plot.estMigConnectivity: Basic plot function for estMigConnectivity objects

In SMBC-NZP/MigConnectivity: Estimate Migratory Connectivity for Migratory Animals

Basic plot function for estMigConnectivity objects

Description

Basic plot function for estMigConnectivity objects

Usage

## S3 method for class '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,
  ...
)

Arguments

x	an estMigConnectivity object (output of estTransition, estStrength, estMC, or estMantel)
plot.which	which parameter (psi, MC, rM, or r) to graph. Defaults to psi for estMC objects, to rM (Mantel correlation) otherwise
point	points on graph can represent mean, median, or point estimates (not considering error). Defaults to mean, the standard estimate from resampling
range	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
xlab	label for the x-axis. Defaults to "Origin" for psi, otherwise ""
ylab	label for the y-axis. Defaults to the parameter being plotted
originNames	names of the origin sites (for plotting psi). If left NULL, the function attempts to get these from the estimate
targetNames	names of the target sites (for plotting psi or r). If left NULL, the function attempts to get these from the estimate
ageNames	names of the age classes (for plotting r with more than one age). If left NULL, the function uses 1:[number of ages]
col	colors to use for labeling transition probabilities for different target sites. If left NULL, defaults to 1:[number of target sites]
pch	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)
las	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
gap	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
sfrac	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
legend	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")
map	placeholder for eventually allowing users to plot psi estimates on a map
...	Additional parameters passed to plotCI

Value

No return value, called to generate plot.

See Also

estMC, estMantel

SMBC-NZP/MigConnectivity documentation built on March 26, 2024, 4:22 p.m.