These functions plot objects created by IsoriX.
# S3 method for isoscape
plot(x, which = "mean", sources = list(draw = TRUE, cex =
0.5, pch = 2, lwd = 1, col = "red"), borders = list(borders = NA, lwd = 0.5,
col = "black"), mask = list(mask = NA, lwd = 0, col = "black", fill =
"black"), palette = list(step = NA, range = c(NA, NA), n.labels = 11, digits
= 2, fn = NA), 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 = NA, lwd = 0.5, col =
"black"), mask = list(mask = NA, lwd = 0, col = "black", fill = "black"),
mask2 = list(mask = NA, lwd = 0, col = "purple", fill = "purple"),
palette = list(step = NA, range = c(0, 1), n.labels = 11, digits = 2, fn =
NA), plot = TRUE, ...)
# S3 method for isofit
plot(x, cex.scale = 0.2, ...)
# S3 method for calibfit
plot(x, ...)
A string indicating the name of the raster to be plotted (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 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 the colours for the isoscape (see details)
A logical indicating whether the plot shall be plotted or just returned
Additional arguments (not in use)
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 calibration sampling area (see details)
A list containing information for the display of a mask (e.g. a distribution mask) (see details)
A numeric giving a scalling factor for the points in the plots
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 the 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 elements 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 CountryBorders 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).
The argument palette is used to define how to colour the isoscape and
assignment plot. Within this list, step defines the number of units on the
z-scale that shares a given colour; range can be used to constrain the
minimum and/or maximum values to be drawn (e.g. range = c(0, 1)) (this latter
argument is usefull if one wants to create several plots with the same
z-scale); n.labels allows for the user to approximatively define the
maximum number of numbers plotted on the z-scale; digits defines the number
of digits displayed for the numbers used as labels; and fn is used to
specify the function that is used to sample the colours. If fn is NULL
(default) the palette functions derived from isopalette1 and
isopalette2 are used when ploting isoscape and assignments,
respectivelly.
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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