This function divides a plot (or several plots) into subplots in the relative coordinates system, and returns the coordinates of subplot corners.
Usage
divide_plot(
corner_data,
rel_coord,
proj_coord = NULL,
longlat = NULL,
grid_size,
tree_data = NULL,
tree_coords = NULL,
corner_plot_ID = NULL,
tree_plot_ID = NULL,
grid_tol = 0.1,
centred_grid = FALSE,
sd_coord = NULL,
n = 100
)Arguments
- corner_data
A data frame, data frame extension, containing the plot corner coordinates. Typically, the output
$corner_coordof thecheck_plot_coord()function.- rel_coord
A character vector of length 2, specifying the column names (resp. x, y) of the corner relative coordinates.
- proj_coord
(optional, if longlat is not provided) A character vector of length 2, specifying the column names (resp. x, y) of the corner projected coordinates.
- longlat
(optional, if proj_coord is not provided) A character vector of length 2, specifying the column names of the corner geographic coordinates (long,lat).
- grid_size
A vector indicating the dimensions of grid cells (resp. X and Y dimensions). If only one value is given, grid cells will be considered as squares.
- tree_data
A data frame containing tree relative coordinates and other optional tree metrics (one row per tree).
- tree_coords
A character vector of length 2, specifying the column names of the relative coordinates of the trees.
- corner_plot_ID
If dealing with several plots: a vector indicating plot IDs for corners.
- tree_plot_ID
If dealing with several plots: a vector indicating tree plot IDs.
- grid_tol
A numeric between (0;1) corresponding to the percentage of the plot area allowed to be excluded from the plot division (when grid_size doesn't match exactly plot dimensions).
- centred_grid
When grid_size doesn't match exactly plot dimensions, a logical indicating if the subplot grid should be centered on the plot.
- sd_coord
used to propagate GPS measurements uncertainties to the subplot polygon areas and the ref_raster footprint in
subplot_summary(). See Details.- n
used to propagate GPS measurements uncertainties: the number of iterations to be used (as in
AGBmonteCarlo()). Cannot be smaller than 50 or larger than 1000.
Value
Returns a list containing:
$sub_corner_coord: a data-frame (or a list of data.table if sd_coord is provided) containing as many rows as there are corners corresponding to the subplots, and the following columns :
plot_ID: If dealing with multiple plots: the plot code, else, a column containing an empty charactersubplot_ID: The automatically generated subplot code, using the following rule : subplot_X_Yx_relandy_rel: the relative X-axis and Y-axis coordinates of subplots corners.x_projandy_proj: if proj_coord is provided, the projected X-axis and Y-axis coordinates of subplots corners
$tree_data: the tree_data argument with the subplot_ID of each tree in the last column
$UTM_code: if 'longlat' is provided, a data.frame containing the UTM code of the corner GPS coordinates for each plot
Details
If corner coordinates in the projected coordinate system are provided (proj_coord), projected coordinates of subplot corners are calculated by a bilinear interpolation in relation with relative coordinates of plot corners. Be aware that this bilinear interpolation only works if the plot in the relative coordinates system is rectangular (ie, has 4 right angles).
In order to propagate GPS measurement uncertainties, the sd_coord argument has to be provided and must contains the average standard deviation of the GPS measurements for each corner on the X and Y axes (typically, the output $sd_coord of the check_plot_coord() function). If corner_data contains only one plot, sd_coord must be a numeric. If dealing with several plot, sd_coord must be a data frame of two columns named 'plot_ID' and 'sd_coord' containing respectively the plot IDs and the previous metric (again, see the output $sd_coord of the check_plot_coord() function).
Examples
# One plot with repeated measurements of each corner
data("NouraguesPlot201")
check_plot201 <- check_plot_coord(
corner_data = NouraguesPlot201,
proj_coord = c("Xutm","Yutm"), rel_coord = c("Xfield","Yfield"),
trust_GPS_corners = TRUE, draw_plot = FALSE)
subplots_201 <- divide_plot(
corner_data = check_plot201$corner_coord,
rel_coord = c("x_rel","y_rel"), proj_coord = c("x_proj","y_proj"),
grid_size = 50)
subplots_201
#> $sub_corner_coord
#> plot_ID subplot_ID x_rel y_rel x_proj y_proj
#> 1 subplot_0_0 0 0 313005.7 451723.2
#> 2 subplot_0_0 50 0 312981.3 451676.7
#> 3 subplot_0_0 50 50 313028.4 451650.5
#> 4 subplot_0_0 0 50 313053.1 451694.5
#> 5 subplot_1_0 50 0 312981.3 451676.7
#> 6 subplot_1_0 100 0 312956.9 451630.2
#> 7 subplot_1_0 100 50 313003.6 451606.4
#> 8 subplot_1_0 50 50 313028.4 451650.5
#> 9 subplot_0_1 0 50 313053.1 451694.5
#> 10 subplot_0_1 50 50 313028.4 451650.5
#> 11 subplot_0_1 50 100 313075.4 451624.2
#> 12 subplot_0_1 0 100 313100.5 451665.9
#> 13 subplot_1_1 50 50 313028.4 451650.5
#> 14 subplot_1_1 100 50 313003.6 451606.4
#> 15 subplot_1_1 100 100 313050.2 451582.6
#> 16 subplot_1_1 50 100 313075.4 451624.2
#>
# Assigning trees to subplots
data("NouraguesTrees")
plot201_trees <- NouraguesTrees[NouraguesTrees$Plot == 201,]
subplots_201 <- suppressWarnings(
divide_plot(
corner_data = check_plot201$corner_coord,
rel_coord = c("x_rel","y_rel"), proj_coord = c("x_proj","y_proj"),
grid_size = 50,
tree_data = plot201_trees, tree_coords = c("Xfield","Yfield")))
head(subplots_201$sub_corner_coord)
#> plot_ID subplot_ID x_rel y_rel x_proj y_proj
#> 1 subplot_0_0 0 0 313005.7 451723.2
#> 2 subplot_0_0 50 0 312981.3 451676.7
#> 3 subplot_0_0 50 50 313028.4 451650.5
#> 4 subplot_0_0 0 50 313053.1 451694.5
#> 5 subplot_1_0 50 0 312981.3 451676.7
#> 6 subplot_1_0 100 0 312956.9 451630.2
head(subplots_201$tree_data)
#> Site Plot x_rel y_rel Family Genus Species
#> 1 Petit_Plateau 201 0.0 31.5 Burseraceae Protium surinamense
#> 2 Petit_Plateau 201 0.1 75.2 Anacardiaceae Tapirira guianensis
#> 3 Petit_Plateau 201 0.2 27.6 Lecythidaceae Indet.Lecythidaceae Indet.
