Merge pull request #57 from umr-amap/subplot_summary

Subplot summary

DESCRIPTION

@@ -48,6 +48,7 @@ Suggests:
 	rmarkdown,
 	prettydoc,
 	testthat,
+	vdiffr,
 	curl,
 	geodata,
 	httr2,

NAMESPACE

@@ -24,6 +24,7 @@ export(modelHD)
 export(numberCorner)
 export(predictHeight)
 export(retrieveH)
+export(subplot_summary)
 export(summaryByPlot)
 importFrom(data.table,"%between%")
 importFrom(data.table,"%chin%")
@@ -51,12 +52,14 @@ importFrom(ggplot2,element_text)
 importFrom(ggplot2,geom_point)
 importFrom(ggplot2,geom_polygon)
 importFrom(ggplot2,geom_segment)
+importFrom(ggplot2,geom_sf)
 importFrom(ggplot2,geom_smooth)
 importFrom(ggplot2,geom_text)
 importFrom(ggplot2,ggplot)
 importFrom(ggplot2,ggtitle)
 importFrom(ggplot2,labs)
 importFrom(ggplot2,scale_color_manual)
+importFrom(ggplot2,scale_fill_gradientn)
 importFrom(ggplot2,scale_shape_manual)
 importFrom(ggplot2,scale_x_continuous)
 importFrom(ggplot2,scale_y_continuous)
@@ -84,6 +87,7 @@ importFrom(sf,st_sfc)
 importFrom(stats,SSmicmen)
 importFrom(stats,as.formula)
 importFrom(stats,coef)
+importFrom(stats,dist)
 importFrom(stats,formula)
 importFrom(stats,lm)
 importFrom(stats,median)
@@ -102,5 +106,6 @@ importFrom(terra,vect)
 importFrom(utils,askYesNo)
 importFrom(utils,data)
 importFrom(utils,download.file)
+importFrom(utils,globalVariables)
 importFrom(utils,head)
 importFrom(utils,unzip)

NEWS

@@ -1,3 +1,23 @@
+* version 2.2
+- Modified bilinear interpolation to generalized bilinear interpolation that can deal with rectangular plot and non (0;0) origin corner plot
+- Added check_plot_coord function which will replace correctCoordGPS() :
+  - calculation of projected coordinates of plot corners depend on trust_GPS_corners argument : if TRUE, a bilinear interpolation is applied (after averaging plot corners and removing outliers) to retrieve tree projected coordinates, if FALSE a procrust analyses is applied as before
+  - rangeX and rangeY are no longer needed : they are calculated using relative coordinates dimensions of the plot corners
+  - a ggplot is returned as output instead of a plot of the plot
+  - calculation of the projected coordinates of the trees is done, using tree_df and tree_coords arguments
+- Added divide_plot function which will replace cutPlot()
+  - No corner numerotation is needed anymore, neither dimX and dimY (the dimensions of the plot)
+  - plot division is made on relative coordinates and then transformed in projected coordinates (if supplied) with a bilinear interpolation
+  - trees are attributed to each subplot using tree_df and tree_coords agruments
+  - Message warning if the grid dimensions don't match the plot dimensions
+  - Used of the argument grid_tol to control the plot area which is included in the grid
+  - The grid can be plot-centred using centred_grid argument
+- Added subplot_summary which will replace summaryByPlot
+  - the function can take any tree metric using the value argument
+  - any valid function can be applied as a summary
+  - a ggplot is returned as output instead of just plot the plot division
+- Added "Spatialized trees and forest stands metrics with BIOMASS" vignette which will replace the "Manage trees and plot coordinates with BIOMASS" vignette
+
 * version 2.1.14
 - Fix an issue about the inversion of subplot locations in cutPlot
 - Change the automatic corner numbering from counter-clockwise to clockise direction in cutPlot

R/BIOMASS-package.R

@@ -0,0 +1,9 @@
+#' @keywords internal
+"_PACKAGE"
+
+# The following block is used by usethis to automatically manage
+# roxygen namespace tags. Modify with care!
+## usethis namespace: start
+## usethis namespace: end
+
+NULL

R/bilinear_interpolation.R

@@ -66,7 +66,7 @@ bilinear_interpolation = function(coord, from_corner_coord, to_corner_coord, ord
   }
 
