plot.intrinsicAssign {MigConnectivity}

Basic plot function for the different isoAssign outputs

Description

Generates a basic plot of the isotope assignments. If map = 'population' generates a single map. If map = 'probability' or map = 'odds' generates a map for each individual is generated. User is asked for input before each individual is drawn.

Usage

## S3 method for class 'intrinsicAssign'
plot(x, map, ...)

Arguments

x

an isoAssign object

map

which isoAssign output to plot either 'probability', 'population' or 'odds'

...

additional arguments passed to plot function

Value

No return value, called to generate plot(s).

See Also

isoAssign

Examples

  extensions <- c("shp", "shx", "dbf", "sbn", "sbx")
  tmp <- tempdir()
  for (ext in extensions) {
  download.file(paste0(
              "https://raw.githubusercontent.com/SMBC-NZP/MigConnectivity",
                     "/master/data-raw/Spatial_Layers/OVENdist.",
                     ext),
              destfile = paste0(tmp, "/OVENdist.", ext), mode = "wb")
  }
  OVENdist <- sf::st_read(paste0(tmp, "/OVENdist.shp"))
  OVENdist <- OVENdist[OVENdist$ORIGIN==2,] # only breeding
  sf::st_crs(OVENdist) <- sf::st_crs(4326)

  download.file(paste0(
    "https://raw.githubusercontent.com/SMBC-NZP/MigConnectivity",
                     "/master/data-raw/deltaDvalues.csv"),
              destfile = paste0(tmp, "/deltaDvalues.csv"))
  OVENvals <- read.csv(paste0(tmp, "/deltaDvalues.csv"))

  b <- isoAssign(isovalues = OVENvals[,2],
                 isoSTD = 12,
                 intercept = -10,
                 slope = 0.8,
                 odds = NULL,
                 restrict2Likely = TRUE,
                 nSamples = 1000,
                 sppShapefile = OVENdist,
                 assignExtent = c(-179,-60,15,89),
                 element = "Hydrogen",
                 period = "GrowingSeason") # setting for demonstration only

  plot(b, map = "population")