Nothing
## ----message=FALSE, warning=FALSE---------------------------------------------
library(QFASA)
library(dplyr)
library(compositions)
## -----------------------------------------------------------------------------
data(FAset)
fa.set = as.vector(unlist(FAset))
## -----------------------------------------------------------------------------
data(predatorFAs)
tombstone.info = predatorFAs[,1:4]
predator.matrix = predatorFAs[,5:(ncol(predatorFAs))]
npredators = nrow(predator.matrix)
## -----------------------------------------------------------------------------
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)
## -----------------------------------------------------------------------------
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]
## ----eval=FALSE---------------------------------------------------------------
# smufasa.est <- p.SMUFASA(predator.matrix, prey.red, FC.red, fa.set)
## ----eval=FALSE---------------------------------------------------------------
# CalEst <- smufasa.est$Cal_Estimates
## ----eval=FALSE---------------------------------------------------------------
# DietEst <- smufasa.est$Diet_Estimates
## ----eval=FALSE---------------------------------------------------------------
# nll <- smufasa.est$nll
## ----eval=FALSE---------------------------------------------------------------
# VarEps <- smufasa.est$Var_Epsilon
## ----eval=FALSE---------------------------------------------------------------
# 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)
## ----eval=FALSE---------------------------------------------------------------
# DietEst.Q <- Q$'Diet Estimates'
## ----eval=FALSE---------------------------------------------------------------
# M <- p.SMUFASA(predator.matrix, prey.red, cal.est, FC.red, fa.set)
# DietEst.M <- M$Diet_Estimates
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