   # Verification of a rectangular plot for from_corner_coord
-  if(!all(abs(dist(rbind(from_corner_coord[,1:2],centroid))[c(4,7,9,10)] - mean(dist(rbind(from_corner_coord[,1:2],centroid))[c(4,7,9,10)]))<0.1)) {
+  if(!all(abs(stats::dist(rbind(from_corner_coord[,1:2],centroid))[c(4,7,9,10)] - mean(stats::dist(rbind(from_corner_coord[,1:2],centroid))[c(4,7,9,10)]))<0.1)) {
     stop("The plot in the relative coordinate system is not a rectangle (or a square). You may consider using trustGPScorners = F")
   }
 

R/checkPlotCoord.R

@@ -236,7 +236,7 @@ checkPlotCoord <- function(projCoord = NULL, longlat = NULL, relCoord, trustGPSc
 
     cornerCoord <- data.frame(cbind(cornerProjCoord[,1:2], cornerRelCoord[,1:2]))
     colnames(cornerCoord) <- c("x_proj","y_proj","x_rel","y_rel")
-    
+
     if(!is.null(cornerID)) cornerCoord$cornerID <- unique(cornerID)
   } # End trustGPScorners = "FALSE"
 

R/check_plot_coord.R

@@ -76,7 +76,6 @@
 #'   draw_plot = TRUE
 #' )
 #' }
-#'
 check_plot_coord <- function(proj_coord = NULL, longlat = NULL, rel_coord, trust_GPS_corners, corner_ID=NULL, max_dist = 15, rm_outliers = TRUE,  draw_plot = TRUE, tree_df = NULL, tree_coords=NULL) {
 
   # Checking arguments -------------------------------------------------
@@ -136,7 +135,6 @@ check_plot_coord <- function(proj_coord = NULL, longlat = NULL, rel_coord, trust
     stop(paste(length((unique(corner_ID))),"unique corners are detected in corner_ID instead of 4"))
   }
 
-
   # function -------------------------------------------------------------------
 
   # Transform the geographic coordinates into UTM coordinates

R/correctTaxo.R

@@ -45,7 +45,7 @@ if (getRversion() >= "2.15.1") {
 #' @author Ariane TANGUY, Arthur PERE, Maxime REJOU-MECHAIN, Guillaume CORNU
 #'
 #' @examples
-#' \donttest{
+#' \dontrun{
 #' correctTaxo(genus = "Astrocarium", species = "standleanum")
 #' correctTaxo(genus = "Astrocarium standleanum")
 #' }

R/divide_plot.R

@@ -6,8 +6,8 @@
 #' @details
 #'  If corner coordinates in the projected coordinate system are supplied (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).
 #' 
-#' @param rel_coord a data frame containing the relative (local) coordinates of plot corners, with X and Y corresponding to the first and second column respectively
-#' @param proj_coord a data frame containing the projected coordinates of plot corners, with X and Y corresponding to the first and second column respectively, and with the same row order than rel_coord
+#' @param rel_coord a matrix or data frame containing the relative (local) coordinates of plot corners, with X and Y corresponding to the first and second column respectively
+#' @param proj_coord a matrix or data frame containing the projected coordinates of plot corners, with X and Y corresponding to the first and second column respectively, and with the same row order than rel_coord
 #' @param 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.
 #' @param tree_df a data frame containing tree relative coordinates and other tree metrics (one row per tree).
 #' @param tree_coords a character vector of size 2 containing the column names of the relative coordinates of the trees.
@@ -29,6 +29,7 @@
 #' @export
 #' @author Arthur PERE, Arthur BAILLY
 #' @importFrom data.table data.table := setcolorder 
+#' @importFrom stats dist
 #' @examples
 #'
 #' # Rectangular plot and grid cells
@@ -37,12 +38,13 @@
 #' 
 #' # Squared plot and projected coordinates associated
 #' rel_coord <- data.frame(x_rel = c(0, 200, 0, 200), y_rel = c(0, 0, 200, 200))
-#' proj_coord <- data.frame(x_proj = c(110, 190, 60, 145), y_proj = c(110, 160, 196, 245))
+#' proj_coord <- data.frame(x_proj = c(210, 383, 110, 283), y_proj = c(210, 310, 383, 483))
 #' subplots <- divide_plot(rel_coord, proj_coord = proj_coord, grid_size = 100)
 #' 
 #' # Assigning trees to subplots
 #' tree_df <- data.frame(x_tree = runif(50,0,200), y_tree = runif(50,0,200))
-#' subplots <- divide_plot(rel_coord, proj_coord, 100, tree_df = tree_df, tree_coords = c("x_tree","y_tree"))
+#' subplots <- divide_plot(rel_coord, proj_coord, 100,
+#'                         tree_df = tree_df, tree_coords = c("x_tree","y_tree"))
 #' subplots$sub_corner_coord
 #' subplots$tree_df
 #' 
@@ -56,17 +58,19 @@
 #' tree_df <- rbind(tree_df, data.frame(x_tree = runif(50,0,200), y_tree = runif(50,0,200)))
 #' corner_plot_ID <- rep(c("plot1","plot2"), e=4)
 #' tree_plot_ID <- rep(c("plot1","plot2"), e=50)
-#' subplots <- divide_plot(rel_coord, proj_coord, 100, tree_df, c("x_tree","y_tree"), corner_plot_ID, tree_plot_ID)
+#' subplots <- divide_plot(rel_coord, proj_coord, 100,
+#'                         tree_df, c("x_tree","y_tree"),
+#'                         corner_plot_ID, tree_plot_ID)
 #'
 
