plot_hisafe_cycle_ts: Plot daily timeseries of major cycles
In kevinwolz/hisafer: An R Toolbox for the Hi-sAFe Biophysical Agroforestry Model

Description Usage Arguments Value See Also Examples

Plots a daily timeseries of tree carbon pools, water uptake, nitrogen uptake, light capture, or tree carbon incrememnt.

plot_hisafe_cycle_ts(
  hop,
  cycle,
  years,
  simu.names = "all",
  tree.ids = "all",
  doy.lim = c(1, 366),
  color.palette = NULL,
  crop.names = c("Main crop", "Inter crop"),
  pheno.lines = TRUE,
  branch.pruning.lines = TRUE,
  root.pruning.lines = TRUE,
  trim = TRUE,
  plot = TRUE
)

`hop`	An object of class hop or face.
`cycle`	One of "carbon", "nitrogen", "water", "light", "yield" "carbon-increment", or "carbon-allocation".
`years`	A numeric vector of the calendar years to include. If more than one year is provided, years are used as facets, and only a single value can be supplied to `simu.names`. Use "all" to include all available values.
`simu.names`	A character vector of the SimulationNames within `hop` to include. Use "all" to include all available values. If more than one value is supplied to `years`, then a single value must be suppied to `simu.names`.
`tree.ids`	A numeric vector indicating a subset of tree ids to plot. Use "all" to include all available values. This only applies when `cycle` is "carbon". Must only include a single tree id for "carbon-allocation".
`doy.lim`	A numeric vector of length two providing the `c(minimum, maximum)` of julian days to plot.
`color.palette`	A character stirng of hex values or R standard color names defining the color palette to use in plots with multiple simulations. If `NULL`, the default, then the default color palette is a color-blind-friendly color palette.
`crop.names`	A character vector of length 2 containing the names to use in the legend for the mainCrop and interCrop of Hi-sAFe, in that order.
`pheno.lines`	Logical indicating whether or not vertical lines should be plotted on dates of tree phenoloigical stage changes
`branch.pruning.lines`	Logical indicating whether or not vertical lines should be plotted on dates of branch pruning
`root.pruning.lines`	Logical indicating whether or not vertical lines should be plotted on dates of root pruning
`trim`	Logical indicating whether or not to trim white space before and after the tree growth season when `cycle` is "carbon-increment"
`plot`	If `TRUE`, the default, a ggplot object is returned. If `FALSE`, the data that would create the plot is returned.

If plot = TRUE, returns a ggplot object. If plot = FALSE, returns the data that would create the plot. If hop contains more than one simulation, the plot will be faceted by SimulationName.

Other hisafe analysis functions: LER_summary(), LER(), analyze_hisafe(), cycle_summary(), hisafe_budget(), plot_hisafe_cycle_bar(), stics_budget_comp(), write_hop()

## Not run: 
# To plot the simulated light capture in the year 2000:
light.capture.plot <- plot_hisafe_cycle_ts(myhop, "light", 2000)

# Once you have the plot object, you can display it and save it:
water.plot
ggsave_fitmax("light_capture.png", light.capture.plot)

## End(Not run)