These functions plot objects created by IsoriX.
# S3 method for isofit
plot(
x,
cex.scale=0.2,
...
)# S3 method for calibfit
plot(
x,
...
)
# S3 method for isoscape
plot(
x,
which="mean",
sources=list(draw=TRUE, cex=0.5, pch=2, lwd=1, col="red"),
borders=list(borders=NULL, lwd=0.5, col="black"),
mask= list(mask=NULL, lwd=0, col="black", fill="black"),
palette=terrain.colors(20),
plot=TRUE,
...
)
# S3 method for isorix
plot(
x,
who="group",
what="pv",
cutoff= list(draw=TRUE, level=0.05, col="#909090"),
sources=list(draw=TRUE, cex=0.5, pch=2, lwd=1, col="red"),
calib= list(draw=TRUE, cex=0.5, pch=4, lwd=1, col="blue"),
borders=list(borders=NULL, lwd=0.5, col="black"),
mask= list(mask=NULL, lwd=0, col="black", fill="black"),
mask2= list(mask=NULL, lwd=0, col="purple", fill="purple"),
palette=rev(terrain.colors(100)),
plot=TRUE,
...
)
a numeric giving a scalling factor for the points in the plots
A string indicating the name of the raster to be plotted (see details)
Either "group", or a vector of indices (e.g. 1:3) or names of the individuals (e.g. c("Mbe_1", "Mbe_3")) to be considered in assignment plots
A string indicating the name of the raster to be plotted (should remain "pv" if who="group", otherwise could be "stat", "stat.var", or "pv")
A list containing information for the display of the region outside the prediction interval (see details)
A list containing information for the display of the location of the sources (see details)
A list containing information for the display of the location of the calibration sampling area (see details)
A list containing information for the display of borders (e.g. country borders) (see details)
A list containing information for the display of a mask (e.g. an ocean mask) (see details)
A list containing information for the display of a mask (e.g. a distribution mask) (see details)
A vector of colours (character)
A logical indicating whether the plot shall be plotted or just returned
Additional arguments (not in use)
When called upon an object of class isofit, the plot function draws diagnostic information for the fits of the isoscape geostatistical model.
When called upon an object of class calibfit, the plot function draws the fitted calibration function.
When called upon an object of class isoscape, the plot function draws a fine-tuned plot of the isoscape. When used on a fitted isoscape, the user can choose between plotting the predictions (which = "mean"; default), the prediction variance (which = "mean.predVar"), the residual variance (which = "mean.residVar"), or the response variance (which = "mean.respVar") for the mean model; or the corresponding information for the residual dispersion variance model ("disp", "disp.predVar", "disp.residVar", or "disp.respVar"). When used on a simulated isoscape, the user can choose between plotting the mean isotopic value (which = "mean") or the dispersion (which = "disp").
When called upon an object of class isorix, the plot function draws a fine-tuned plot of the assignment. You can use the argument "who" to choose between plotting the assignment for the group or for some individuals (check the vignette "Workflow" for examples).
The arguments "cutoff", "sources", "calib", "borders", "mask" and "mask2" are used to fine-tune additional layers that can be added to the main plot to embellish it. These arguments must be lists that provide details on how to draw, respectively, the area outside the prediction interval (for assignment plots), the locations of sources (for both isoscape and assignment plots), the locations of the calibration sampling area (for assignment plots, the borders (for both types of plots) and a mask (again, for both)). For assignment maps, an extra mask can be used (mask2), as one may want to add a mask covering the area outside the biological range of the species. Within these lists, the element "lwd", "col", "cex", "pch" and "fill" influences their respective objects as in traditional R plotting functions (see par for details). The element "draw" should be a logical that indicates whether the layer must be created or not. The argument "borders" (within the list borders) expects an object of the class SpatialPolygons such as the object "countries" provided with this package. The argument "mask" (within the list maks) expects an object of the class SpatialPolygons such as the object oceanmask provided with this package (see examples).
isofit for the function fitting the isoscape
isoscape for the function building the isoscape
calibfit for the function fitting the calibration function
isofind for the function performing the assignment
IsoriX for the complete work-flow
# NOT RUN {
## See ?isoscape or ?isofind for examples
# }
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