context("Does LRIBI Match the WiDNR Calculator")
test_that("LRIBI() with no data discrepancies",{
## read external data files
fmdb56 <- read.FMDB(system.file("extdata","fish_raw_data_Survey375049456.csv",
package="fishWiDNR"),expandCounts=TRUE)
agg56 <- utils::read.csv(system.file("extdata","aggdata_Survey375049456.csv",
package="fishWiDNR"))
## read test files (results from WiDNR Calculator)
sum56 <- utils::read.csv(system.file("extdata","test_375049456_summary.csv",
package="fishWiDNR"),stringsAsFactors=FALSE)
met56 <- utils::read.csv(system.file("extdata","test_375049456_metric_scores.csv",
package="fishWiDNR"),stringsAsFactors=FALSE)
## Calculate IBI (assumes effort is 0.9)
res <- LRIBI(fmdb56,agg56,effort=0.9)
## Do overall IBIs match
expect_equal(res$IBI,60)
## Do species summaries match
expect_equal(res$sum.data$Species1,sum56$Species)
expect_equal(res$sum.data$Count,sum56$Counts)
expect_equal(round(res$sum.data$Biomass,3),round(sum56$Biomass/1000,3))
expect_equal(res$n.fish,sum(sum56$Counts))
expect_equal(round(res$ttl.Biomass,3),round(sum(sum56$Biomass)/1000,3))
## Do metric summaries match
expect_equal(res$IBI.data$Metric,met56$Metric)
expect_equal(round(res$IBI.data$Value[1],1),round(met56$Value[1],1)) #just WPUE
expect_equal(round(res$IBI.data$Value,0),round(met56$Value,0))
expect_equal(res$IBI.data$Score,met56$Score)
## Check that no problems were identified
expect_true(res$noProblems)
expect_true(is.null(res$countsProblems))
expect_true(is.null(res$weightsProblems))
})
test_that("LRIBI() with data discrepancies",{
## read external data files
fmdb18 <- read.FMDB(system.file("extdata","fish_raw_data_Survey375334018.csv",
package="fishWiDNR"),expandCounts=TRUE)
agg18 <- utils::read.csv(system.file("extdata","aggdata_Survey375334018.csv",
package="fishWiDNR"))
## read test files (results from WiDNR Calculator)
sum18 <- utils::read.csv(system.file("extdata","test_375334018_summary.csv",
package="fishWiDNR"),stringsAsFactors=FALSE)
met18 <- utils::read.csv(system.file("extdata","test_375334018_metric_scores.csv",
package="fishWiDNR"),stringsAsFactors=FALSE)
## Calculate IBI (assumes effort is 0.9)
expect_warning(res <- LRIBI(fmdb18,agg18,effort=0.9),"do not match")
## Do overall IBIs match
expect_equal(res$IBI,65)
## Do species summaries match
expect_equal(res$sum.data$Species1,sum18$Species)
expect_equal(res$sum.data$Count,sum18$Counts)
expect_equal(round(res$sum.data$Biomass,3),round(sum18$Biomass/1000,3))
expect_equal(res$n.fish,sum(sum18$Counts))
expect_equal(round(res$ttl.Biomass,3),round(sum(sum18$Biomass)/1000,3))
## Do metric summaries match
expect_equal(res$IBI.data$Metric,met18$Metric)
expect_equal(round(res$IBI.data$Value[1],1),round(met18$Value[1],1)) #just WPUE
expect_equal(round(res$IBI.data$Value,0),round(met18$Value,0))
expect_equal(res$IBI.data$Score,met18$Score)
## Check that no problems were identified
expect_true(!res$noProblems)
expect_true(!is.null(res$countsProblems))
expect_equal(res$countsProblems,c("Common Shiner","Northern Hog Sucker","White Sucker"))
expect_true(is.null(res$weightsProblems))
})
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.