Display annual growth rates using ggplot2

display_growth(
  growth,
  type = "ribbon",
  time_col = "time",
  color_col = "Plot",
  growth_variable = "mean",
  faceting = FALSE,
  title = "Annual growth in function of census intervals.",
  subtitle = NULL,
  save_graph = FALSE,
  device = "png",
  path_save = file.path("ForestGraphs", paste0("annual_mortality_recruitment_", type,
    ".png")),
  name = "annual_growth.png",
  create_folder = FALSE,
  overwrite = FALSE,
  ordered_percentiles = c("P5", "P95"),
  ...
)

Arguments

growth	A data.frame outputed from compute_growth
type	Character, the type of graph (recommended: "line" or "ribbon")
time_col	Character, name of the column corresponding to census time
color_col	Character, name of the colomn used to define lines' colors, defaults to "Plot".
growth_variable	Character
faceting	Character, name of the variable used for faceting -see after- but defaults to FALSE i.e. no faceting. NB: faceting refers to using a grouping variable to layout multiple plots, each corresponding to a category of the grouping variable. See details for a pratical explanation. The scales are free on the x axis: t correspond to several groups not necessarily having the same censusing temporal resolution; but are bound on the y-axis: the values are displayed on the same scale for comparison purposes.
title	Character,title of the graph.
subtitle	Character, subtitle of the graph. Defaults to `NULL`
save_graph	Logical, indicates whether the graph must be saved or not. Defaults to `FALSE`. If `TRUE`, please set the above described arguments in an appropriate way.
device	Relevant if `save_graph=TRUE`. Character, the graphical device to be used to save the graph.
path_save	Relevant if `save_graph=TRUE`. Character, a path indicating in which FOLDER the graph has to be saved.
name	Relevant if `save_graph=TRUE`. Character, the name of the folder containing the graph. It can be followd by the extension corresponding to the device - avoid .jpg for the jpeg device, use .jpeg instead. If the extension is missing, it is automatically added according to the selected device.
create_folder	Relevant if `save_graph=TRUE`. Logical, indicated whether the folders in the given path must be created in case they do not exist yet, or not.
overwrite	Relevant if `save_graph=TRUE`. Logical, indicating whether a file already existing under the same name must be overwritten, or kept. In the second case, the function aborts with an explicit error message.
ordered_percentiles	Numeric, if plotting a ribbon, please indicate the percentiles used when aggregating the data.
...	Additional arguments. Notably, verbose = F turns most warnings off

Value

A ggplot graph

Examples


data(example_size_corr)
growth <- suppressWarnings(compute_growth(example_size_corr,
                         size_col = "size_corr",
                         measure_type = "cir",
                         status_col = "CodeAlive",
                         id_col= "idTree",
                         time_col = "CensusYear",
                         what_output = "annual",
                         aggregate = TRUE,
                         by = c("Plot"),
                         stat = "mean",
                         percentiles = c(5,95)))
#> The growth rates were not computed when tree life status was 0 (dead) or NA (unseen or uncertain), thus the growth rate on these lines was set to NA
 display_growth(growth)
#> $mapping
#> Aesthetic mapping: 
#> * `ymin` -> `P95`
#> * `ymax` -> `P5`
#> * `fill` -> `Plot`
#> * `x`    -> `time`
#> 
#> $alpha
#> [1] 0.4
#>