plot.estMigConnectivity {MigConnectivity}

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