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

## -----------------------------------------------------------------------------
library(oce)

## -----------------------------------------------------------------------------
library(oce)
data(ctdRaw)

## ----fig.cap="Figure 1. Summary plot for raw CTD profile.", fig.width=5, fig.height=5, dpi=72, dev.args=list(pointsize=13)----
plot(ctdRaw)

## -----------------------------------------------------------------------------
badS <- with(ctdRaw[["data"]], salinity < 25 | 40 < salinity)
badT <- with(ctdRaw[["data"]], temperature < -2 | 40 < temperature)

## -----------------------------------------------------------------------------
salinity <- ctdRaw[["salinity"]]
temperature <- ctdRaw[["temperature"]]
bad <- (salinity < 25 | 40 < salinity) | (temperature < -2 | 40 < temperature)

## -----------------------------------------------------------------------------
qc <- ctdRaw

## -----------------------------------------------------------------------------
qc <- initializeFlagScheme(qc, "WHP CTD")

## -----------------------------------------------------------------------------
qc <- initializeFlags(qc, "salinity", 2)
qc <- initializeFlags(qc, "temperature", 2)

## -----------------------------------------------------------------------------
qc <- setFlags(qc, "salinity", badS, value = "bad")

## -----------------------------------------------------------------------------
names(qc[["flags"]])

## -----------------------------------------------------------------------------
qc <- setFlags(qc, "temperature", badT, value = "bad")

## -----------------------------------------------------------------------------
qch <- handleFlags(qc, flags = list(c(1, 3:9)))

## ----fig.cap="Figure 2. Summary plot for range-checked CTD profile.", fig.width=5, fig.height=5, dpi=72, dev.args=list(pointsize=13)----
plot(qch)

## ----eval=FALSE---------------------------------------------------------------
#  options(eos = "gsw")
#  data(ctd)
#  qc <- ctd
#  qc <- initializeFlagScheme(qc, "WHP CTD")
#  qc <- initializeFlags(qc, "salinity", 2)
#  Sspan <- diff(range(qc[["SA"]]))
#  Tspan <- diff(range(qc[["CT"]]))
#  n <- length(qc[["SA"]])
#  par(mfrow = c(1, 1))
#  plotTS(qc, type = "o")
#  message("Click on bad points; quit by clicking to right of plot")
#  for (i in seq_len(n)) {
#      xy <- locator(1)
#      if (xy$x > par("usr")[2]) {
#          break
#      }
#      i <- which.min(abs(qc[["SA"]] - xy$x) / Sspan + abs(qc[["CT"]] - xy$y) / Tspan)
#      qc <- setFlags(qc, "salinity", i = i, value = "bad")
#      qc <- handleFlags(qc)
#      plotTS(qc, type = "o")
#  }

## ----fig.cap="Temperature-salinity diagram for section data, with flags ignored (top) and handled (bottom).", fig.width=5, fig.height=5, dpi=72, dev.args=list(pointsize=13)----
data(section)
s <- handleFlags(section, flags = list(c(1, 3:9)))
par(mfrow = c(2, 1))
plotTS(section)
plotTS(s)

## ----fig.cap="Near-surface eastward component of ADP velocity, unaltered (top) and after handling flags (bottom).", fig.width=6, fig.height=4, dpi=72, dev.args=list(pointsize=13)----
data(adp)
v <- adp[["v"]]
i2 <- array(FALSE, dim = dim(v)) # construct array to match 'v'
g <- adp[["g", "numeric"]]
G <- 25 # for percent-good field, named 'g'
V4 <- 0.45 # for error velocity field, in beam 4
for (k in 1:3) {
    i2[, , k] <- ((g[, , k] + g[, , 4]) < G) | (v[, , 4] > V4)
}
adpQC2 <- initializeFlags(adp, "v", 2)
adpQC2 <- setFlags(adpQC2, "v", i2, 3)
adpClean2 <- handleFlags(adpQC2, flags = list(3), actions = list("NA"))
par(mfrow = c(2, 1))
plot(subset(adp, distance > 35), which = "u1") # original
plot(subset(adpClean2, distance > 35), which = "u1") # altered