PBSmapping: addBubbles – R documentation

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addBubbles

Add Bubbles to Maps

Description

Add bubbles proportional to some EventData's Z column (e.g., catch or effort) to an existing plot, where each unique EID describes a bubble.

Usage

addBubbles(events, type=c("perceptual","surface","volume"),
   z.max=NULL, min.size=0, max.size=0.8, symbol.zero="+",
   symbol.fg=rgb(0,0,0,0.60), symbol.bg=rgb(0,0,0,0.30),
   legend.pos="bottomleft", legend.breaks=NULL,
   show.actual=FALSE, legend.type=c("nested","horiz","vert"),
   legend.title="Abundance", legend.cex=.8, neg.col="RYB", ...)

Arguments

`events`	EventData to use (required).
`type`	`character` – scaling option for bubbles where `"perceptual"` emphasizes large z-values, `"volume"` emphasizes small z-values, and `"surface"` lies in between.
`z.max`	`numeric` – maximum value for z (default = `max(events$Z)`); determines the largest bubble; keeps the same legend for different maps.
`min.size`	`numeric` – minimum size (inches) for a bubble representing `min(events$Z)`. The legend may not actually include a bubble of this size because the calculated legend.breaks does not include the `min(events$Z)`.
`max.size`	`numeric` – maximum size (inches) for a bubble representing `z.max`. A legend bubble may exceed this size when `show.actual` is `FALSE` (on account of using `pretty(...)`).
`symbol.zero`	`character` – symbol to represent z-values equal to 0.
`symbol.fg`	`character` – bubble outline (border) colour.
`symbol.bg`	`character` – bubble interior (fill) colour. If a vector, the first element represents `min(legend.breaks)` and the last element represents `max(legend.breaks)`; colours are interpolated for values of `events$Z` between those boundaries. For values outside of those boundaries, interiors remain unfilled.
`legend.pos`	`character\|numeric` – position for the legend.
`legend.breaks`	`numeric` – break values for categorizing the z-values. The automatic method should work if zeroes are present; otherwise, you can specify your own break values for the legend. If a single number, specifies the number of breaks; if a vector, specifies the breaks.
`show.actual`	`logical` – if `FALSE`, legend values are obtained using `pretty(...)`, and consequently, the largest bubble may be larger than `z.max`; if `TRUE`, the largest bubble in the legend will correspond to `z.max`.
`legend.type`	`character` – display format for legend.
`legend.title`	`character` – title for legend.
`legend.cex`	`numeric` – size of legend text.
`neg.col`	`character` – bubble colour for any potential negative values.
`...`	`dots` – additional arguments for `points` function that plots zero-value symbols.

Details

Modified from (and for the legend, strongly inspired by) Tanimura et al. (2006) by Denis Chabot to work with PBSmapping.

Furthermore, Chabot's modifications make it possible to draw several maps with bubbles that all have the same scale (instead of each bubble plot having a scale that depends on the maximum z-value for that plot). This is done by making z.max equal to the largest z-value from all maps that will be plotted.

The user can also add a legend in one of four corners (see legend) or at a specific c(X,Y) position. If legend.pos is NULL, no legend is drawn.

Author(s)

Denis Chabot, Research Scientist
Maurice-Lamontagne Institute, Fisheries & Oceans Canada (DFO), Mont-Joli QC

Maintainer: Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Institute of Ocean Sciences (IOS), Sidney BC
Last modified Rd: 2021-01-11

References

Tanimura, S., Kuroiwa, C., and Mizota, T. (2006) Proportional symbol mapping in R. Journal of Statistical Software 15(5).

Examples

local(envir=.PBSmapEnv,expr={
  oldpar = par(no.readonly=TRUE)
  #--- common code for both examples below
  data(nepacLL,surveyData,envir=.PBSmapEnv)
  surveyData$Z <- surveyData$catch

  #--- plot a version that only varies the size
  plotMap(nepacLL, xlim=c(-131.8,-127.2), ylim=c(50.5,52.7),
    col="gainsboro",plt=c(.08,.99,.08,.99), cex.axis=1.2, cex.lab=1.5)
  addBubbles(surveyData, symbol.bg=rgb(.9,.5,0,.6),
    legend.type="nested", symbol.zero="+", col="grey")

  #--- plot a version that uses different symbol colours
  plotMap(nepacLL, xlim=c(-131.8,-127.2), ylim=c(50.5,52.7),
  col="gainsboro",plt=c(.08,.99,.08,.99), cex.axis=1.2, cex.lab=1.5)
  subset <- surveyData[surveyData$Z <= 1000, ]
  addBubbles(subset, symbol.bg=c("red", "yellow", "green"),
    legend.type="horiz", legend.breaks=pretty(range(subset$Z), n=11),
    symbol.zero=FALSE, col="grey", min.size=0.1, max.size=0.4)
  par(oldpar)
})

PBSmapping

Mapping Fisheries Data and Spatial Analysis Tools

v2.73.0

GPL (>= 2)

Authors

Jon T. Schnute [aut], Nicholas Boers [aut], Rowan Haigh [aut, cre], Alex Couture-Beil [ctb], Denis Chabot [ctb], Chris Grandin [ctb], Angus Johnson [ctb], Paul Wessel [ctb], Franklin Antonio [ctb], Nicholas J. Lewin-Koh [ctb], Roger Bivand [ctb]

Initial release

2021-01-12