In inbo/watervogelanalysis: Analysis of the Wintering Birds

Index based on monthly population totals, grouped by area

p_index <- function(x, se, reference, p) {
  100 * exp(qnorm(p = p, mean = x - reference, sd = se))
}
results %>%
  filter(ModelType == "yearly imputed index: Total ~ Year + Month") -> index
index %>%
  arrange(Parameter) %>%
  group_by(LocationGroupID, SpeciesGroupID) %>%
  slice(1) %>%
  ungroup() %>%
  select(LocationGroupID, SpeciesGroupID, Reference = Estimate) %>%
  inner_join(index, by = c("LocationGroupID", "SpeciesGroupID")) %>%
  transmute(
    LocationGroup,
    genus = str_replace(scientific_name, "([[:alpha:]]*) .*", "\\1"),
    species = str_replace(scientific_name, "[[:alpha:]]* (.*)", "\\1") %>%
      str_replace(" ", "\n"),
    year = as.integer(as.character(Parameter)),
    p05 = p_index(Estimate, SE, Reference, 0.05),
    p10 = p_index(Estimate, SE, Reference, 0.1),
    p30 = p_index(Estimate, SE, Reference, 0.3),
    p50 = p_index(Estimate, SE, Reference, 0.5),
    p70 = p_index(Estimate, SE, Reference, 0.7),
    p90 = p_index(Estimate, SE, Reference, 0.9),
    p95 = p_index(Estimate, SE, Reference, 0.95),
    Order
  ) %>%
  arrange(LocationGroup, Order) %>%
  group_by(LocationGroup, genus) %>%
  nest() %>%
  mutate(
    id = str_replace(LocationGroup, " ", "-") %>%
      interaction(genus, sep = "-") %>%
      as.character(),
    Previous = lag(LocationGroup),
    Title = ifelse(
      is.na(Previous) | Previous != LocationGroup,
      sprintf("## %s\n\n### %s", LocationGroup, genus),
      sprintf("### %s", genus)
    )
  ) -> monthly_population
monthly_population %>%
  pull(id) %>%
  sapply(
    function(id) {
      knit_expand("_area_genus_montly_index.Rmd", id = id)
    }
  ) %>%
  paste(collapse = "\n\n") -> rmd
knit(text = rmd, quiet = TRUE) %>%
  cat()