Plotting functions for IsoriX
## S3 method for class 'ISOSCAPE' plot( x, which = "mean", y_title = list(which = TRUE, title = bquote(delta^2 * H)), 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, sphere = list(build = FALSE, keep_image = FALSE), ... ) ## S3 method for class 'ISOFIND' plot( x, who = "group", cutoff = list(draw = TRUE, level = 0.05, col = "#909090"), sources = list(draw = TRUE, cex = 0.5, pch = 2, lwd = 1, col = "red"), calibs = list(draw = TRUE, cex = 0.5, pch = 4, lwd = 1, col = "blue"), assigns = list(draw = TRUE, cex = 0.5, pch = 5, lwd = 1, col = "white"), 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, sphere = list(build = FALSE, keep_image = FALSE), ... ) ## S3 method for class 'ISOFIT' plot(x, cex_scale = 0.2, ...) ## S3 method for class 'CALIBFIT' plot( x, pch = 1, col = "black", xlab = "Predicted isotopic value in the environment", ylab = "Isotopic value in the calibration sample", ylim = NULL, CI = list(show = TRUE, col = "blue"), ... ) ## S3 method for class 'CALIBFIT' points(x, pch = 2, col = "red", CI = list(show = TRUE, col = "red"), ...) ## S3 method for class 'RasterLayer' plot(x, ...)
x |
The return object of an |
which |
A string indicating the name of the raster to be plotted (see details) |
y_title |
A list containing information for the display of the title (see details) |
sources |
A list containing information for the display of the location of the sources (see details) |
borders |
A list containing information for the display of borders (e.g. country borders) (see details) |
mask |
A list containing information for the display of a mask (e.g. an ocean mask) (see details) |
palette |
A list containing information for the display of the colours for the isoscape (see details) |
plot |
A logical indicating whether the plot shall be plotted or just returned |
sphere |
A list containing information whether the raster should be returned as a rotating sphere and if the image created during the process should be saved in your current working directory. The default settings are FALSE. |
... |
Additional arguments (only in use in plot.CALIBFIT and plot.RasterLayer) |
who |
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 |
cutoff |
A list containing information for the display of the region outside the prediction interval (see details) |
calibs |
A list containing information for the display of the location of the calibration sampling location (see details) |
assigns |
A list containing information for the display of the location of the assingment sampling location (see details) |
mask2 |
A list containing information for the display of a mask (e.g. a distribution mask) (see details) |
cex_scale |
A numeric giving a scaling factor for the points in the plots |
pch |
The argument pch as in |
col |
The argument col as in |
xlab |
A string the x-axis label in plot.CALIBFIT |
ylab |
A string the y-axis label in plot.CALIBFIT |
ylim |
A range defining the extreme coordinates for the the y-axis in plot.CALIBFIT |
CI |
A list containing two elements: |
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 called upon an object of class RasterLayer, the plot function displays the raster (just for checking things fast and dirty).
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 produced with the function
isosim, the user can choose between plotting the mean isotopic
value (which = "mean") or the residual dispersion (which =
"disp").
When called upon an object of class ISOFIND, 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 online tutorial for examples).
The argument y_title can be used to customise the title of isoscapes. The
element which is a logical indicating if the name of the layer should
be displayed or not. The element title is a string or a call used to
define the rest of the title. By default it draws the delta value for
hydrogen. Check the syntax of this default before trying to modify it.
The arguments cutoff, sources, calibs, assigns, 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
samples (for assignment plots), the locations of the assignment
samples (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 useful 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 plotting
isoscape and assignments, respectivelly. If fn is NA the function used
is the palette viridis.
When called upon an object of class RasterLayer, the plot function is a
simple shortcut to levelplot.
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
## See ?isoscape or ?isofind for examples
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