make_plot: A general plotting function
In jBernardADFG/telprep: Quick and automatic processing of aerial telemetry data

A general plotting function

make_plot(
  sldf,
  detects,
  extent = NA,
  open_maps = T,
  type = "bing",
  darken = 1,
  col_by_fish = F,
  flight_num = NA,
  channel = NA,
  tag_id = NA,
  viterbi = F,
  return_background = F
)

`sldf`	Shapefile or SpatialLinesDataFrame representation of the river network.
`detects`	Output of `combine_data`, `rm_land_detects`, `get_best_locations`, `flag_dead_fish`, `flag_dead_fish`, or `hmm_survival`.
`extent`	A vector of length four specifying the plotting extent c(x_min, x_max, y_min, y_max)
`open_maps`	If open_maps=T, a background will be plotted using (`openmap`). If open_maps=F, a black background will be used.
`type`	The background to use (see `openmap`) for more information. Argument is ignored if open_maps=F.
`darken`	Increase to darken the background when open_maps=T. Defaults to 1.
`col_by_fish`	col_by_fish=T assigns each fish a unique color. This color will be preserved between mappings (i.e. between different flight periods).
`flight_num`	Numerical argument specifying the flight period to plot. Defaults to all.
`channel`	Vector with the channel numbers to plot. If channel=NA, all channels will be used.
`tag_id`	Vector with the tag ids to plot. If tag_id=NA, all tag ids will be used.
`viterbi`	Use viterbi=T to color by survival state using the viterbi path (detects needs to be the viterbi output from `hmm_survival`; see examples). Expired fish will be plotted in green.

# plotting all detections
par(mfrow=c(1,1))
make_plot(sldf, all_data)

# real detections only
make_plot(sldf, best_detects)

# darken background
make_plot(sldf, best_detects, darken=2.5)

# change style of background
make_plot(sldf, best_detects, type="esri-topo")

# remove background -- can be useful if OpenStreetMap is unavailable on your machine
make_plot(sldf, best_detects, open_maps=F)

# give each fish a unique color preserved through flights -- unfortunately there are only so many colors
par(mfrow=c(3,1))
make_plot(sldf, best_detects, col_by_fish=T, flight=1, darken=2.5)
make_plot(sldf, best_detects, col_by_fish=T, flight=2, darken=2.5)
make_plot(sldf, best_detects, col_by_fish=T, flight=3, darken=2.5)

# to plot the locations for a single fish
par(mfrow=c(1,1))
make_plot(sldf, best_detects, channel=10, tag_id=11, darken=2.5)

# to zoom in to a specified extent
extent <- c(x_min=466060, x_max=1174579, y_min=6835662, y_max=7499016)
temp<-make_plot(sldf, best_detects, extent, darken=2.5)

# plotting live and dead fish by flight period -- green fish have expired
par(mfrow=c(3,1))
viterbi <- hmm_survival(best_detects)$viterbi
make_plot(sldf, viterbi, type="bing", darken=2.5, viterbi=T, flight=1)
make_plot(sldf, viterbi, type="bing", darken=2.5, viterbi=T, flight=3)
make_plot(sldf, viterbi, type="bing", darken=2.5, viterbi=T, flight=5)