multifunc (version 0.9.4)

getFuncMaxed: getFuncMaxed

Description

getFuncMaxed the number of functions greater than or equal to a single threshold in one experimental unit

Usage

getFuncMaxed(
  adf,
  vars = NA,
  thresh = 0.7,
  proportion = FALSE,
  prepend = "Diversity",
  maxN = 1
)

Arguments

adf

A data frame with functions.

vars

The column names of the functions to be assessed.

thresh

The threshold value to assess.

proportion

Whether the output will be returned as a proportion 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 proportions of the largest value measured for a function. If maxN=8, then it's the proportion of the mean of the highest 8 measurements.

Value

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

Details

Create a data frame that has the value of number or proportion of functions greater than a single threshold.

Examples

# NOT RUN {
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 <- getFuncMaxed(germany, vars, 
                              thresh = 0.5, 
                              prepend = c("plot", "Diversity"), 
                              maxN = 7)


# A function that will return a data frame with the first several columns
# being information the user wants for identification purposes (prepend)
# which defaults to Diversity and the final column the number of columns
# which pass a predefined threshold, defined as some proportion of the maximim
# observed for each column.  vars=the names of the vars being specified
# thresh is the threshold, between 0 and 1, of proportion of the max that needs
# to be passed to be counted.

# changelog
# 2014-03-24 Fixed -1 error in getMaxValue
# 2015-06-24 Fixed column name from prepend error https://github.com/jebyrnes/multifunc/issues/1
# 2022-04-14 Updated to use dplyr
# }