create_data/echosounder/create_echosounder.R

In dankelley/oce: Analysis of Oceanographic Data

library(oce)
library(testthat)
data(echosounder)
echosounderOLD <- echosounder
## I would like to make dataset have dim(ECHOSOUNDER@data$a) = c(736,88) but doing that with decimate()
## does not yield the smoothness in the existing datafile. The present code is useless except perhaps
## to remind me where the original file resided, what times I used for chopping, etc.

## echosounder <- read.oce("/data/archive/sleiwex/2008/fielddata/2008-07-01/Merlu/Biosonics/20080701_161403.dt4")
files <- c(
    "/data/archive/sleiwex/2008/fielddata/2008-07-01/Merlu/Biosonics/20080701_163942.dt4",
    "~/Dropbox/data/archive/sleiwex/2008/fielddata/2008-07-01/Merlu/Biosonics/20080701_163942.dt4"
)
ok <- FALSE
for (file in files) {
    if (file.exists(file)) {
        message(file)
        echosounder <- read.oce(file)
        ok <- TRUE
        break
    }
}
if (!ok) {
    stop("cannot find file in c(", paste(files, collapse = ","), ")")
}

# echosounder <- read.oce("dood/Dropbox/data/archive/sleiwex/2008/fielddata/2008-07-01/Merlu/Biosonics/20080701_163942.dt4")
## echosounder <- read.oce("/data/archive/sleiwex/2008/fielddata/2008-07-01/Merlu/Biosonics/20080701_164323.dt4")
## echosounder <- read.oce("/data/archive/sleiwex/2008/fielddata/2008-07-01/Merlu/Biosonics/20080701_163942.dt4")
## echosounder <- read.oce("/data/archive/sleiwex/2008/fielddata/2008-07-01/Merlu/Biosonics/20080701_164742.dt4")
## echosounder <- read.oce("/data/archive/sleiwex/2008/fielddata/2008-07-01/Merlu/Biosonics/20080701_165611.dt4")

echosounder <- subset(echosounder, depth < 40)
## echosounder <- subset(echosounder, time > as.POSIXct("2008-07-01 16:44:30", tz="UTC"))
echosounder <- decimate(echosounder, c(2, 40))
# plot(echosounder)

e <- echosounder
if (!interactive()) png("echosounder-new.png")
plot(echosounder, drawBottom = TRUE, despike = TRUE, which = "zx image")
if (!interactive()) dev.off()
if (!interactive()) png("echosounder-old.png")
plot(echosounderOLD, drawBottom = TRUE, despike = TRUE, which = "zx image")
if (!interactive()) dev.off()

expect_equal(
    echosounder[["a"]][10, 10:15],
    c(1101.6125, 818.9500, 892.3500, 1393.0625, 2320.9500, 5840.2750)
)
expect_equal(
    echosounder[["a"]][10:15, 10],
    c(1101.6125, 1164.5500, 875.3750, 842.5750, 959.6250, 1076.6500)
)

expect_equal(
    head(echosounder[["time"]]),
    as.POSIXct(
        c(
            "2008-07-01 16:39:41.019", "2008-07-01 16:39:41.509",
            "2008-07-01 16:39:42.000", "2008-07-01 16:39:42.485",
            "2008-07-01 16:39:42.974", "2008-07-01 16:39:43.464"
        ),
        tz = "UTC"
    )
)
expect_equal(head(echosounder[["latitude"]]),
    c(
        47.87948333, 47.87948333, 47.87948333, 47.87948825, 47.87949642,
        47.87950000
    ),
    tolerance = 0.000001
)
expect_equal(
    head(echosounder[["longitude"]]),
    c(
        -69.72364436, -69.72366061, -69.72367686, -69.72368808,
        -69.72369625, -69.72370900
    ),
    tolerance = 0.000001
)

## Save in version 2, because otherwise users with R 3.5.x and earlier will not
## be able to use data("echosounder")
if (utils::compareVersion(paste0(R.Version()$major, ".", R.Version()$minor), "3.6.0") >= 0) {
    message("saving with version=2 since R version is 3.6.0 or later")
    save(echosounder, file = "echosounder.rda", version = 2)
    tools::resaveRdaFiles("echosounder.rda", version = 2)
} else {
    save(echosounder, file = "echosounder.rda")
    tools::resaveRdaFiles("echosounder.rda")
}