plotSpatialTerm: Plot Spatial Term
In aquaMetrics/fcs2: Fisheries Classification Scheme 2 For SNIFFER

Description Usage Arguments Warning See Also

Plots summaries of the spatial term estimates from a fitted FCS2 model on a map of the spatial regions.

plotSpatialTerm(
  map,
  fit,
  type = "mean",
  abundance = TRUE,
  prevalence = TRUE,
  posterior = !is.null(fit$bugsFit),
  inla = !posterior,
  ...
)

`map`	a `SpatialPolygonsDataFrame` object containing polygons and a data frame corresponding to the regions used for a spatial term in the FCS2 model. This will usually be generated from an ESRI shapefile using `readShapePoly`.
`fit`	an `"fcs2Fit"` object containing INLA or BUGS model fits, as returned from `fcs2FitModel`. The model should include a `spatial` term in the abundance and/or prevalence component which is based upon the region given by `map`.
`type`	which summary to plot. Either `"mean"` for the mean or `"sd"` for the standard deviation, or both.
`abundance`	whether the spatial term (with these regions) is in the abundance regression component and should be plotted.
`prevalence`	whether the spatial term (with these regions) is in the prevalence regression component and should be plotted.
`posterior`	whether to plot the posterior estimates of the spatial term (if available).
`inla`	whether to plot the approximate INLA estimates of the spatial term.
`...`	further arguments passed to `spplot` and perhaps on further to `levelplot`. For example, the colour pallete can be changed using `col.regions` which by default is set using `cm.colors`.

This function requires the additional package sp to provide the SpatialPolygonsDataFrame map. This package is one of the requirements of the package maptools which may also be useful for creating map from an ESRI shapefile using the function readShapePoly.

fcs2SpatialSummary which this function uses to attach the spatial summaries to the map before plotting.

aquaMetrics/fcs2 documentation built on Aug. 21, 2021, 12:55 p.m.