Nothing
## ----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
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