oce: Analysis of Oceanographic Data

# vim:textwidth=80:expandtab:shiftwidth=4:softtabstop=4
library(oce)

file <- system.file("extdata", "CTD_BCD2014666_008_1_DN.ODF.gz", package="oce")
CRATwarning <- "\"conductivity\" \\(code name \"CRAT_01\"\\)" # portion of the warning

test_that("ODF CTD file", {
    expect_warning(d <- read.odf(file), CRATwarning)
    expect_equal(d[["temperatureUnit"]]$unit, expression(degree*C))
    expect_equal(d[["temperatureUnit"]]$scale, "IPTS-68")
    expect_equal(d[["conductivityUnit"]]$unit, expression(S/m))
    expect_equal(d[["pressureType"]], "sea")
    expect_equal(d[["ship"]], "CCGS SIGMA T (Call Sign: unknown)")
    expect_equal(d[["cruise"]], "Scotian Shelf")
    expect_equal(d[["scientist"]], "Catherine Johnson")
    # expect_null(d[["waterDepth"]])
    expect_equal(d[["latitude"]], 44.267500)
    expect_equal(d[["longitude"]], -63.317500)
    expect_equal(d[["temperature"]][1:3], c(5.883587939, 5.910981364, 5.917379829))
    expect_equal(d[["salinity"]][1:3], c(30.8514, 30.8593, 30.8596))
    # there are some flagged data in this file
    expect_equal(which(d[["salinityFlag"]]!=1), 121)
    expect_equal(c(110, 120, 121, 142), which(d[["sigmaThetaFlag"]]!=1))
})

test_that("ODF CTD file (not as CTD)", {
    expect_warning(d <- read.odf(file), CRATwarning)
    # Test whether the file marked sigmaTheta as bad, when salinity was
    # bad (line 121)
    badSTp <- which(d[["salinityFlag"]]!=1 | d[["temperatureFlag"]]!=1 | d[["pressureFlag"]]!=1)
    expect_equal(3, d@metadata$flags$sigmaTheta[badSTp])
})

test_that("ODF header", {
    expect_warning(d <- read.odf(file), CRATwarning)
    expect_true(is.list((d[["header"]])))
    expect_equal(length(d[["header"]]), 32)
    expect_warning(d <- read.odf(file, header="character"), CRATwarning)
    expect_true(is.vector(d[["header"]]))
    expect_equal(32, length(grep("^[A-Z].*,$", d[["header"]])))
    expect_true(is.character(d[["header"]]))
    expect_warning(d <- read.odf(file, header="list"), CRATwarning)
    expect_true(is.list(d[["header"]]))
    expect_equal(32, length(d[["header"]]))
    expect_true(is.list(d[["header"]][[1]]))
})

# temperature unit/scale (issue 1601)
# https://github.com/dankelley/oce/issues/1801
test_that("ODF temperature scale, IPTS68 and ITS90", {
    # Get IPTS68 temperature, ITS90, and unit, all needed for tests.
    # Note that all read() calls need to check for a warning that results
    # from an error in this ODF file (and quite a few ODF files, it seems).
    Tref68 <- read.table(file, skip=675, header=FALSE)$V4
    Tref90 <- T90fromT68(Tref68)
    unit <- list(unit=expression(degree*C), scale="IPTS-68")
    # read.odf()
    expect_warning(ctd1 <- read.odf(file), CRATwarning)
    expect_equal(ctd1@metadata$units$temperature, unit)
    expect_equal(ctd1@data$temperature, Tref68)
    expect_equal(ctd1[["temperature"]], Tref90)
    # read.ctd.odf()
    expect_warning(ctd2 <- read.ctd.odf(file), CRATwarning)
    expect_equal(ctd2@metadata$units$temperature, unit)
    expect_equal(ctd2@data$temperature, Tref68)
    expect_equal(ctd2[["temperature"]], Tref90)
    # read.oce()
    expect_warning(ctd3 <- read.oce(file), CRATwarning)
    expect_equal(ctd3@metadata$units$temperature, unit)
    expect_equal(ctd3@data$temperature, Tref68)
    expect_equal(ctd3[["temperature"]], Tref90)
    # as.ctd(read.odf())
    ctd1B <- as.ctd(ctd1)
    expect_equal(ctd1B@metadata$units$temperature, unit)
    expect_equal(ctd1B@data$temperature, Tref68)
    expect_equal(ctd1B[["temperature"]], Tref90)
    # as.ctd(read.ctd.odf())
    ctd2B <- as.ctd(ctd2)
    expect_equal(ctd2B@metadata$units$temperature, unit)
    expect_equal(ctd2B@data$temperature, Tref68)
    expect_equal(ctd2B[["temperature"]], Tref90)
    # as.ctd(read.oce())
    ctd3B <- as.ctd(ctd3)
    expect_equal(ctd3B@metadata$units$temperature, unit)
    expect_equal(ctd3B@data$temperature, Tref68)
    expect_equal(ctd3B[["temperature"]], Tref90)
})