inst/extdat/raw-data-classification.R

In ecodata1/whpt: Predict WHPT scores

library(tidyr)
library(dplyr)
library(purrr)
library(rlang)
library(utils)
library(readr)
ntaxa_report <- read_csv("inst/extdat/ntaxa-classification-water-body.csv")
aspt_report <- read_csv("inst/extdat/aspt-classification-water-body.csv")

class_report <- bind_rows(ntaxa_report, aspt_report)

year_report <- pivot_longer(class_report,names_to = c("year"),
                            cols = c(as.character(paste(2008:2018))))
year_report <- select(year_report, -ends_with("confidence"))
year_report$question <- "class"

confidence_report <- pivot_longer(class_report,
                                  names_to = "year",
                                  cols =
                                    as.character(paste0(
                                      2008:2018, "_confidence")))
confidence_report <- select(confidence_report,
                            -ends_with(as.character(paste0(2008:2018))))
confidence_report$question <- "confidence"
confidence_report$year <- gsub(pattern = "_confidence" ,
                               "",
                               confidence_report$year)
report <- bind_rows(year_report, confidence_report)

report$year <- as.numeric(report$year)

filtered_report <- map_df(split(report, report$Location), function(id) {

  max_year <- max(id$year[id$question == 'class' & !is.na(id$value)])
  max_rows <- id[id$year == max_year,]
  return(max_rows)
})

filtered_report <- pivot_wider(filtered_report,
                               names_from = question,
                               values_from = value)

filtered_report <- pivot_wider(filtered_report,
                               names_from = Parameter,
                               values_from = c(class, confidence))

filtered_report <- rename(filtered_report,
                          "ASPT class" = `class_1-3-2-3-3-1: Macroinvertebrates (ASPT)`,
                          "NTAXA class" = `class_1-3-2-3-3-2: Macroinvertebrates (NTAXA)`,
                          "ASPT confidence" = `confidence_1-3-2-3-3-1: Macroinvertebrates (ASPT)`,
                          "NTAXA confidence" = `confidence_1-3-2-3-3-2: Macroinvertebrates (NTAXA)`)

write.csv(filtered_report, file='inst/extdat/typical-class.csv')