#' Summarise the dataset used to calculate the index.
#'
#' @param target_taxa
#'
#' @return A text output of summary information about the quantity and characteristics of species included in the index.
#' @export
#'
summarise_index_data <- function(target_taxa){
# get time series and taxonomic info to observations
obs <- dplyr::left_join(ratlas::get_timeseries(),
ratlas::get_gen(endpoint="taxa"),
by = c("id_taxa" = "id"))
obs$id <- as.character(obs$id)
# subset to observations with at least 6 observations in time
obs <- obs[unlist(lapply(obs$years, length)) >= 6,]
# Subset to selected taxa
stopifnot(target_taxa %in% c("Poissons", "Amphibiens", "Oiseaux", "Mammifères", "Reptiles", "Tous"))
if (target_taxa != "Tous") {
obs <- subset(obs, obs$species_gr %in% target_taxa)
}
# Make a named list of summary stats
d <- list(
"n_sp" = length(unique(obs$id_taxa)),
"sp" = unique(obs$scientific_name),
"n_pop" = length(unique(obs$id)),
"sp_status" = table(factor(obs$qc_status, levels = c("Susceptible", "Menacée", "Vulnérable"))),
"sp_vul" = obs$scientific_name[which(obs$qc_status == "Vulnérable")],
"sp_men" = obs$scientific_name[which(obs$qc_status == "Menacée")],
"sp_sus" = obs$scientific_name[which(obs$qc_status == "Susceptible")],
"summ_tslength" = unlist(lapply(obs$years, length)) %>% summary(na.rm = TRUE) %>% floor(),
"range_years" = range(unlist(obs$years))
)
summary_text <- paste(
"L'Indice Planète Vivante montrée ci-dessous représente la tendance moyenne des changements d'abondances de",
d$n_pop, 'populations de', d$n_sp, "espèces différentes, suivis pendant, en moyenne,", d$summ_tslength[4], "ans.",
"\n\nDe ces", d$n_sp, "espèces,",
unname(d$sp_status)[1], "espèces sont considérées Susceptibles,",
unname(d$sp_status)[2], "espèces sont considérées Menacées, et",
unname(d$sp_status)[3], "espèces sont considérées Vulnérable."
)
return(summary_text)
}
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