.m2, light3, N.Soil, wood3, cotton3)

germany <- subset(all_biodepth, all_biodepth$location == "Germany")

vars <- whichVars(germany, allVars)

# re-normalize N.Soil so that everything is on the same
# sign-scale (e.g. the maximum level of a function is
# the "best" function)
germany$N.Soil <- -1 * germany$N.Soil + 
                  max(germany$N.Soil, na.rm = TRUE)

germanyThresh <- getFuncsMaxed(germany, vars,
  threshmin = 0.50,
  threshmax = 0.60, prepend = c("plot", "Diversity"), maxN = 7
)

jebyrnes/multifunc documentation built on May 25, 2022, 9:43 p.m.