Plot methods

Plot methods for different bSims objects.

Usage

# S3 method for bsims_landscape
plot(x,
  col_H, col_E, col_R,
  xlim = NULL, ylim = NULL, ...)

# S3 method for bsims_population
plot(x,
  pch_nest, col_nest, cex_nest, ...)

# S3 method for bsims_events
plot(x,
  event_type=c("vocal", "move", "both"), tlim = NULL,
  pch_nest, col_nest, cex_nest,
  pch_vocal, col_vocal, cex_vocal,
  lty_move, col_move, lwd_move, ...)

# S3 method for bsims_detections
plot(x,
  event_type=NULL, tlim = NULL,
  pch_nest, col_nest, cex_nest,
  pch_vocal, col_vocal, cex_vocal,
  lty_move, col_move, lwd_move,
  lty_det_vocal, col_det_vocal, lwd_det_vocal,
  lty_det_move, col_det_move, lwd_det_move,
  condition = "event1", ...)

# S3 method for bsims_transcript
plot(x,
  pch_nest, col_nest, cex_nest,
  pch_vocal, col_vocal, cex_vocal,
  lty_move, col_move, lwd_move,
  lty_det_vocal, col_det_vocal, lwd_det_vocal,
  lty_det_move, col_det_move, lwd_det_move,
  show_tint=TRUE, show_rint=TRUE,
  col_tint, col_rint, ...)

# S3 method for bsims_events
lines(x, tlim = NULL, ...)
# S3 method for bsims_detections
lines(x,
  event_type=NULL, tlim=NULL, condition="event1", ...)
# S3 method for bsims_transcript
lines(x,
  event_type=NULL, tlim=NULL, ...)

# S3 method for bsims_population
points(x, ...)
# S3 method for bsims_events
points(x,
  event_type=c("vocal", "move", "both"), tlim = NULL, ...)
# S3 method for bsims_detections
points(x,
  event_type=NULL, tlim=NULL, condition="event1", ...)

col2hex(col, alpha = FALSE)

# S3 method for bsims_events_table
plot(x,
  xlab, ylab, xlim, ylim, col_det_vocal, col_det_move, ...)
# S3 method for bsims_detections_table
plot(x,
  type=c("time", "distance"), xlab, ylab, xlim, ylim,
  col_det_vocal, col_det_move, ...)

Arguments

x: simulation object.
col: color values.
col_H, col_E, col_R: color values for the Habitat, Edge, and Road strata.
event_type: type of events to access. The value is inferred from the input object when NULL.
xlim, ylim, tlim: x, y, time intervals.
xlab, ylab: x and y axis labels.
pch_nest, col_nest, cex_nest: visual characteristics of nest locations.
pch_vocal, col_vocal, cex_vocal: visual characteristics of vocalization events.
lty_move, col_move, lwd_move: visual characteristics of movement events.
lty_det_vocal, col_det_vocal, lwd_det_vocal: visual characteristics of detection events related to vocalizations.
lty_det_move, col_det_move, lwd_det_move: visual characteristics of detection events related to movements.
alpha: alpha channel for colors.
show_tint, show_rint: whether time and distance intervals should be displayed.
col_tint, col_rint: colors for time and distance intervals.
condition: conditioning type to define availability for each individual, see bsims_detect.
type: what the x axis should be: time or distance.
...: other graphical arguments.

Details

The main plotting functions use a theme defined in the option getOption("bsims_theme"). Overriding these default settings allows customization.

Value

These plotting functions are called for their side effects and silently return the input object.

col2hex is modeled after col2rgb

and returns a character vector giving hexadecimal color codes with or without alpha channel values.

Author

Peter Solymos

Examples

b <- bsims_all(road=1, edge=2, move_rate=1, movement=0.2)$new()
o <- getOption("bsims_theme")
str(o)
#> List of 20
#>  $ col_H        : chr "darkolivegreen1"
#>  $ col_E        : chr "burlywood1"
#>  $ col_R        : chr "lightgrey"
#>  $ col_nest     : chr "darkgreen"
#>  $ pch_nest     : num 3
#>  $ cex_nest     : num 1
#>  $ col_vocal    : chr "blue"
#>  $ pch_vocal    : num 21
#>  $ cex_vocal    : num 0.5
#>  $ col_move     : chr "orange"
#>  $ lty_move     : num 1
#>  $ lwd_move     : num 1
#>  $ col_det_vocal: chr "black"
#>  $ lty_det_vocal: num 1
#>  $ lwd_det_vocal: num 1
#>  $ col_det_move : chr "purple"
#>  $ lty_det_move : num 1
#>  $ lwd_det_move : num 1
#>  $ col_tint     : chr "red"
#>  $ col_rint     : chr "red"
n <- o
n$col_H <- "gold"
n$col_E <- "magenta"
n$col_R <- "black"
op <- par(mfrow=c(1, 2))
plot(b)
options("bsims_theme" = n) # apply new theme
plot(b)

par(op)
options("bsims_theme" = o) # reset old theme

col2hex(c(blu = "royalblue", reddish = "tomato"), alpha = FALSE)
#>       blu   reddish 
#> "#4169E1" "#FF6347" 
col2hex(c(blu = "royalblue", reddish = "tomato"), alpha = TRUE)
#>         blu     reddish 
#> "#4169E1FF" "#FF6347FF"