setFlags,adp-method {oce} | R Documentation |
This function changes specified entries in the data-quality
flags of a adp object, which are stored within
a list named flags
that resides in the metadata
slot. If the object already has a flag set up for name
,
then only the specified entries are altered. If not, the flag
entry is first created and its entries set to default
,
after which the entries specified by i
are changed to value
.
The specification is made with i
, the form of which
is determined by the data item in question. Generally,
the rules are as follows:
If the data item is a vector, then i
must be (a)
an integer vector specifying indices to be set to value
,
(b) a logical vector of length matching the data item, with
TRUE
meaning to set the flag to value
, or (c)
a function that takes an oce
object as its single
argument, and returns a vector in either of the forms
just described.
If the data item is an array, then i
must be
(a) a data frame of integers whose rows specify spots to change
(where the number of columns matches the number of dimensions
of the data item), (b) a logical array that has dimension equal to
that of the data item, or (c) a function that takes an oce
object as its single input and returns such a data frame or array.
See “Details” for the particular case of
adp-class
objects.
## S4 method for signature 'adp' setFlags(object, name = NULL, i = NULL, value = NULL, debug = getOption("oceDebug"))
object |
An oce object. |
name |
Character string indicating the name of the variable to be flagged. If
this variable is not contained in the object's |
i |
Indication of where to insert the flags; see “Description” for
general rules and “Details” for rules for |
value |
The value to be inserted in the flag. |
debug |
Integer set to 0 for quiet action or to 1 for some debugging. |
The only flag that may be set is v
, for the array holding velocity. See “Indexing rules”, noting that adp data are stored in 3D arrays; Example 1 shows using a data frame for i
, while Example 2 shows using an array.
An object with flags set as indicated.
This function was added in early May, 2018, and is likely to undergo changes until the mid-summer of that year. Use with caution.
Other functions relating to data-quality flags: defaultFlags
,
handleFlags,adp-method
,
handleFlags,argo-method
,
handleFlags,ctd-method
,
handleFlags,section-method
,
handleFlags
,
initializeFlagScheme,ctd-method
,
initializeFlagScheme,oce-method
,
initializeFlagScheme,section-method
,
initializeFlagScheme
,
initializeFlags,adp-method
,
initializeFlags,oce-method
,
initializeFlags
,
setFlags,ctd-method
,
setFlags,oce-method
, setFlags
Other things related to adp
data: [[,adp-method
,
[[<-,adp-method
, adp-class
,
adpEnsembleAverage
, adp
,
as.adp
, beamName
,
beamToXyzAdp
, beamToXyzAdv
,
beamToXyz
, beamUnspreadAdp
,
binmapAdp
, enuToOtherAdp
,
enuToOther
,
handleFlags,adp-method
,
plot,adp-method
, read.ad2cp
,
read.adp.nortek
,
read.adp.rdi
,
read.adp.sontek.serial
,
read.adp.sontek
, read.adp
,
read.aquadoppHR
,
read.aquadoppProfiler
,
read.aquadopp
, rotateAboutZ
,
subset,adp-method
,
summary,adp-method
, toEnuAdp
,
toEnu
, velocityStatistics
,
xyzToEnuAdp
, xyzToEnu
library(oce) data(adp) ## Example 1: flag first 10 samples in a mid-depth bin of beam 1 i1 <- data.frame(1:20, 40, 1) adpQC <- initializeFlags(adp, "v", 2) adpQC <- setFlags(adpQC, "v", i1, 3) adpClean1 <- handleFlags(adpQC, flags=list(3), actions=list("NA")) par(mfrow=c(2, 1)) ## Top: original, bottom: altered plot(adp, which="u1") plot(adpClean1, which="u1") ## Example 2: percent-good and error-beam scheme v <- adp[["v"]] i2 <- array(FALSE, dim=dim(v)) g <- adp[["g", "numeric"]] # Thresholds on percent "goodness" and error "velocity" G <- 25 V4 <- 0.45 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")) ## Top: original, bottom: altered plot(adp, which="u1") plot(adpClean2, which="u1") # differs at 8h and 20h