tests/testthat/test_makeLH.R

In rFAMS: Fisheries Analysis and Modeling Simulator

# ## Get some simple results
# ## get some LVB results (as an example)
# data(SpotVA1,package="FSA")
# SpotVA1 <- SpotVA1 |> dplyr::mutate(tl=tl*25.4)
# vb1 <- FSA::vbFuns()
# fit1 <- nls(tl~vb1(age,Linf,K,t0),data=SpotVA1,start=FSA::vbStarts(tl~age,data=SpotVA1))
# vb2 <- FSA::vbFuns(param="Original")
# fit2 <- nls(tl~vb1(age,Linf,K,L0),data=SpotVA1,start=list(Linf=337,K=0.4,L0=10))
#
#
# ## get some LW results (as an example)
# data(BluegillLM,package="FSAdata")
# BluegillLM <- BluegillLM |>
#   dplyr::mutate(logW=log10(wght),logL=log10(tl))
# fit3 <- lm(logW~logL,data=BluegillLM)
#
#
# test_that("makeLH() messages",{
#   expect_no_error(makeLH(N0=100,maxage=15,Linf=2000,K=0.50,t0=-0.616,
#                          LWalpha=-5.453,LWbeta=3.10))
#   expect_error(makeLH(Linf=2000,maxage=15,K=0.50,t0=-0.616,
#                       LWalpha=-5.453,LWbeta=3.10),
#                "Need to specify an initial number of fish")
#   expect_error(makeLH(N0=100,maxage=15,K=0.50,t0=-0.616,
#                       LWalpha=-5.453,LWbeta=3.10),
#                "Need to specify a mean asymptotic length")
#
#   ## A few checks on reasonableness of values, there are more tests in internals
#   expect_error(makeLH(N0=-100,maxage=15,Linf=2000,K=0.50,t0=-0.616,
#                       LWalpha=-5.453,LWbeta=3.10),
#                "'N0' must be >=0")
#   expect_error(makeLH(N0=100,maxage=15,Linf=-2000,K=0.50,t0=-0.616,
#                       LWalpha=-5.453,LWbeta=3.10),
#                "'Linf' must be >=0")
#   expect_error(makeLH(N0=c(100,200),maxage=15,Linf=2000,K=0.50,t0=-0.616,
#                       LWalpha=-5.453,LWbeta=3.10),
#                "Only use one value in 'N0'")
#   expect_error(makeLH(N0=100,maxage=15,Linf="a",K=0.50,t0=-0.616,
#                       LWalpha=-5.453,LWbeta=3.10),
#                "'Linf' must be a number")
#   expect_warning(makeLH(N0=100,maxage=15,Linf=20000,K=0.50,t0=-0.616,
#                         LWalpha=-5.453,LWbeta=3.10),
#                  "A mean asymptotic length of 20000 mm seems too large")
#   expect_error(makeLH(N0=100,maxage=15,Linf=fit2,LWalpha=-5.453,LWbeta=3.10),
#                "Names of parameters in 'nls' object are not 'Linf', 'K', and 't0'")
#   expect_error(makeLH(N0=100,maxage=15,Linf=fit3,LWalpha=-5.453,LWbeta=3.10),
#                "'Linf' given object from 'lm")
#   expect_error(makeLH(N0=100,maxage=15,Linf=fit1,LWalpha=fit1),
#                "'LWalpha' given object from 'nls")
# })
#
# test_that("makeLH() results",{
#   ## as a list
#   tmp <- makeLH(N0=100,maxage=15,Linf=2000,K=0.50,t0=-0.616,LWalpha=-5.453,LWbeta=3.10)
#   expect_true(isa(tmp,"list"))
#   expect_equal(length(names(tmp)),7)
#   expect_equal(names(tmp),c("N0","maxage","Linf","K","t0","LWalpha","LWbeta"))
#
#   ## as a vector
#   tmp <- makeLH(N0=100,maxage=15,Linf=2000,K=0.50,t0=-0.616,LWalpha=-5.453,LWbeta=3.10,
#                 restype="vector")
#   expect_true(is.numeric(tmp))
#   expect_equal(length(names(tmp)),7)
#   expect_equal(names(tmp),c("N0","maxage","Linf","K","t0","LWalpha","LWbeta"))
#
#   ## as a list but using model results
#   tmp <- makeLH(N0=100,maxage=15,Linf=fit1,LWalpha=fit3)
#   expect_true(isa(tmp,"list"))
#   expect_equal(length(names(tmp)),7)
#   expect_equal(names(tmp),c("N0","maxage","Linf","K","t0","LWalpha","LWbeta"))
# })