#' Occurrence analysis
#'
#' Occurrence analysis for individual species.
#'
#' @param x output of [an1_gain_loss()].
#'
#' @return
#' A data frame with info about species
#'
#' @export
# res <- an2_occurrence_species(an1_gain_loss(sf_bsm_ahi))
an2_occurrence_species <- function(x) {
## Occurrence of selected species
occAHI <- apply(x[[1]][x[[5]]], 2, sum)
occBSM <- apply(x[[1]][x[[6]]], 2, sum)
# tmp data frame
tmp_occ <- data.frame(idOnt = getIdsNum(names(occBSM)),
occAHI = occAHI, occBSM = occBSM)
# gain / lost per species
df_gain_loss_sp <- ec_temporal_betadiversity(t(x[[1]][x[[5]]]),
t(x[[1]][x[[6]]]), methods = c("ra", "wi", "bc", "ja"),
site_names = getIdsNum(x[[5]]))
names(df_gain_loss_sp)[1:3] <- c("idOnt", "lost", "gain")
##
tmp_occ <- merge(tmp_occ, df_gain_loss_sp[, 1:4], by = "idOnt") %>%
merge(df_species_info[, c("idOnt", "order", "family",
"species", "commonName", "GameFish", "baitOntario", "FTP", "ULIT",
"log10BS_bsm", "thermalGuild_bsm", "meanDepth_bsm",
"Updated_Trophic_Level", "LongevityWild", "stocked")], by = "idOnt")
tmp_occ <- tmp_occ[order(tmp_occ$occAHI), ]
tmp_occ$id_graph <- rev(seq_nrow(tmp_occ))
tmp_occ
}
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