##' Generate biomass estimates
##' (\url{https://github.com/SrivastavaLab/bwgbiomass/}) from allometry data
##' (\url{https://github.com/SrivastavaLab/allometrydata/})
##' @title Generate biomass estimates
##'
##' @param data_dir A local data directory in which to save the biomass data
##'
##' @param version Optional data version number
##'
##' @import fwdata
##' @importFrom dplyr %>%
##' @export
gen_biomass <- function(data_dir = "_data", version = NULL){
# I/O Variables
# Biomass filename generated from allometry data version and biomass data
# version, if provided.
allometry_version <- allometry_version_current()
if(is.null(version)){
biomass_filename <- paste(
data_dir, "/biomass_", format(Sys.time(),"%Y%m%d"), "_", allometry_version, ".rds",
sep = ""
)
} else {
biomass_filename <- paste(
data_dir, "/biomass_v.", version, "_", allometry_version, ".rds",
sep = ""
)
}
# The clean allometry matrix
allometry_matrix <- create_allometry_matrix()
# Taxonomy info to go with species IDs
species_ids <- get_species_ids()
# Equation bank for calculating biomass
equation_bank <- create_equation_bank(allometry_matrix)
# Category lookup table
category_lookup <- create_category_lookup()
# Clean the original biomass table
biomass_table <- create_biomass_table(species_ids)
# Get the table of closest relatives
# Successfully compared with original
closest_relatives <- get_closest_relatives(
biomass_data = biomass_table,
allometry_data = allometry_matrix,
species_data = species_ids
)
# Populate the biomass table
biomass_estimates <- populate_biomass_table(
allometry_data = allometry_matrix,
equation_bank = equation_bank,
biomass_data = biomass_table,
species_data = species_ids,
category_data = category_lookup,
closest_relatives = closest_relatives
)
# Save the new data in the local data_dir for uploading
saveRDS(biomass_estimates, file = biomass_filename)
return(biomass_estimates)
}
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