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Summarise and display tree information by subplot

Source: R/subplot_summary.R
subplot_summary.Rd

After applying the divide_plot() function, this function summarises with any defined function the desired tree metric by sub-plot and displays the plot representation.

Usage

subplot_summary(
  subplots,
  value = NULL,
  draw_plot = TRUE,
  per_ha = TRUE,
  fun = sum,
  ...
)

Arguments

subplots

output of the divide_plot() function

value

a character indicating the column in subplots$tree_data to be summarised (or character vector to summarise several metrics at once)

draw_plot

a logical indicating whether the plot design should be displayed

per_ha

a logical indicating whether the metric summary should be per hectare (or, if summarising several metrics at once: a logical vector corresponding to each metric (see examples))

fun

the function to be applied (or, if summarising several metrics at once: a list of functions named according to each metric (see examples))

...

optional arguments to fun

Value

a list containing the following elements :

  • tree_summary : a summary of the metric per subplot

  • polygon : an sf object : simple feature collection of the subplot's polygon

  • plot_design : a ggplot object (or a list of ggplot objects) that can easily be modified

Author

Arthur Bailly

Examples

# One plot with repeated measurements of each corner
data("NouraguesPlot201")
data("NouraguesTrees")
check_plot201 <- check_plot_coord(
  corner_data = NouraguesPlot201,
  proj_coord = c("Xutm","Yutm"), rel_coord = c("Xfield","Yfield"),
  trust_GPS_corners = TRUE, draw_plot = FALSE)
subplots_201 <- suppressWarnings(
  divide_plot(
    corner_data = check_plot201$corner_coord, 
    rel_coord = c("x_rel","y_rel"), proj_coord = c("x_proj","y_proj"),
    grid_size = 50,
    tree_data =  NouraguesTrees[NouraguesTrees$Plot == 201,],
    tree_coords = c("Xfield","Yfield")))
# Sum summary (by default) of diameter
subplots_201_sum <- subplot_summary(subplots_201 , value = "D", draw_plot = FALSE)
subplots_201_sum$tree_summary
#>              subplot_ID D_sum_per_ha
#> subplot_0_0 subplot_0_0     10656.19
#> subplot_0_1 subplot_0_1     10708.82
#> subplot_1_0 subplot_1_0     12103.82
#> subplot_1_1 subplot_1_1     12972.33
subplots_201_sum$polygon
#> Simple feature collection with 4 features and 2 fields
#> Geometry type: POLYGON
#> Dimension:     XY
#> Bounding box:  xmin: 312956.9 ymin: 451582.6 xmax: 313100.5 ymax: 451723.2
#> CRS:           NA
#>              subplot_ID D_sum_per_ha             sf_subplot_polygon
#> subplot_0_0 subplot_0_0     10656.19 POLYGON ((313005.7 451723.2...
#> subplot_0_1 subplot_0_1     10708.82 POLYGON ((313053.1 451694.5...
#> subplot_1_0 subplot_1_0     12103.82 POLYGON ((312981.3 451676.7...
#> subplot_1_1 subplot_1_1     12972.33 POLYGON ((313028.4 451650.5...
# \donttest{
  subplots_201_sum$plot_design

# }
# 9th quantile summary (for example) of diameter
subplots_201_quant <- subplot_summary(subplots_201 , value = "D", draw_plot = FALSE,
                                      fun = quantile, probs=0.9)
  

# Dealing with multiple plots
if (FALSE) { # \dontrun{
  data("NouraguesCoords")
  nouragues_subplots <- suppressWarnings(
  divide_plot(
     corner_data = NouraguesCoords,
    rel_coord = c("Xfield","Yfield"), proj_coord = c("Xutm","Yutm"),
    corner_plot_ID = "Plot",
    grid_size = 50,
    tree_data = NouraguesTrees, tree_coords =  c("Xfield","Yfield"),
    tree_plot_ID = "Plot"))
  # Sum summary (by default)
  nouragues_sum <- subplot_summary(nouragues_subplots , value = "D", draw_plot = FALSE)
  nouragues_sum$tree_summary
  nouragues_sum$plot_design
} # }

if (FALSE) { # \dontrun{
  data("NouraguesCoords")
  nouragues_subplots <- suppressWarnings(
  divide_plot(
     corner_data = NouraguesCoords,
    rel_coord = c("Xfield","Yfield"), proj_coord = c("Xutm","Yutm"),
    corner_plot_ID = "Plot",
    grid_size = 50,
    tree_data = NouraguesTrees, tree_coords =  c("Xfield","Yfield"),
    tree_plot_ID = "Plot"))
  # Sum summary (by default)
  nouragues_mult <- subplot_summary(nouragues_subplots , 
                                   value = c("D","D","x_rel"),
                                   fun = list(D=sum,D=mean,x_rel=mean),
                                   per_ha = c(T,F,F),
                                   draw_plot = FALSE)
  nouragues_mult$tree_summary
  nouragues_mult$plot_design$`201`[[1]]
  nouragues_mult$plot_design$`201`[[2]]
  nouragues_mult$plot_design$`201`[[3]]
} # }