plotZOC,TDR,matrix-method | R Documentation |
Plots for comparing the zero-offset corrected depth from a
TDRcalibrate
object with the uncorrected data in a
TDR
object, or the progress in each of the filters during
recursive filtering for ZOC (calibrateDepth
).
## S4 method for signature 'TDR,matrix' plotZOC(x, y, xlim, ylim, ylab = "Depth (m)", ...) ## S4 method for signature 'TDR,TDRcalibrate' plotZOC(x, y, xlim, ylim, ylab = "Depth (m)", ...)
x |
|
y |
matrix with the same number of rows as there are observations
in |
xlim |
|
ylim |
numeric vector of length 2 (upper, lower) with axis limits. Defaults to range of input. |
ylab |
character strings to label the corresponding y-axis. |
... |
Arguments passed to |
The TDR
,matrix
method produces a plot like those shown in
Luque and Fried (2011).
The TDR
,TDRcalibrate
method overlays the corrected depth
from the second argument over that from the first.
Nothing; a plot as side effect.
x = TDR,y = matrix
: This plot helps in finding appropriate parameters
for diveMove:::.depthFilter
, and consists of three panels.
The upper panel shows the original data, the middle panel shows the
filters, and the last panel shows the corrected
data. method=“visual” in calibrateDepth
.
x = TDR,y = TDRcalibrate
: This plots depth from the TDRcalibrate
object over the one from the TDR
object.
Sebastian P. Luque spluque@gmail.com
Luque, S.P. and Fried, R. (2011) Recursive filtering for zero offset correction of diving depth time series. PLoS ONE 6:e15850
calibrateDepth
, .zoc
## Using the Example from '?diveStats': ## Too long for checks utils::example("diveStats", package="diveMove", ask=FALSE, echo=FALSE, run.donttest=TRUE) ## Plot filters for ZOC ## Work on first phase (trip) subset, to save processing time, since ## there's no drift nor shifts between trips tdr <- divesTDR[1:15000] ## Try window widths (K), quantiles (P) and bound the search (db) K <- c(3, 360); P <- c(0.5, 0.02); db <- c(0, 5) d.filter <- diveMove:::.depthFilter(depth=getDepth(tdr), k=K, probs=P, depth.bounds=db, na.rm=TRUE) old.par <- par(no.readonly=TRUE) plotZOC(tdr, d.filter, ylim=c(0, 6)) par(old.par) ## Plot corrected and uncorrected depth, regardless of method ## Look at three different scales xlim1 <- c(getTime(divesTDR)[7100], getTime(divesTDR)[11700]) xlim2 <- c(getTime(divesTDR)[7100], getTime(divesTDR)[7400]) xlim3 <- c(getTime(divesTDR)[7100], getTime(divesTDR)[7200]) par(mar=c(3, 4, 0, 1) + 0.1, cex=1.1, las=1) layout(seq(3)) plotZOC(divesTDR, dcalib, xlim=xlim1, ylim=c(0, 6)) plotZOC(divesTDR, dcalib, xlim=xlim2, ylim=c(0, 70)) plotZOC(divesTDR, dcalib, xlim=xlim3, ylim=c(0, 70)) par(old.par)
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