plot_seasonality_beast: Plot seasonal overlays
In mdkarcher/phylodyn: Statistical Tools for Phylodynamics

Plot seasonal overlays

plot_seasonality_beast(BEAST_out, zero_date, start = 0, years = NULL,
  period = 1, ylim = NULL, nbreaks = 40, lty = 1, lwd = 2,
  col_years = "gray", col_median = "black", main = "",
  axlabs = NULL, xlab = "Time", xmarline = 1,
  ylab = "Effective Population Size", log_y = TRUE,
  samp_times = NULL, n_sampled = NULL, heatmaps = TRUE,
  heatmap_labels = TRUE, heatmap_labels_side = "right",
  heatmap_width = 7, legend = NULL, yscale = 1, ...)

`BEAST_out`	list containing 'midpts', 'medianEffPop', 'q975EffPop', and 'q025EffPop'.
`zero_date`	numeric date (in decimal years) representing 't=0' in 'BEAST_out'
`start`	numeric value between 0 and 'period' controlling the right side of the plot.
`years`	numeric how many years or periods to overlay.
`period`	numeric representing how long one year or other seasonal period is in the units of 'BEAST_out'.
`ylim`	numeric y-axis interval.
`nbreaks`	integer number of bins in the sampling time histogram heatmap.
`lty`	numeric line type.
`lwd`	numeric line width.
`col_years`	color of individual trajectory
`col_median`	color of the median estimate.
`main`	character main figure title.
`axlabs`	character vector x-axis labels.
`xlab`	character x-axis label.
`xmarline`	numeric if not using default x-axis labels, how far to put the labels from the axis.
`ylab`	character y-axis label.
`log_y`	logical whether to log-scale the y-axis.
`samp_times`	numeric vector of sampling times.
`n_sampled`	integer vector of number of samples taken at each element of samp_times.
`heatmaps`	boolean whether to display sampling and coalescent heatmaps.
`heatmap_labels`	boolean whether to display labels on heatmaps.
`heatmap_labels_side`	string which side of plot to display heatmaps.
`heatmap_width`	numeric vertical width of sampling time histogram heatmap.
`legend`	character legend text. The defauly, NULL, disables.
`yscale`	numeric scaling applied to all effective population calculations.
`...`	additional arguments to be passed onto plot().