Nothing
test_that("Model Workflow Regression KL", {
set.seed(1234)
dist.meas = 1
## Fatty Acids
data(FAset)
fa.set = as.vector(unlist(FAset))
## Predators
data(predatorFAs)
tombstone.info = predatorFAs[,1:4]
predator.matrix = predatorFAs[,5:(ncol(predatorFAs))]
npredators = nrow(predator.matrix)
## Prey
data(preyFAs)
prey.sub=(preyFAs[,4:(ncol(preyFAs))])[fa.set]
prey.sub=prey.sub/apply(prey.sub,1,sum)
group=as.vector(preyFAs$Species)
prey.matrix=cbind(group,prey.sub)
prey.matrix=MEANmeth(prey.matrix)
FC = preyFAs[,c(2,3)]
FC = as.vector(tapply(FC$lipid,FC$Species,mean,na.rm=TRUE))
## Calibration Coefficients
data(CC)
cal.vec = CC[,2]
cal.mat = replicate(npredators, cal.vec)
# Run QFASA
Q = p.QFASA(predator.matrix,
prey.matrix,
cal.mat,
dist.meas,
gamma=1,
FC,
start.val = rep(1,nrow(prey.matrix)),
fa.set)
# Diet Estimates
DietEst = Q$'Diet Estimates'
DietEst = round(DietEst*100,digits=2)
colnames(DietEst) = (as.vector(rownames(prey.matrix)))
DietEst = cbind(tombstone.info,DietEst)
# Check diet estimates
DietEstCheck = read.csv(file=system.file("exdata", "DietEstKL.csv", package="QFASA"),
as.is=TRUE)
expect_equal(DietEst, DietEstCheck, tolerance=1e-6)
# Additional Measures
AdditionalMeasures = plyr::ldply(Q$'Additional Measures', data.frame)
# Check additional measures
AdditionalMeasuresCheck = read.csv(file=system.file("exdata", "AdditionalMeasuresKL.csv", package="QFASA"), as.is=TRUE)
expect_equal(AdditionalMeasures, AdditionalMeasuresCheck, tolerance=1e-4)
})
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