rcarbon: plot.spatialTest – R documentation

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rcarbon

plot.spatialTest

Plot results of the local spatial permutation test of summed probability distributions.

Description

Displays local growth rates, p-values, and q-values retrieved from a spatialTest class object.

Usage

## S3 method for class 'spatialTest'
plot(
  x,
  index = 1,
  option,
  breakRange = NA,
  breakLength = 7,
  rd = 5,
  baseSize = 0.5,
  plim = 0.05,
  qlim = 0.05,
  legend = FALSE,
  legSize = 1,
  location = "bottomright",
  ...
)

Arguments

`x`	A `spatialTest` class object
`index`	A numerical value indicating which transition to display. Ignored when `option="rawlegend"` or `option="testlegend"`. Default is 1.
`option`	Indicates what to display. Either "`raw`" (the local growth rate) or "`test`" (the test results, i.e. q and p values).
`breakRange`	A vector of length 2 defining the minimum and maximum values of growth rate to be displayed in the legend. If set to NA its computed from data range (default).
`breakLength`	A numerical vector defining the number of breaks for growth rates to be displayed in the legend.
`rd`	Number of decimal places of the growth rate to be displayed in the Legend
`baseSize`	Numerical value giving the amount by which points should be magnified relative to the default settings in R. Default is 0.5
`plim`	Threshold value for the p-values. Default is 0.05.
`qlim`	Threshold value for the q-values. Default is 0.05.
`legend`	Logical values specifying whether the legend should be displayed or not. Default is FALSE.
`legSize`	Numerical value giving the amount by which points should be magnified relative to the default settings in R for the Legend. Default is 1.
`location`	A single keyword from the list "bottomright", "bottom", "bottomleft", "left", "topleft", "top", "topright", "right" and "center" to specify the location of the Legend. Default is "bottomright".
`...`	Graphical parameters to be passed to methods.

Details

The function displays a distribution map of local growth rates (when option="raw"), q- and p-values (when option="test"), and the associated legends (when option="rawlegend" or option="testlegend").