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Style code and document #484

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Oct 19, 2023
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Style code and document #484

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46 changes: 23 additions & 23 deletions tests/testthat/test-fims-estimation.R
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Original file line number Diff line number Diff line change
Expand Up @@ -413,22 +413,22 @@ test_that("estimation test of fims", {
)

# Biomass
sdr_biomass <- sdr_report[which(rownames(sdr_report) == "Biomass"),]
sdr_biomass <- sdr_report[which(rownames(sdr_report) == "Biomass"), ]
biomass_are <- rep(0, length(om_output$biomass.mt))
for (i in 1:length(om_output$biomass.mt)) {
biomass_are[i] <- abs(sdr_biomass[i,1] - om_output$biomass.mt[i])# / om_output$biomass.mt[i]
# expect_lte(biomass_are[i], 0.15)
biomass_are[i] <- abs(sdr_biomass[i, 1] - om_output$biomass.mt[i]) # / om_output$biomass.mt[i]
# expect_lte(biomass_are[i], 0.15)
}
expect_lte(
sum(biomass_are > qnorm(.975) * sdr_biomass[1:length(om_output$biomass.mt),2]),
0.05*length(om_output$biomass.mt)
sum(biomass_are > qnorm(.975) * sdr_biomass[1:length(om_output$biomass.mt), 2]),
0.05 * length(om_output$biomass.mt)
)

# Spawning biomass
sdr_sb <- sdr_report[which(rownames(sdr_report) == "SSB"), ]
sb_are <- rep(0, length(om_output$SSB))
for (i in 1:length(om_output$SSB)) {
sb_are[i] <- abs(sdr_sb[i,1] - om_output$SSB[i])# / om_output$SSB[i]
sb_are[i] <- abs(sdr_sb[i, 1] - om_output$SSB[i]) # / om_output$SSB[i]
# expect_lte(sb_are[i], 0.15)
}
expect_lte(
Expand All @@ -444,9 +444,9 @@ test_that("estimation test of fims", {
sdr_naa1 <- sdr_naa1_vec[seq(1, om_input$nyr * om_input$nages, by = om_input$nages)]
fims_naa1_are <- rep(0, length(om_output$N.age[, 1]))
for (i in 1:length(om_output$N.age[, 1])) {
fims_naa1_are[i] <- abs(fims_naa[i,1] - om_output$N.age[i, 1])# /
# om_output$N.age[i, 1]
#expect_lte(fims_naa1_are[i], 0.25)
fims_naa1_are[i] <- abs(fims_naa[i, 1] - om_output$N.age[i, 1]) # /
# om_output$N.age[i, 1]
# expect_lte(fims_naa1_are[i], 0.25)
}
expect_lte(
sum(fims_naa1_are > qnorm(.975) * sdr_naa1[1:length(om_output$SSB)]),
Expand All @@ -463,8 +463,8 @@ test_that("estimation test of fims", {
rdev_are <- rep(0, length(om_input$logR.resid))

for (i in 1:length(om_input$logR.resid)) {
rdev_are[i] <- abs(report$rec_dev[[1]][i] - exp(om_input$logR.resid[i]))# /
# exp(om_input$logR.resid[i])
rdev_are[i] <- abs(report$rec_dev[[1]][i] - exp(om_input$logR.resid[i])) # /
# exp(om_input$logR.resid[i])
# expect_lte(rdev_are[i], 1) # 1
}
expect_lte(
Expand All @@ -476,7 +476,7 @@ test_that("estimation test of fims", {
sdr_F <- sdr_report[which(rownames(sdr_report) == "FMort"), ]
f_are <- rep(0, length(om_output$f))
for (i in 1:length(om_output$f)) {
f_are[i] <- abs(sdr_F[i,1] - om_output$f[i])
f_are[i] <- abs(sdr_F[i, 1] - om_output$f[i])
}
# Expect 95% of absolute error to be within 2*SE of Fmort
expect_lte(
Expand All @@ -486,24 +486,24 @@ test_that("estimation test of fims", {

