## ----echo=FALSE---------------------------------------------------------------
knitr::opts_chunk$set(collapse=TRUE, comment="#>")

## ----eval=FALSE---------------------------------------------------------------
# library(argoFloats)
# load_all()
# browseVignettes("argoFloats")

## ----echo=FALSE---------------------------------------------------------------
ID <- "1901584"

## ----warning=FALSE, error=FALSE, message=FALSE, eval=FALSE--------------------
# library(argoFloats)
# data("index")
# index1 <- subset(index, ID="1901584")
# profiles <- getProfiles(index1)
# argos <- readProfiles(profiles)
# plot(argos, which="QC", parameter="temperature")

## ----message=FALSE, error=FALSE, warning=FALSE, eval=FALSE--------------------
# index2 <- subset(index1, cycle="124")
# profiles2 <- getProfiles(index2)
# argos2 <- readProfiles(profiles2)
# showQCTests(argos2[[1]])

## ----eval=FALSE---------------------------------------------------------------
# A <- argos[[1]]
# D <- data.frame(T=A[["temperature"]], TF=A[["temperatureFlag"]],
#                 S=A[["salinity"]], SF=A[["salinityFlag"]],
#                 P=A[["pressure"]], PF=A[["pressureFlag"]])

## ----message=FALSE, error=FALSE, warning=FALSE, eval=FALSE--------------------
# clean <- applyQC(argos)
# oldpar <- par(no.readonly=TRUE)
# par(mfrow=c(1, 2))
# plot(argos, which="TS")
# plot(clean, which="TS")
# par(oldpar)

## ----eval=FALSE---------------------------------------------------------------
# remotes::install_github("dankelley/oce", ref="develop")

## ----warning=FALSE, message=FALSE, error=FALSE, fig.cap="*Figure 5.* Comparison of raw and adjusted oxygen profiles for built-in float file `SD5903586_001.nc`."----
if (packageVersion("oce") > "1.2.0") {
    library(argoFloats)
    raw <- readProfiles(system.file("extdata", "SD5903586_001.nc", package="argoFloats"))
    adjusted <- useAdjusted(raw)
    rawOxygen <- unlist(raw[["oxygen"]])
    rawPressure <- unlist(raw[["pressure"]])
    adjustedOxygen <- unlist(adjusted[["oxygen"]])
    adjustedPressure <- unlist(adjusted[["pressure"]])
    xlim <- range(c(rawOxygen, adjustedOxygen), na.rm=TRUE)
    plot(rawOxygen, rawPressure,
         pch=1, col=1,
         xlim=xlim, ylim=rev(range(rawPressure, na.rm=TRUE)),
         xlab=expression("Raw Oxygen ["*mu*mol/kg*"]"),
         ylab="Pressure (dbar)")
    points(adjustedOxygen, adjustedPressure,
           pch=3, col=2)
    legend("bottomright", pch=c(1,3), col=c(1,2), c("Raw", "Adjusted"))
}

## ----warning=FALSE, error=FALSE, message=FALSE, fig.cap="*Figure 6.* Comparison of raw and adjusted oxygen for built-in float file `SD5903586_001.nc`.  The dotted line is a 1:1 relationship, and the red line is the result of linear regression (see text)."----
if (packageVersion("oce") > "1.2.0") {
    plot(rawOxygen, adjustedOxygen,
         xlab=expression("Raw Oxygen ["*mu*mol/kg*"]"),
         ylab=expression("Adjusted Oxygen ["*mu*mol/kg*"]"))
    abline(0, 1, lty=3)
    model <- lm(adjustedOxygen ~ rawOxygen)
    abline(model, col=2)
}

## ----echo=FALSE---------------------------------------------------------------
if (packageVersion("oce") > "1.2.0") {
    residual <- round(mean(abs((model$residuals))),8)
} else {
    residual <- 9.8e-7 # value obtained with oce 1.3.0
}

## -----------------------------------------------------------------------------
if (packageVersion("oce") > "1.2.0") {
    summary(model)
}

## ----eval=FALSE---------------------------------------------------------------
# library(argoFloats)
# data("indexSynthetic")
# index1 <- subset(indexSynthetic, ID="4900845")
# profiles <- getProfiles(index1)
# argos <- readProfiles(profiles)
# plot(argos, which="QC", parameter="temperature")

## ----eval=FALSE---------------------------------------------------------------
# library(argoFloats)
# data("indexSynthetic")
# index1 <- subset(indexSynthetic, ID="4900845")
# profiles <- getProfiles(index1)
# argos <- readProfiles(profiles)
# a1 <- argos[[1]]
# showQCTests(a1)

## ----eval=FALSE---------------------------------------------------------------
# library(argoFloats)
# # Contrast TS diagrams for raw and flag-handled data
# data(indexSynthetic)
# index1 <- subset(indexSynthetic, ID="4900845")
# argos <- readProfiles(getProfiles(index1))
# clean <- applyQC(argos)
# oldpar <- par(no.readonly=TRUE)
# par(mfrow=c(1, 2))
# plot(argos, which="TS")
# plot(clean, which="TS")
# par(oldpar)

## ----eval=FALSE---------------------------------------------------------------
# summary(unlist(argos[["temperature"]]))
# summary(unlist(clean[["temperature"]]))
# summary(unlist(argos[["salinity"]]))
# summary(unlist(clean[["salinity"]]))

## ----eval=FALSE---------------------------------------------------------------
# library(argoFloats)
# raw <- readProfiles(system.file("extdata", "SD5903586_001.nc", package="argoFloats"))
# adjusted <- useAdjusted(raw)
# rawC <- unlist(raw[["chlorophyllA"]])
# rawPressure <- unlist(raw[["pressure"]])
# adjustedC <- unlist(adjusted[["chlorophyllA"]])
# adjustedPressure <- unlist(adjusted[["pressure"]])
# plot(rawC, rawPressure, ylim=rev(range(rawPressure, na.rm=TRUE)), pch=16, col="blue", xlab=expression("Raw Chlorophyll A (mg/m3)"), ylab="Pressure (dbar)")
# points(adjustedC, adjustedPressure, ylim=rev(range(unlist(adjusted[["pressure"]]), na.rm=TRUE)), pch=16, col="red")
# legend("bottomright", col=c("blue","red"), c("Raw", "Adjusted"), pch=c(16, 16))

## ----eval=FALSE---------------------------------------------------------------
# plot(rawC, adjustedC,
#      xlab=expression("Raw Chlorophyll (mg/m3)"),
#      ylab=expression("Adjusted Chlorophyll (mg/m3)"))
# abline(0, 1, lty=3)
# model <- lm(adjustedC ~ rawC)
# abline(model, col=2)
# summary(model)