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

## 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))))
#> Error in st_polygon(list(rbind(c(0, 0), c(0, 1), c(1, 1), c(1, 0), c(0,     0)))): could not find function "st_polygon"
square2 <- st_polygon(list(rbind(c(2,2), c(2,3), c(3,3), c(3,2), c(2,2))))
#> Error in st_polygon(list(rbind(c(2, 2), c(2, 3), c(3, 3), c(3, 2), c(2,     2)))): could not find function "st_polygon"

# 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)}

    }

  }
}
#> Error in 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)))): could not find function "st_polygon"


# 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()))
)
#> Error in 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()))): could not find function "st_sf"

for (j in 1:25) {sub_plot$geometry[j] <- mget(ls(pattern = "smaller_square1"))[[j]]}
#> Error in mget(ls(pattern = "smaller_square1"))[[j]]: subscript out of bounds
for (j in 1:25) {sub_plot$geometry[j+25] <- mget(ls(pattern = "smaller_square2"))[[j]]}
#> Error in mget(ls(pattern = "smaller_square2"))[[j]]: subscript out of bounds

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)))
#> Error in ggplot(sub_plot): could not find function "ggplot"

# Check the order of subplots
test.order.subplot(df, sub_plot)
#> Error in group_by(., plot_name, quadrat): Must group by variables found in `.data`.
#> ✖ Column `quadrat` is not found.

## Test 2

library(CafriplotsR)

# Extract datas
x <- query_plots(locality_name = "Mbalmayo", extract_individuals = TRUE, show_all_coordinates = TRUE)
#> Error in get_password_secure("Enter database password: "): Cannot prompt for password in non-interactive session. Please provide password parameter.

coordinates_sf <- x$coordinates_sf
#> Error in x$coordinates_sf: $ operator is invalid for atomic vectors
ind.extract <- x$extract
#> Error in x$extract: $ operator is invalid for atomic vectors

sub_plot <- divid_plot(coordinates_sf,'plot_name')
#> Error in divid_plot(coordinates_sf, "plot_name"): unused argument ("plot_name")
test.order.subplot(ind.extract, sub_plot)
#> Error: object 'ind.extract' not found