inst/tinytest/test-bioticdiff.R

In StoXProject/RstoxFDA: Fisheries Dependent Analysis with RstoX

#context("Test bioticdiff")

library(RstoxData) #workaround for issue in RstoxData (https://github.com/StoXProject/RstoxData/issues/253)

bioticfile <- system.file("testresources", "biotic_v3_example.xml", package="RstoxFDA")
nmdbiotic <- RstoxData::ReadBiotic(bioticfile)
nmdbiotic$biotic_v3_example.xml$catchsample$catchproducttype <- 1
nmdbiotic$biotic_v3_example.xml$catchsample$sampleproducttype <- 1
nmdbiotic$biotic_v3_example.xml$individual$individualproducttype <- 1
nmdbiotic$biotic_v3_example.xml$catchsample$lengthmeasurement <- "E"
nmdbiotic$biotic_v3_example.xml$mission$cruise[1] <- "20170202"
StoxBiotic <- RstoxData::StoxBiotic(nmdbiotic)

diff <- RstoxFDA:::bioticDiff(nmdbiotic, StoxBiotic)
expect_equal(nrow(diff$mission), 0)
expect_equal(nrow(diff$fishstation), 0)
expect_equal(nrow(diff$catchsample), 0)
expect_equal(nrow(diff$individual), 0)

StoxBioticStation <- StoxBiotic
StoxBioticStation$Haul <- StoxBioticStation$Haul[2,]
diff <- RstoxFDA:::bioticDiff(nmdbiotic, StoxBioticStation)
expect_equal(nrow(diff$mission), 0)
expect_equal(nrow(diff$fishstation), 1)
expect_equal(nrow(diff$catchsample), 0)
expect_equal(nrow(diff$individual), 0)

StoxBioticCatchsample <- StoxBiotic
StoxBioticCatchsample$Sample <- StoxBioticCatchsample$Sample[c(1,3,5),]
diff <- RstoxFDA:::bioticDiff(nmdbiotic, StoxBioticCatchsample)
expect_equal(nrow(diff$mission), 0)
expect_equal(nrow(diff$fishstation), 0)
expect_equal(nrow(diff$catchsample), nrow(StoxBiotic$Sample)-3)
expect_equal(nrow(diff$individual), 0)

StoxBioticIndividual <- StoxBiotic
StoxBioticIndividual$Individual <- StoxBioticIndividual$Individual[5:25,]
diff <- RstoxFDA:::bioticDiff(nmdbiotic, StoxBioticIndividual)
expect_equal(nrow(diff$mission), 0)
expect_equal(nrow(diff$fishstation), 0)
expect_equal(nrow(diff$catchsample), 0)
expect_equal(nrow(diff$individual), nrow(StoxBiotic$Individual)-21)