Visualize results from a survey index model fitted with get_surveyidx().

Usage

plot_surveyidx(
  x,
  dat,
  alt.idx = NULL,
  myids,
  cols = 1:length(x$pModels),
  select = c("index", "map", "residuals", "fitVsRes"),
  par = list(mfrow = c(3, 3)),
  colors = rev(grDevices::heat.colors(6)),
  map.cex = 1,
  plotByAge = TRUE,
  legend = TRUE,
  predD = NULL,
  year = NULL,
  main = NULL,
  legend.signif = 3,
  legend.pos = "topright",
  restoreOldPar = FALSE,
  mapBubbles = FALSE,
  cutp = NULL,
  ...
)

Arguments

x: Survey index as produced by getsdmgamindex()
dat: DATRASraw object
alt.idx: optional matrix with alternative index
myids: vector of haul ids that constitute the grid
cols: which age columns to consider?
select: character vector of chosen plots. Either one of "index","map","absolutemap","CVmap","residuals","fitVsRes",""resVsYear","resVsShip","spatialResiduals", or a number. Numbers refer to smooths in the order they appear in the formula.
par: 'par' settings for plotting (a named list).
colors: colors for spatial effect.
map.cex: size of grid points on maps
plotByAge: boolean (default=TRUE). If true, par(par) is called for each age group.
legend: boolean (default=TRUE). add legends to plot?
predD: DATRASraw object with grid (optional). Overrides 'myids' if supplied.
year: numeric scalar or vector (default=NULL). If 'select' equals 'map' a specific year can be chosen (only meaningful for time-varying spatial effects). If select equals 'absolutemap' or 'CVmap' then year must be a vector.
main: optional main title (overrides default title)
legend.signif: Number of significant digits in map legends
legend.pos: Position of legend (e.g. "bottomleft") see ?legend
restoreOldPar: restore old par() on exit? Default=FALSE
mapBubbles: boolean (default=FALSE) add observation bubbles?
cutp: optional vector of break points for the color scale on maps
...: Additional parameters for plot()

Value

series of production plots

Examples

# plot_surveyidx()