test.order.subplot: Check the order of subplots in a given data frame

In gdauby/bdd_plots_central_africa: Exploring and updating the Central Africa plot database

Check the order of subplots in a given data frame

Description

This function checks the order of subplots in a given data frame against a predefined order. It also checks if there are any missing or too much subplots. If there is any issue, it plots the mean of the indicator variable 'ind_num_sous_plot' for each subplot and displays it in a spatial plot to see where the errors from thanks to an indicator 'check.

Usage

test.order.subplot(ind.extract, sub_plot)

Arguments

ind.extract	A data frame containing the indicator variable 'ind_num_sous_plot' and the names of the plots and subplots in the columns 'plot_name' and 'sous_plot_name' respectively.
sub_plot	A sf object containing the names of the plots and subplots in the columns 'plot_name' and 'sous_plot_name' respectively.

Value

The function returns a message indicating if the order of subplots in the data frame is correct or if there is a problem with the order. If there is any issue, it plots the errors.

Author(s)

Hugo Leblanc

Examples

## Test 1
# Define the data for 2 plots
df <- data.frame(plot_name = c(rep("plot1", each = 250),rep("plot2", each = 250)),
                 sous_plot_name = rep(c("0_0","20_0","40_0","60_0","80_0",
                                        "80_20","60_20", "40_20","20_20","0_20",
                                        "0_40","20_40","40_40","60_40","80_40",
                                        "80_60","60_60","40_60","20_60","0_60",
                                        "0_80","20_80","40_80","60_80","80_80"),
                                      each = 10),
                 ind_num_sous_plot = c(1:250, 1:50, 76:100, 51:75, 101:250))

# Define the 2 plots geometry
square1 <- st_polygon(list(rbind(c(0,0), c(0,1), c(1,1), c(1,0), c(0,0))))
square2 <- st_polygon(list(rbind(c(2,2), c(2,3), c(3,3), c(3,2), c(2,2))))

# Define the size of the subplot sides
n <- 5
side_length <- 1/n

# Define the subplot geometries
for (j in c(0,2)){

  for (x in 1:n){

    for (i in 1:n){

      tmp  <-   st_polygon(
        list(
          rbind(
            c(j+(i-1)*side_length,j+(x-1)*side_length),
            c(j+(i-1)*side_length,j+x*side_length),
            c(j+i*side_length,j+x*side_length),
            c(j+i*side_length,j+(x-1)*side_length),
            c(j+(i-1)*side_length,j+(x-1)*side_length)
          )
        )
      )

      if(j == 0){assign (paste('smaller_square1',x,i, sep = "_"), tmp)}
      else{assign (paste('smaller_square2',x,i, sep = "_"), tmp)}

    }

  }
}


# Define the predefinite order of subplots
order <- c("0_0",
           "20_0",
           "40_0",
           "60_0",
           "80_0",
           "0_20",
           "20_20",
           "40_20",
           "60_20",
           "80_20",
           "0_40",
           "20_40",
           "40_40",
           "60_40",
           "80_40",
           "0_60",
           "20_60",
           "40_60",
           "60_60",
           "80_60",
           "0_80",
           "20_80",
           "40_80",
           "60_80",
           "80_80")

# Assign names to geometries
sub_plot <- st_sf(
  plot_name = rep(c("plot1","plot2"),each = 25),
  sous_plot_name = rep(order,2),
  geometry = st_sfc(lapply(1:25,function(x) st_geometrycollection()))
)

for (j in 1:25) {sub_plot$geometry[j] <- mget(ls(pattern = "smaller_square1"))[[j]]}
for (j in 1:25) {sub_plot$geometry[j+25] <- mget(ls(pattern = "smaller_square2"))[[j]]}

rm(list=ls(pattern = "smaller_square1"))
rm(list=ls(pattern = "smaller_square2"))

# Plot
ggplot(sub_plot)  +
  #geom_sf() +
  scale_fill_continuous(type = 'viridis')+
  geom_sf_label(aes(label = as.character(sous_plot_name)))  +
  ggtitle(paste(unique(tmp$plot_name)))

# Check the order of subplots
test.order.subplot(df, sub_plot)

## Test 2

library(plotsdatabase)

# Extract datas
x <- query_plots(locality_name = "Mbalmayo", extract_individuals = TRUE, show_all_coordinates = TRUE)

coordinates_sf <- x$coordinates_sf
ind.extract <- x$extract

sub_plot <- divid_plot(coordinates_sf,'plot_name')
test.order.subplot(ind.extract, sub_plot)

gdauby/bdd_plots_central_africa documentation built on April 12, 2024, 1:15 a.m.