Basic plot function for estMigConnectivity objects
# S3 method for estMigConnectivity
plot(
x,
plot.which = ifelse(inherits(x, "estPsi"), "psi", ifelse(inherits(x, "estMC"), "MC",
ifelse(inherits(x, "estGamma"), "gamma", "rM"))),
point = c("mean", "median", "point"),
range = c("simpleCI", "bcCI", "se"),
xlab = NULL,
ylab = plot.which,
originNames = NULL,
targetNames = NULL,
ageNames = NULL,
col = NULL,
pch = NULL,
las = 1,
gap = 0,
sfrac = ifelse(range == "se", 0.01, 0),
legend = FALSE,
map = FALSE,
...
)No return value, called to generate plot.
an estMigConnectivity object (output of estTransition, estStrength, estMC, or estMantel)
which parameter (psi, MC, rM, or r) to graph. Defaults to psi for estMC objects, to rM (Mantel correlation) otherwise
points on graph can represent mean, median, or point estimates (not considering error). Defaults to mean, the standard estimate from resampling
lines / error bars drawn around points can represent simple quantile-based confidence intervals (simpleCI), bias-corrected quantile- based confidence intervals (bcCI), or +- standard error (se). Defaults to simpleCI
label for the x-axis. Defaults to "Origin" for psi, otherwise ""
label for the y-axis. Defaults to the parameter being plotted
names of the origin sites (for plotting psi). If left NULL, the function attempts to get these from the estimate
names of the target sites (for plotting psi or r). If left NULL, the function attempts to get these from the estimate
names of the age classes (for plotting r with more than one age). If left NULL, the function uses 1:[number of ages]
colors to use for labeling transition probabilities for different target sites. If left NULL, defaults to 1:[number of target sites]
symbols to use for labeling transition probabilities for different target sites. If left NULL, defaults to 21:25, then 0:([number of target sites]-5)
style of axis labels (0-3). We set the default at 1 (always horizontal) here, but if you prefer your labels parallel to the axis, set at 0
space left between the center of the error bar and the lines marking the error bar in units of the height (width) of the letter "O". Defaults to 0
width of "crossbar" at the end of error bar as a fraction of the x plotting region. Defaults to 0, unless range is set to "se", in which case it defaults to 0.01
leave as FALSE to not print a legend. Otherwise the position of the legend (for psi or r (multi-age) only; one of "bottomright", "bottom", "bottomleft", "left", "topleft", "top", "topright", "right", or "center")
placeholder for eventually allowing users to plot psi estimates on a map
Additional parameters passed to plotCI
estMC, estMantel