tests/residuals.R

In flr/FLa4a: A Simple and Robust Statistical Catch at Age Model

library(FLa4a)
data(ple4)
data(ple4.indices)
ple4.indices <- ple4.indices[c(3,4,5)]
data(ple4.index)

# creating idx 1
bioidx <- FLIndexBiomass(FLQuant(NA, dimnames=list(age="all", year=range(ple4)["minyear"]:range(ple4)["maxyear"])))
index(bioidx) <- stock(ple4)*0.001
index(bioidx) <- index(bioidx)*exp(rnorm(index(bioidx), sd=0.1))
range(bioidx)[c("startf","endf")] <- c(0,0)

# creating idx 2
stkn <- stock.n(ple4)*exp(-z(ple4))*0.5
bioidx2 <- FLIndexBiomass(FLQuant(NA, dimnames=list(age="all", year=range(ple4)["minyear"]:range(ple4)["maxyear"])))
index(bioidx2) <- quantSums(stkn*stock.wt(ple4))*0.001
index(bioidx2) <- index(bioidx2)*exp(rnorm(index(bioidx2), sd=0.1))
range(bioidx2)[c("startf","endf")] <- c(0,1)

# FLIndices
idxs <- FLIndices(c(ple4.indices, b1 = bioidx, b2 = bioidx2))

# fitting the model
fit <- sca(ple4, idxs, qmodel=list(~s(age, k=4), ~s(age, k=4), ~s(age, k=3), ~1, ~1))
res <- residuals(fit, ple4, idxs)
length(res) == 7

# FLIndex
fit <- sca(ple4, ple4.index)
res <- try(residuals(fit, ple4, ple4.index))
!is(res, 'try-error')

# flquantdistr
catch.n(ple4) <- FLQuantDistr(catch.n(ple4), catch.n(ple4))
var(catch.n(ple4))[] <- 0.2
index.var(ple4.index)[] <- 0.2

fit <-  sca(ple4, FLIndices(ple4.index), qmodel=list(~1))
res <- residuals(fit, ple4, FLIndices(ple4.index))
length(res) == 3