getIndices: getIndices

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

getIndices

Description

getIndices Generates a variety of indices describing multifunctionality based on the number of functions greater than a threshold for many different threshold and coefficients describing the relationship between diversity and number of functoins greater than a threshold.

Usage

getIndices(
  slopedata,
  threshdata,
  eqn,
  fun = stats::glm,
  divvar = "Diversity",
  groupVar = "thresholds",
  showNfunc = T
)

Arguments

slopedata	A data frame with slopes of the relationship between diversity and number of functions greather than or equal to a threshold from getCoefTab.
threshdata	A data frame with the number of functions greater than a threshold for each plot at each threshold from getFuncsMaxed.
eqn	The formula used for fitting the models in slopedata.
fun	The function used to refit the threshold data at key points to get intercepts, etc., that are needed for the table.
divvar	The name of the variable that has the measure of diversity or other driver in the threshdata data frame.
groupVar	The name of a variable by which data is grouped in the threshdata data frame. Typically "thresholds" from getFuncsMaxed.
showNfunc	Show the functions at Tmin, Tmax, and Tmde. Defaults to TRUE.

Details

See Byrnes et al. In Review.

Value

A data frame of indices

Author(s)

Jarrett Byrnes.

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)

germanyThresh <- getFuncsMaxed(germany, vars,
  threshmin = 0.05,
  threshmax = 0.99, prepend = c("plot", "Diversity"), maxN = 7
)

germanyLinearSlopes <- getCoefTab(funcMaxed ~ Diversity,
  data = germanyThresh,
  coefVar = "Diversity", family = quasipoisson(link = "identity")
)

getIndices(germanyLinearSlopes, germanyThresh, funcMaxed ~ Diversity)


## End(Not run)

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