Scripts/Creating_messy_datasets.R

In sgraham9319/ForestPlotR: Tree growth as a function of its neighbors

# This script creates the messy_mapping and messy_tree datasets that are used
# for testing and demonstrating the data checking functions

#-------------------------------
# Create some messy mapping data
#-------------------------------

# Load old mapping data
map_old <- read.csv("Data/Mapping_2017.csv", stringsAsFactors = F)

# Repeat some rows
map_add <- map_old[sample(1:nrow(map_old), 10), ]

# Combine repeats and original
map_old <- bind_rows(map_old, map_add)

# Give some trees NAs for x, y, or x and y coordinates
map_old[sample(1:nrow(map_old), 5), c("x_coord", "y_coord")] <- NA
map_old[sample(1:nrow(map_old), 5), "x_coord"] <- NA
map_old[sample(1:nrow(map_old), 5), "y_coord"] <- NA

# Give some trees x or y coordinates beyond expected range
# No need to do this because they already exist!

# Give some trees an NA for stand_id
map_old[sample(1:nrow(map_old), 10), "stand_id"] <- NA

# Give some trees an NA for species
map_old[sample(1:nrow(map_old), 10), "species"] <- NA

# Remove unneeded columns
map_old <- map_old %>%
  select(-c(plot, tree_status))

# Write messy mapping to file
#write.csv(map_old, "Data/messy_mapping.csv", row.names = F)

# Rename dataset
messy_mapping <- map_old

# Add dataset to package
#usethis::use_data(messy_mapping)

#----------------------------
# Create some messy tree data
#----------------------------

# Load cleaned tree data
messy_tree <- tree

# Subset to two stands to reduce dataset size
messy_tree <- messy_tree %>%
  filter(stand_id %in% c("AB08", "PP17"))

# Duplicate some trees
set.seed(100)
dups <- messy_tree[sample(1:nrow(messy_tree), 10), ]

# Make changes so all have errors in stand, species, or both
dups$stand_id <- "AB08"
dups$species <- "PSME"

# Rejoin with other tree data
messy_tree <- bind_rows(messy_tree, dups)

# Create some trees without mapping data
set.seed(500)
no_map <- messy_tree[sample(1:nrow(messy_tree), 10), ]
no_map$tree_id <- paste("TEST000", 0:9, sep = "")

# Rejoin with other tree data
messy_tree <- bind_rows(messy_tree, no_map)

# Give some tree records an NA for dbh
messy_tree[sample(1:nrow(messy_tree), 10), "dbh"] <- NA

# Give some tree records an NA for stand_id
messy_tree[sample(1:nrow(messy_tree), 10), "stand_id"] <- NA

# Give some tree records an NA for species
messy_tree[sample(1:nrow(messy_tree), 10), "species"] <- NA

# Give some tree records an NA for year
messy_tree[sample(1:nrow(messy_tree), 10), "year"] <- NA

# Add dataset to package
#usethis::use_data(messy_tree)