test_accessors.R
In oce: Analysis of Oceanographic Data

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

test_that("[[\"?\"]] is handled by all object classes", {
    # The object names was created by saving the output of `git grep setClass R`
    # and reformulating into R code.
    objectNames <- c("adp", "adv", "amsr", "argo", "bremen", "cm", "coastline",
        "ctd", "echosounder", "satellite", "g1sst", "gps", "ladp", "landsat",
        "lisst", "lobo", "met", "odf", "rsk", "satellite", "sealevel",
        "section", "tidem", "topo", "windrose", "xbt")
    for (objectName in objectNames) {
        o <- new(objectName)
        expect_equal(4, length(o[["?"]]))
    }
})

test_that("get/set/delete data", {
    data("ctd")
    S <- oceGetData(ctd, "salinity")
    ctd2 <- oceSetData(ctd, name="fake", value=2*S,
        unit=list(unit=expression(), scale=""),
        originalName="FAKE")
    expect_equal(2*S, ctd2[["fake"]])
    expect_equal(S, ctd@data$salinity)
    expect_equal(S, ctd2@data$salinity)
    ## deletion
    d <- oceDeleteData(ctd, "fake")
    expect_false("fake" %in% names(d[["data"]]))
    expect_false("fake" %in% names(d@data))
})

test_that("get/set/delete metadata", {
    data("ctd")
    type <- oceGetMetadata(ctd, name="type")
    expect_equal(type, "SBE")
    ctd2 <- oceSetMetadata(ctd, name="type", value="fake")
    expect_equal(oceGetMetadata(ctd2, "type"), "fake")
    expect_equal(ctd2[["metadata"]]$type, "fake")
    ctd3 <- oceDeleteMetadata(ctd2, "type")
    expect_false("fake" %in% names(ctd3[["metadata"]]))
})


test_that("data", {
    data("ctd")
    d <- oceGetData(ctd, "salinity")
    expect_equal(d, ctd[["salinity"]])
    expect_equal(d, ctd@data$salinity)
})


test_that("retrieve units", {
    data("ctd")
    ## pre 20160430 expect_equal(ctd[["temperatureUnit"]], list(unit=expression(degree*C), scale="ITS-90"))
    ## pre 20160430 expect_equal(ctd[["temperature unit"]], expression(degree*C))
    ## pre 20160430 expect_equal(ctd[["temperature scale"]], "ITS-90")
    expect_equal(ctd[["temperatureUnit"]], list(unit=expression(degree*C), scale="IPTS-68"))
    expect_equal(ctd[["temperature unit"]], expression(degree*C))
    expect_equal(ctd[["temperature scale"]], "IPTS-68")
    expect_equal(ctd[["pressureUnit"]], list(unit=expression(dbar), scale=""))
    expect_equal(ctd[["pressure unit"]], expression(dbar))
    expect_equal(ctd[["pressure scale"]], "")
})

test_that("alter units", {
    data("ctd")
    ctd[["metadata"]]$units$salinity <- list(unit=expression(foo), scale="bar")
    expect_equal(ctd[["salinityUnit"]], list(unit=expression(foo), scale="bar"))
})


test_that("three methods for specifying units", {
    data(ctd)
    freezing <- swTFreeze(ctd)
    ctd <- oceSetData(ctd, "freezing", freezing, list(unit=expression(degree*C), scale="ITS-90"))
    feet <- 3.28048 * swDepth(ctd)
    ctd <- oceSetData(ctd, "depthInFeet", feet, expression(feet))
    expect_identical(ctd[["units"]]$depthInFeet, list(unit=expression(feet), scale=""))
    fathoms <- feet / 6
    ctd <- oceSetData(ctd, "depthInFathoms", fathoms, "fathoms")
    expect_identical(ctd[["units"]]$depthInFathoms, list(unit=expression(fathoms), scale=""))
})

test_that("can use original names", {
    data("ctd")
    ## next two tests relate to issues 1460 and 1547
    expect_equal(diff(ctd[["timeS"]]), diff(as.numeric(ctd[["time"]])))
    expect_equal(length(ctd[["time"]]), length(ctd[["pressure"]])) # 1460,1547
    expect_equal(ctd[["pressure"]], ctd[["pr"]])
    expect_equal(ctd[["depth"]], ctd[["depS"]])
    expect_equal(ctd[["temperature"]], T90fromT68(ctd[["t068"]]))
    expect_equal(ctd[["salinity"]], ctd[["sal00"]])
})

test_that("alter ctd profiles within a section", {
    data("section")
    section[["station", 1]][["S2"]] <- 2 * section[["station", 1]][["salinity"]]
    expect_equal(section[["station", 1]][["S2"]],
        2 * section[["station", 1]][["salinity"]])
})

## Tests with a funky file, from 1154 (we may need to chop these,
## since it does not make sense to use space in a CRAN package
## with a broken file.

