fcs2SpatialSummary: Summary of Spatial Terms in FCS2 Model
In aquaMetrics/fcs2: Fisheries Classification Scheme 2 For SNIFFER

Description Usage Arguments Value Warning See Also

Summarises the spatial terms in a fitted FCS2 model and attaches the summary to a map of the spatial region used.

fcs2SpatialSummary(
  map,
  fit,
  posterior = !is.null(fit$bugsFit),
  inla = !posterior,
  abundance = TRUE,
  prevalence = TRUE
)

`map`	a `sp::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`.
`posterior`	whether to summarise the posterior estimates of each region (if available).
`inla`	whether to summarise the approximate INLA estimates of each region.
`abundance`	whether the spatial term (with these regions) is in the abundance regression component.
`prevalence`	whether the spatial term (with these regions) is in the prevalence regression component.

the sp::SpatialPolygonsDataFrame object map with additional columns in the data frame component map@data containing the requested summaries. Each summary is given as two columns, one for the mean of each variable named mean.* and another for the standard deviation named sd.*, where * is the name of the spatial variable.

This function requires the additional package maptools which may also be useful for creating map from an ESRI shapefile using the function maptools::readShapePoly.

plotSpatialTerm which uses this function to plot the spatial term summaries on a map.

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