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since spocc::occ() converts the polygon to BBOX
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@oggioniale
oggioniale committed Nov 15, 2024
1 parent 7768f5e commit 33f22b1
Showing 1 changed file with 41 additions and 36 deletions.
77 changes: 41 additions & 36 deletions R/get_site_speciesOccurrences.R
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Original file line number Diff line number Diff line change
Expand Up @@ -91,13 +91,7 @@ get_site_speciesOccurrences <- function(
print("No boundary for requested DEIMS site.")
return(NULL)
} else {
bbox_wkt <- sf::st_as_text(
sf::st_as_sfc(
sf::st_bbox(
boundary
)
)
)
site_geom <- boundary$geometry
}

# download occurrence by SPOCC by provide data sources ----
Expand All @@ -106,7 +100,7 @@ get_site_speciesOccurrences <- function(
if (any(c("gbif", "inat") %in% list_DS)) {
site_occ_spocc <- spocc::occ(
from = list_DS,
geometry = bbox_wkt,
geometry = site_geom,
limit = limit,
has_coords = TRUE
)
Expand All @@ -126,40 +120,50 @@ get_site_speciesOccurrences <- function(
if (!is.null(site_occ_spocc) && is.null(site_occ_spocc$inat$meta$returned)) {
list_DS_exclude <- c(list_DS_exclude, "inat")
}
if (is.null(site_occ_spocc_obis) && is.null(site_occ_spocc_obis$results)) {
if (is.null(site_occ_spocc_obis) &&
is.null(site_occ_spocc_obis$results)) {
list_DS_exclude <- c(list_DS_exclude, "obis")
}
if (length(site_occ_spocc_obis$results) == 0) {
list_DS_exclude <- c(list_DS_exclude, "obis")
}
list_DS <- list_DS[!(list_DS %in% list_DS_exclude)]

# harmonization of date and time GBIF
if (!is.null(site_occ_spocc$gbif$data[[1]]$lastCrawled)) {
site_occ_spocc$gbif$data[[1]]$lastCrawled <- lubridate::as_datetime(site_occ_spocc$gbif$data[[1]]$lastCrawled)
}
if (!is.null(site_occ_spocc$gbif$data[[1]]$lastParsed)) {
if ("gbif" %in% list_DS) {
if (!is.null(site_occ_spocc$gbif$data[[1]]$lastCrawled)) {
site_occ_spocc$gbif$data[[1]]$lastCrawled <- lubridate::as_datetime(site_occ_spocc$gbif$data[[1]]$lastCrawled)
}
if (!is.null(site_occ_spocc$gbif$data[[1]]$lastParsed)) {
site_occ_spocc$gbif$data[[1]]$lastParsed <- lubridate::as_datetime(site_occ_spocc$gbif$data[[1]]$lastParsed)
}
if (!is.null(site_occ_spocc$gbif$data[[1]]$dateIdentified)) {
site_occ_spocc$gbif$data[[1]]$dateIdentified <- lubridate::as_datetime(site_occ_spocc$gbif$data[[1]]$dateIdentified)
}
if (!is.null(site_occ_spocc$gbif$data[[1]]$eventDate)) {
site_occ_spocc$gbif$data[[1]]$eventDate <- lubridate::as_date(site_occ_spocc$gbif$data[[1]]$eventDate)
}
if (!is.null(site_occ_spocc$gbif$data[[1]]$modified)) {
site_occ_spocc$gbif$data[[1]]$modified <- lubridate::as_datetime(site_occ_spocc$gbif$data[[1]]$modified)
}
if (!is.null(site_occ_spocc$gbif$data[[1]]$dateIdentified)) {
site_occ_spocc$gbif$data[[1]]$dateIdentified <- lubridate::as_datetime(site_occ_spocc$gbif$data[[1]]$dateIdentified)
}
if (!is.null(site_occ_spocc$gbif$data[[1]]$eventDate)) {
site_occ_spocc$gbif$data[[1]]$eventDate <- lubridate::as_date(site_occ_spocc$gbif$data[[1]]$eventDate)
}
if (!is.null(site_occ_spocc$gbif$data[[1]]$modified)) {
site_occ_spocc$gbif$data[[1]]$modified <- lubridate::as_datetime(site_occ_spocc$gbif$data[[1]]$modified)
}
}
# harmonization of date and time iNat
if (!is.null(site_occ_spocc$inat$data[[1]]$time_observed_at)) {
site_occ_spocc$inat$data[[1]]$time_observed_at <- lubridate::as_datetime(site_occ_spocc$inat$data[[1]]$time_observed_at)
}
if (!is.null(site_occ_spocc$inat$data[[1]]$created_at)) {
site_occ_spocc$inat$data[[1]]$created_at <- lubridate::as_datetime(site_occ_spocc$inat$data[[1]]$created_at)
}
if (!is.null(site_occ_spocc$inat$data[[1]]$updated_at)) {
site_occ_spocc$inat$data[[1]]$updated_at <- lubridate::as_datetime(site_occ_spocc$inat$data[[1]]$updated_at)
if ("inat" %in% list_DS) {
if (!is.null(site_occ_spocc$inat$data[[1]]$time_observed_at)) {
site_occ_spocc$inat$data[[1]]$time_observed_at <- lubridate::as_datetime(site_occ_spocc$inat$data[[1]]$time_observed_at)
}
if (!is.null(site_occ_spocc$inat$data[[1]]$created_at)) {
site_occ_spocc$inat$data[[1]]$created_at <- lubridate::as_datetime(site_occ_spocc$inat$data[[1]]$created_at)
}
if (!is.null(site_occ_spocc$inat$data[[1]]$updated_at)) {
site_occ_spocc$inat$data[[1]]$updated_at <- lubridate::as_datetime(site_occ_spocc$inat$data[[1]]$updated_at)
}
}
# harmonization of date and time OBIS
if (!is.null(site_occ_spocc_obis$results$modified)) {
site_occ_spocc_obis$results$modified <- lubridate::as_datetime(site_occ_spocc_obis$results$modified)
if ("obis" %in% list_DS) {
if (!is.null(site_occ_spocc_obis$results$modified)) {
site_occ_spocc_obis$results$modified <- lubridate::as_datetime(site_occ_spocc_obis$results$modified)
}
}
# combine results from occ calls to a single data.frame ----
occ_df <- NULL
Expand Down Expand Up @@ -187,9 +191,7 @@ get_site_speciesOccurrences <- function(

if (nrow(occ_df_gbif) > 0) {
occ_df <- rbind(occ_df, occ_df_gbif)
} #else {
# list_DS <- list_DS[!(list_DS == "gbif")]
# }
}
}

if ("inat" %in% list_DS) {
Expand All @@ -202,11 +204,14 @@ get_site_speciesOccurrences <- function(
prov,
date = observed_on,
key = id
) %>%
dplyr::mutate(
date = as.character(date)
)
occ_df <- rbind(occ_df, occ_df_inat)
}

if ("obis" %in% list_DS && !length(site_occ_spocc_obis$results)==0) {
if ("obis" %in% list_DS && !length(site_occ_spocc_obis$results) == 0) {
occ_df_obis <- site_occ_spocc_obis$results %>%
dplyr::mutate(
prov = rep("obis", nrow(site_occ_spocc_obis$results))
Expand Down

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