Check the order of subplots in a given data frame

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 'tag' 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 'tag' 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

Hugo Leblanc

Examples

if (FALSE) { # \dontrun{
## 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),
                 tag = 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(CafriplotsR)

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