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SMUFASA Workflow Example

Jennifer McNichol

2023-11-15

Load Packages

library(QFASA)
library(dplyr)
library(compositions)

Modeling Inputs

Prior to starting make sure that:

Fatty Acid Set

data(FAset)
fa.set = as.vector(unlist(FAset))

Matrix of Predator FA Signatures

data(predatorFAs)
tombstone.info = predatorFAs[,1:4]
predator.matrix = predatorFAs[,5:(ncol(predatorFAs))]
npredators = nrow(predator.matrix)

Matrix of Prey FA Signatures

data(preyFAs)
prey.matrix = preyFAs[,-c(1,3)]

# Selecting 5 prey species to include
spec.red <-c("capelin", "herring", "mackerel", "pilchard", "sandlance")
spec.red <- sort(spec.red)
prey.red <- prey.matrix %>%
  filter(Species %in% spec.red)

Prey Lipid Content

FC = preyFAs[,c(2,3)] 
FC = FC %>%
  arrange(Species)
FC.vec = tapply(FC$lipid,FC$Species,mean,na.rm=TRUE)
FC.red <- FC.vec[spec.red]

Running SMUFASA

smufasa.est <- p.SMUFASA(predator.matrix, prey.red, FC.red, fa.set)

p.SMUFASA Output

The MUFASA output is a list with 4 components:

Calibration Coefficient Estimates

A vector of length equal to the number of FAs used and whose sum is the total number of FAs used. Thos is a set of calibration coefficients common to all predators used.

CalEst <- smufasa.est$Cal_Estimates

Diet Estimates

The diet estimate vector returned by p.SMUFASA represents an overall common diet for all predators in predator.matrix . Note: If you wish to obtain diet estimates for each individual predator see the steps below.

DietEst <- smufasa.est$Diet_Estimates

nll

This is a vector of the negative log likelihood values at each iteration of the optimizer.

nll <- smufasa.est$nll

Var_Epsilon

This is the optimized diagonal values of the variance-covariance matrix of the errors. See reference in help file for details.

VarEps <- smufasa.est$Var_Epsilon

Obtaining Diet Estimates

Once a vector of calibration coefficients is obtained via p.SMUFASA you can pass this vector to p.QFASA or p.MUFASA to obtain individual diet estimates.

QFASA

Q = p.QFASA(predator.matrix=predator.matrix, prey.matrix=prey.matrix, 
            cal.mat=CalEst, dist.meas=2, gamma=1, FC=FC.red, 
            start.val=rep(1,nrow(prey.red)), ext.fa=fa.set)

QFASA Diet Estimates:

DietEst.Q <- Q$'Diet Estimates'

See p.QFASA documnetation for further details.

MUFASA

M <- p.SMUFASA(predator.matrix, prey.red, cal.est, FC.red, fa.set)
DietEst.M <- M$Diet_Estimates

See p.MUFASA documnetation for further details.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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