# Expected fishery catch and survey index
fims_index <- sdr_report[which(rownames(sdr_report) == "ExpectedIndex"), ]
fims_catch <- fims_index[1:om_input$nyr,]
fims_survey <- fims_index[(om_input$nyr+1):(om_input$nyr*2),]
fims_catch <- fims_index[1:om_input$nyr, ]
fims_survey <- fims_index[(om_input$nyr + 1):(om_input$nyr * 2), ]

#Expected fishery catch - om_output
# Expected fishery catch - om_output
catch_are <- rep(0, length(om_output$L.mt$fleet1))
for (i in 1:length(om_output$L.mt$fleet1)) {
catch_are[i] <- abs(fims_catch[i,1] - om_output$L.mt$fleet1[i])
catch_are[i] <- abs(fims_catch[i, 1] - om_output$L.mt$fleet1[i])
}
# Expect 95% of absolute error to be within 2*SE of fishery catch
expect_lte(
sum(catch_are > qnorm(.975) * fims_catch[, 2]),
0.05 * length(om_output$L.mt$fleet1)
)

#Expected fishery catch - em_input
# Expected fishery catch - em_input
catch_are <- rep(0, length(em_input$L.obs$fleet1))
for (i in 1:length(em_input$L.obs$fleet1)) {
catch_are[i] <- abs(fims_catch[i,1] - em_input$L.obs$fleet1[i])
catch_are[i] <- abs(fims_catch[i, 1] - em_input$L.obs$fleet1[i])
}
# Expect 95% of absolute error to be within 2*SE of fishery catch
expect_lte(
Expand All @@ -516,7 +516,7 @@ test_that("estimation test of fims", {
sdr_cnaa <- sdr_report[which(rownames(sdr_report) == "CNAA"), ]
cnaa_are <- rep(0, length(c(t(om_output$L.age$fleet1))))
for (i in 1:length(c(t(om_output$L.age$fleet1)))) {
cnaa_are[i] <- abs(sdr_cnaa[i,1] - c(t(om_output$L.age$fleet1))[i])
cnaa_are[i] <- abs(sdr_cnaa[i, 1] - c(t(om_output$L.age$fleet1))[i])
}
# Expect 95% of absolute error to be within 2*SE of CNAA
expect_lte(
Expand Down Expand Up @@ -544,18 +544,18 @@ test_that("estimation test of fims", {
# Expected survey index - om_output
index_are <- rep(0, length(om_output$survey_index_biomass$survey1))
for (i in 1:length(om_output$survey_index_biomass$survey1)) {
index_are[i] <- abs(fims_survey[i,1] - om_output$survey_index_biomass$survey1[i])
index_are[i] <- abs(fims_survey[i, 1] - om_output$survey_index_biomass$survey1[i])
}
# Expect 95% of absolute error to be within 2*SE of survey index
expect_lte(
sum(index_are > qnorm(.975) * fims_survey[, 2]),
0.05 * length(om_output$survey_index_biomass$survey1)
)

#Expected survey index - em_input
# Expected survey index - em_input
index_are <- rep(0, length(em_input$surveyB.obs$survey1))
for (i in 1:length(em_input$surveyB.obs$survey1)) {
index_are[i] <- abs(fims_survey[i,1] - em_input$surveyB.obs$survey1[i])
index_are[i] <- abs(fims_survey[i, 1] - em_input$surveyB.obs$survey1[i])
}
# Expect 95% of absolute error to be within 2*SE of survey index
# expect_lte(
Expand All @@ -564,7 +564,7 @@ test_that("estimation test of fims", {
# )

for (i in 1:length(em_input$surveyB.obs$survey1)) {
expect_lte(abs(fims_survey[i,1] - em_input$surveyB.obs$survey1[i]) /
expect_lte(abs(fims_survey[i, 1] - em_input$surveyB.obs$survey1[i]) /
em_input$surveyB.obs$survey1[i], 0.25)
}

Expand Down
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