 divide_plot <- function(rel_coord, proj_coord = NULL, grid_size, tree_df = NULL, tree_coords = NULL, corner_plot_ID = NULL, tree_plot_ID = NULL, grid_tol = 0.1, centred_grid = F) {
 
-  # Parameters verification ----------------------------------------------------
+  # Checking parameters --------------------------------------------------------
   if (is.matrix(rel_coord)) {
-    rel_coord <- data.frame(x_rel=rel_coord[,1],y_rel=rel_coord[,2])
+    rel_coord <- data.frame(rel_coord)
   }
   if (!is.null(proj_coord) && !is.data.frame(proj_coord)) {
-    proj_coord <- data.frame(x_proj=proj_coord[,1], y_proj=proj_coord[,2])
+    proj_coord <- data.frame(proj_coord)
   }
   if (!is.null(corner_plot_ID) && nrow(rel_coord) != length(corner_plot_ID)) {
     stop("The length of corner_plot_ID and the number of rows of rel_coord are different")
@@ -106,7 +110,7 @@ divide_plot <- function(rel_coord, proj_coord = NULL, grid_size, tree_df = NULL,
   }
 
 
-  # Formatting data  -----------------------------------------------------------
+  # Data processing ------------------------------------------------------------
 
   if(length(grid_size)!=2) grid_size = rep(grid_size,2)
 
@@ -117,7 +121,6 @@ divide_plot <- function(rel_coord, proj_coord = NULL, grid_size, tree_df = NULL,
   } else{
     rel_coord[,corner_plot_ID:=""]
   }
-  setcolorder(rel_coord , "corner_plot_ID" , after = 2) # if rel_coord has more than 2 col
 
   # Sorting rows in a counter-clockwise direction and check for non-rectangular plot
   sort_rows <- function(dat) {
@@ -187,6 +190,7 @@ divide_plot <- function(rel_coord, proj_coord = NULL, grid_size, tree_df = NULL,
   sub_corner_coord <- combine_coord[, divide_plot_fct(.SD, grid_size), by = corner_plot_ID, .SDcols = colnames(combine_coord)]
 
   # Assigning trees to subplots -------------------------------------------------------------
+
   if(!is.null(tree_df)) {
     tree_df <- as.data.table(tree_df)
 
@@ -205,13 +209,13 @@ divide_plot <- function(rel_coord, proj_coord = NULL, grid_size, tree_df = NULL,
     if (anyNA(tree_df[, subplot_id])) {
       warning("One or more trees could not be assigned to a subplot (not in a subplot area)")
     }
+
     if(is.null(tree_plot_ID)) {
       tree_df[ , c("subplot_id","plot_id") := list(paste0("subplot",subplot_id),NULL)]
     } 
   }
 
-
-  # returns --------------------------------------------------------------------
+  # Returns --------------------------------------------------------------------
 
   if(is.null(corner_plot_ID)) {
     sub_corner_coord[ , c("subplot_id","corner_plot_ID") := list(paste0("subplot",subplot_id),NULL)]

R/globals.R

@@ -0,0 +1,19 @@
+#' @importFrom utils globalVariables
+
+
+if(getRversion() >= "2.15.1") {
+  # modelHD function 
+  utils::globalVariables(c("x","y"))
+
+  # check_plot_coord function 
+  utils::globalVariables(c("x_proj","y_proj","outlier","Xmean","Ymean","row_number","whatpoint","Xend","Yend"))
+
+  # checkPlotCoord function 
+  utils::globalVariables("nRow")
+
+  # divide_plot function 
+  utils::globalVariables(c("x_rel","y_rel","subplot_id","plot_id"))
+
+  # subplot_summary function 
+  utils::globalVariables(c("subplot_id","plot_id",".data"))
+}