diversity_calc: @encoding UTF-8 Calculate diversity entropies for each replicate

Description

Calculate Shannon's or Simpson's entropies for each replicate while propagating uncertainty in relative abundance estimates through calculations.

Usage

diversity_calc(
  model_output,
  countData,
  params = "pi",
  entropy_measure = "shannon",
  equivalents = T
)

Arguments

model_output

Object from fitted 'Stan' model that has samples describing posteriors of focal parameters.

countData

Dataframe of count data that was modelled. Should be exactly the same as those data modelled! The first field should be sample name and integer count data should be in all other fields. This is passed in so that the names of fields can be used to make the output of differential relative abundance testing more readable.

params

Parameter for which to calculate diversity, can be 'p' or 'pi' or both (e.g., c("pi","p"))

entropy_measure

Diversity entropy to use, can be one of 'shannon' or 'simpson'

equivalents

Convert entropies into number equivalents. Defaults to true. See Jost (2006), "Entropy and diversity"

Value

A list that has samples from posterior distributions of entropy metrics

Examples

Run this code

# NOT RUN {
com_demo <-matrix(0, nrow = 10, ncol = 10)
com_demo[1:5,] <- c(rep(3,5), rep(7,5)) #Alternates 3 and 7
com_demo[6:10,] <- c(rep(7,5), rep(3,5)) #Reverses alternation
names(com_demo) <- rep("name", 10)
out <- varInf(com_demo,starts = c(1,6), ends=c(5,10))
diversity_calc(model_output = out,params = c("pi","p"),
countData = com_demo, entropy_measure = 'shannon')
# }

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