## Next tests are in support of issue 1162, relating to the rules for accessing
## derived quantities.
test_that("accessor operations (ctd)", {
    data(ctd)
    S <- ctd[["salinity"]]
    expect_equal(head(S), c(29.9210, 29.9205, 29.9206, 29.9219, 29.9206, 29.9164))
    ctd[["salinity"]] <- S + 0.01
    SS <- ctd[["salinity"]]
    expect_equal(head(SS), 0.01 + c(29.9210, 29.9205, 29.9206, 29.9219, 29.9206, 29.9164))
    ctd[["SS"]] <- SS
    expect_equal(head(ctd[["SS"]]), 0.01 + c(29.9210, 29.9205, 29.9206, 29.9219, 29.9206, 29.9164))
})

## accessors to metadata or data
## https://github.com/dankelley/oce/issues/1554
test_that("accessor operations, specifying data or metadata", {
    data(ctd)
    expect_equal(ctd[["longitude"]], ctd[["longitude", "metadata"]])
    expect_null(ctd[["longitude", "data"]])
    expect_equal(ctd[["temperature"]], ctd[["temperature", "data"]])
    expect_equal(ctd[["salinity"]], ctd[["salinity", "data"]])
    expect_equal(ctd[["salinity"]], ctd[["sal00", "data"]]) # originalName
    ## Now, create something with conflicts
    o <- new("oce")
    o <- oceSetMetadata(o, "foo", "metadataBar")
    o <- oceSetData(o, "foo", "dataBar")
    expect_equal(o[["foo"]], "metadataBar")
    expect_equal(o[["foo", "metadata"]], "metadataBar")
    expect_equal(o[["foo", "data"]], "dataBar")
    expect_error(o[["foo", "unknown"]], "second arg must be")
})

test_that("derived quantities handled properly (ctd)", {
    ## do we get the same theta by both methods, if the object lacks
    ## theta at the start?
    data(ctd)
    expect_null(ctd[["noSuchThing"]])
    thetaByAccessor <- ctd[["theta"]]
    thetaByFunction <- swTheta(ctd)
    expect_equal(thetaByAccessor, thetaByFunction)
    ## Now, insert theta into the object, and alter salinity, to
    ## check that [[ gets the object value and swTheta() computes
    ## a new value.
    ctd[["theta"]] <- thetaByAccessor
    expect_equal(ctd[["theta"]], thetaByAccessor)
    expect_equal(ctd[["theta"]], swTheta(ctd))
    ctd[["S"]] <- ctd[["S"]] + 0.01 # alter S
    ## next values are just what I got from these data, i.e. they only
    ## form a consistency check, if the data or if swTheta() ever change.
    expect_equal(head(swTheta(ctd, eos="unesco")),
        c(14.2208818496, 14.2262540208, 14.2248015615,
            14.2218758247, 14.2263218577, 14.2328135332))
    ## Try both EOSs; need loction for GSW
    expect_equal(swTheta(ctd, eos="unesco"), swTheta(ctd[["salinity"]],
            ctd[["temperature"]],
            ctd[["pressure"]], eos="unesco"))
    expect_equal(swTheta(ctd, eos="gsw"), swTheta(ctd[["salinity"]],
            ctd[["temperature"]],
            ctd[["pressure"]],
            longitude=ctd[["longitude"]],
            latitude=ctd[["latitude"]], eos="gsw"))
})

test_that("accessor operations (adp)", {
    data(adp)
    v <- adp[["v"]]
    expect_equal(v[1:5, 1, 1], c(-0.11955770778, -0.09925398341, 0.10203801933,
        0.09613003081, 0.24394126236))
    expect_null(adp[["noSuchThing"]])
    adp[["somethingNew"]] <- 1:4
    expect_true("somethingNew" %in% names(adp[["data"]]))
    expect_equal(adp[["somethingNew"]], 1:4)
})

test_that("renaming items in the data slot", {
    data(ctd)
    bad <- oceRenameData(ctd, "salinity", "saltiness", note="a bad idea!")
    expect_error(plot(bad), "data slot lacks 'salinity")
})

test_that("argo original names (issue 1640)", {
    data(argo)
    expect_equal(argo[["temperature"]], argo[["TEMP"]])
})