data-raw/clean_heights.R

In akleinhesselink/sedgwicktraits: Sedgwick Annual Plant Traits

rm(list = ls())
library(tidyverse)
library(stringr)

outfile <- 'data-raw/cleaned_trait_data/clean_heights.csv'
q_height <- 0.95

old_heights <-
  read_csv('data-raw/old-data/tapioca_trait_averages.csv')
new_heights <- read_csv('data-raw/raw_trait_data/plant_heights.csv')
molinari <- read_csv('data-raw/old-data/molinari.csv')
alias <- read_csv('data-raw/alias.csv')

old_heights <-
  old_heights %>%
  select(species, `max_height(cm)`) %>%
  rename('max_height' = `max_height(cm)` , 'alias' = species) %>%
  left_join(alias) %>%
  select(USDA_symbol, max_height) %>%
  distinct() %>%
  mutate(max_height_data_source = 'TAPIOCA')


new_heights %>%
  group_by(USDA_symbol) %>%
  summarise(n = n()) %>%
  arrange(n, USDA_symbol) %>%
  mutate(trait = 'max_height') %>%
  write_csv('data-raw/temp/check_heights.csv')

new_heights <-
  new_heights %>%
  group_by(USDA_symbol) %>%
  summarise(max_height = quantile(height, q_height), mean_height = mean(height)) %>%
  mutate(max_height_data_source = 'AK')


molinari <-
  molinari %>%
  select(USDA_symbol, max_height) %>%
  mutate(max_height_data_source = 'MOLINARI') %>%
  filter(complete.cases(.))

all_heights <- bind_rows(new_heights, molinari, old_heights)

all_heights <-
  all_heights %>%
  arrange(USDA_symbol, max_height_data_source) %>%
  group_by(USDA_symbol) %>%
  filter(row_number() == 1)

write_csv(all_heights, path = outfile)