test_functions/test_functions.R

In zsmith27/Benthos: Benthos

new_pct_taxon <- function(long.df, unique.id.col, taxon.rank, taxon, count.col) {
  sapply(unique(long.df[, unique.id.col]), function(x){
    sub.df <- long.df[long.df[, unique.id.col] %in% x, ]
    if (!taxon %in% sub.df[, taxon.rank]) {
      0
    } else {
      sum(sub.df[sub.df[, taxon.rank] %in% taxon, count.col]) /
        sum(sub.df[, count.col]) * 100
    }
  })
}
library(dplyr)
unique.id.col <- quo(UNIQUE_ID)
taxon.rank <- quo(GENUS)
taxon.x <- quo(EPEORUS)
count.col <- quo(REPORTING_VALUE)
new_pct_taxon2 <- function(long.df, unique.id.col, count.col, taxon.col, taxon) {
  # Prep.
  unique.id.col <- enquo(unique.id.col)
  taxon.col <- enquo(taxon.col)
  count.col <- enquo(count.col)
  #----------------------------------------------------------------------------
  final.vec <- long.df %>% 
    group_by(!!unique.id.col) %>% 
    summarise(TOTAL = sum(!!count.col),
           INDV = sum(UQ(count.col)[UQ(taxon.col) %in% taxon]),
           PCT = INDV / TOTAL * 100) %>% 
    pull(PCT)

  return(final.vec)
}

test2 <- long.df %>% 
  distinct(UNIQUE_ID) %>% 
  arrange(UNIQUE_ID) %>% 
  mutate(CHIRO = new_pct_taxon2(long.df, UNIQUE_ID, REPORTING_VALUE, FAMILY, "CHIRONOMIDAE"),
         EPHEM = new_pct_taxon2(long.df, UNIQUE_ID, REPORTING_VALUE, ORDER, c("EPHEMEROPTERA", "PLECOPTERA", "TRICHOPTERA")),
         EPEORUS = new_pct_taxon2(long.df, UNIQUE_ID, REPORTING_VALUE, GENUS, "EPEORUS"),
         HEXAPODA =new_pct_taxon2(long.df, UNIQUE_ID, REPORTING_VALUE, SUBPHYLUM, "HEXAPODA"))