#> 4 Petit_Plateau 201 -4.0 67.5 Euphorbiaceae Conceveiba guyanensis
#> 5 Petit_Plateau 201 0.3 39.9 Burseraceae Protium altissimum
#> 6 Petit_Plateau 201 -3.5 41.5 Euphorbiaceae Mabea speciosa
#> D plot_ID subplot_ID
#> 1 11.0 subplot_0_0
#> 2 74.4 subplot_0_1
#> 3 25.4 subplot_0_0
#> 4 10.0 <NA>
#> 5 18.9 subplot_0_0
#> 6 10.0 <NA>
# When grid dimensions don't fit perfectly plot dimensions
# \donttest{
divide_plot(
corner_data = check_plot201$corner_coord,
rel_coord = c("x_rel","y_rel"),
grid_size = c(41,41),
grid_tol = 0.4, centred_grid = TRUE)
#> Warning:
#> The x-dimension of the plot is not a multiple of the x-dimension of the grid size
#> Warning:
#> The y-dimension of the plot is not a multiple of the y-dimension of the grid size
#> $sub_corner_coord
#> plot_ID subplot_ID x_rel y_rel
#> 1 subplot_0_0 9 9
#> 2 subplot_0_0 50 9
#> 3 subplot_0_0 50 50
#> 4 subplot_0_0 9 50
#> 5 subplot_1_0 50 9
#> 6 subplot_1_0 91 9
#> 7 subplot_1_0 91 50
#> 8 subplot_1_0 50 50
#> 9 subplot_0_1 9 50
#> 10 subplot_0_1 50 50
#> 11 subplot_0_1 50 91
#> 12 subplot_0_1 9 91
#> 13 subplot_1_1 50 50
#> 14 subplot_1_1 91 50
#> 15 subplot_1_1 91 91
#> 16 subplot_1_1 50 91
#>
# }
# Dealing with multiple plots
data("NouraguesCoords")
nouragues_subplots <- suppressWarnings(
divide_plot(
corner_data = NouraguesCoords,
rel_coord = c("Xfield","Yfield"), proj_coord = c("Xutm","Yutm"),
corner_plot_ID = "Plot",
grid_size = 50,
tree_data = NouraguesTrees, tree_coords = c("Xfield","Yfield"),
tree_plot_ID = "Plot"))
head(nouragues_subplots$sub_corner_coord)
#> plot_ID subplot_ID x_rel y_rel x_proj y_proj
#> 1 201 201_0_0 0 0 313007.9 451717.2
#> 2 201 201_0_0 50 0 312984.0 451673.2
#> 3 201 201_0_0 50 50 313028.0 451649.4
#> 4 201 201_0_0 0 50 313051.8 451693.3
#> 5 201 201_1_0 50 0 312984.0 451673.2
#> 6 201 201_1_0 100 0 312960.2 451629.3
head(nouragues_subplots$tree_data)
#> Site plot_ID x_rel y_rel Family Genus
#> 1 Petit_Plateau 201 0.0 31.5 Burseraceae Protium
#> 2 Petit_Plateau 201 0.1 75.2 Anacardiaceae Tapirira
#> 3 Petit_Plateau 201 0.2 27.6 Lecythidaceae Indet.Lecythidaceae
#> 4 Petit_Plateau 201 -4.0 67.5 Euphorbiaceae Conceveiba
#> 5 Petit_Plateau 201 0.3 39.9 Burseraceae Protium
#> 6 Petit_Plateau 201 -3.5 41.5 Euphorbiaceae Mabea
#> Species D subplot_ID
#> 1 surinamense 11.0 201_0_0
#> 2 guianensis 74.4 201_0_1
#> 3 Indet. 25.4 201_0_0
#> 4 guyanensis 10.0 <NA>
#> 5 altissimum 18.9 201_0_0
#> 6 speciosa 10.0 <NA>