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util-convert_otn_to_att.r
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util-convert_otn_to_att.r
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#' Convert detections, tagging metadata, and deployment metadata to a format
#' that ATT accepts.
#'
#' Convert \code{glatos_detections}, OTN tagging metadata and OTN deployment
#' metadata to \code{ATT} format for use in the Animal Tracking Toolbox
#' <https://github.com/vinayudyawer/ATT>, now part of `VTrack`
#' <https://github.com/RossDwyer/VTrack>.
#'
#' @param detectionObj A `glatos_detections` object (e.g., created by
#' [read_otn_detections] or [read_glatos_detections]) or a `data.frame`
#' containing required columns (see [glatos_detections]).
#'
#' @param taggingSheet a data frame from \code{prepare_tag_sheet}
#'
#' @param deploymentObj a data frame from \code{read_otn_deployments}
#'
#' @param deploymentSheet a data frame from \code{prepare_deploy_sheet}
#'
#' @param timeFilter Whether the data should be filtered using the deployment
#' and recovery/last download times of receivers. Defaults to TRUE, if not all
#' receiver metadata is available, this should be set to FALSE otherwise there
#' will be data loss.
#'
#' @param crs an object of class `crs` (see [sf::st_crs][st_crs]) with
#' geographic coordinate system for all spatial information
#' (latitude/longitude). If none provided or `crs` is not recognized,
#' defaults to WGS84.
#'
#'
#' @details This function takes 3 data frames containing detections, tagging
#' metadata, and deployment metadata from either `read_otn_deployments`
#' or `prepare_deploy_sheet` and transforms them into 3
#' `tibble` objects inside of a list. The input that AAT uses to
#' get this data product is located here:
#' <https://github.com/vinayudyawer/ATT/blob/master/README.md> and our mappings
#' are found here: <https://github.com/ocean-tracking-network/glatos/issues/75#issuecomment-982822886>
#' in a comment by Ryan Gosse.
#'
#' @author Ryan Gosse
#'
#' @return a list of 3 tibbles containing tag detections, tag metadata,
#' and station metadata, to be ingested by VTrack/ATT
#'
#' @examples
#' \dontrun{
#' #--------------------------------------------------
#' # EXAMPLE #1 - loading from Deployment Object
#'
#' library(glatos)
#'
#' dets_path <- system.file("extdata", "blue_shark_detections.csv",
#' package = "glatos"
#' )
#' deploy_path <- system.file("extdata", "hfx_deployments.csv",
#' package = "glatos"
#' )
#' tag_path <- system.file("extdata", "otn_nsbs_tag_metadata.xls",
#' package = "glatos"
#' )
#'
#' dets <- read_otn_detections(dets_path)
#' tags <- prepare_tag_sheet(tag_path, 5, 2)
#' deploy <- read_otn_deployments(deploy_path)
#'
#' ATTdata <- convert_otn_to_att(dets, tags, deploymentObj = deploy)
#' }
#' #--------------------------------------------------
#' # EXAMPLE #2 - loading from Deployment Sheet
#'
#' library(glatos)
#'
#' dets_path <- system.file("extdata", "blue_shark_detections.csv",
#' package = "glatos"
#' )
#' deploy_path <- system.file("extdata", "hfx_deploy_simplified.xlsx",
#' package = "glatos"
#' )
#' tag_path <- system.file("extdata", "otn_nsbs_tag_metadata.xls",
#' package = "glatos"
#' )
#'
#' dets <- read_otn_detections(dets_path)
#' tags <- prepare_tag_sheet(tag_path, 5, 2)
#' deploy <- prepare_deploy_sheet(deploy_path, 1, 1)
#'
#' ATTdata <- convert_otn_to_att(dets, tags, deploymentSheet = deploy)
#'
#' @export
convert_otn_to_att <- function(detectionObj,
taggingSheet,
deploymentObj = NULL,
deploymentSheet = NULL,
timeFilter = TRUE,
crs = sf::st_crs(4326)) {
## Declare global variables for R CMD check
station <- receiver_sn <- deploy_lat <- deploy_long <-
detection_timestamp_utc <- deploy_date_time <- recover_date_time <-
last_download <- instrumenttype <- ins_model_no <- Tag.ID <- Sex <- NULL
if (is.null(deploymentObj) && is.null(deploymentSheet)) {
stop(
"Deployment data must be supplied by either 'deploymentObj' or ",
"'deploymentSheet'"
)
} else if ((!is.null(deploymentObj)) && (!is.null(deploymentSheet))) {
stop(
"Deployment data must be supplied by either 'deploymentObj' or ",
"'deploymentSheet', not both"
)
} else if (!is.null(deploymentSheet)) {
deploymentObj <- deploymentSheet
}
detectionObj <- detectionObj %>% # Remove (lost/found)
dplyr::mutate(
station = gsub("\\(lost\\/found\\)", "", station),
receiver_sn = gsub("\\(lost\\/found\\)", "", receiver_sn)
)
transmitters <-
if (all(grepl("-", detectionObj$transmitter_id, fixed = TRUE))) {
detectionObj$transmitter_id
} else {
concat_list_strings(
detectionObj$transmitter_codespace,
detectionObj$transmitter_id
)
}
tagMetadata <- unique(dplyr::tibble( # Start building Tag.Metadata table
Tag.ID = detectionObj$animal_id,
Transmitter = as.factor(transmitters),
Common.Name = as.factor(detectionObj$common_name_e),
Sci.Name = as.factor(detectionObj$scientificname)
))
tagMetadata <- unique(tagMetadata) # Cut out dupes
detectionObj <- dplyr::left_join(detectionObj, taggingSheet %>%
dplyr::select(-c("animal_id")),
by = "transmitter_id"
)
detectionObj <- dplyr::left_join(
detectionObj %>%
dplyr::select(-deploy_lat, -deploy_long),
deploymentObj,
by = "station"
)
if (timeFilter) {
if (is.null(deploymentSheet)) {
detectionObj <- detectionObj %>% dplyr::filter(
detection_timestamp_utc >= deploy_date_time,
detection_timestamp_utc <= dplyr::coalesce(
recover_date_time,
last_download
),
instrumenttype == "rcvr"
)
} else {
detectionObj <- detectionObj %>% dplyr::filter(
detection_timestamp_utc >= deploy_date_time,
detection_timestamp_utc <= recover_date_time |
recover_date_time %in% c(NA)
)
}
}
detectionObj <- detectionObj %>%
dplyr::mutate(
ReceiverFull = paste(ins_model_no, receiver_sn, sep = "-")
)
detectionObj$est_tag_life[detectionObj$est_tag_life == "NULL"] <- NA
releaseData <- dplyr::tibble( # Get the rest from detectionObj
Tag.ID = detectionObj$animal_id,
Tag.Project = as.factor(detectionObj$collectioncode),
Release.Latitude = as.double(detectionObj$latitude),
Release.Longitude = as.double(detectionObj$longitude),
Release.Date = as.Date(detectionObj$time),
Sex = as.factor(detectionObj$sex),
Tag.Life = as.integer(detectionObj$est_tag_life)
) %>% dplyr::filter(!Tag.ID %in% NA)
releaseData <- dplyr::mutate(releaseData,
# Convert sex text and null missing columns
Sex = convert_sex(Sex),
Tag.Status = as.factor(NA),
Bio = as.factor(NA)
) %>% unique()
detections <- dplyr::tibble(
Date.Time = detectionObj$detection_timestamp_utc,
Transmitter = as.factor(detectionObj$transmitter_id),
Station.Name = as.factor(detectionObj$station),
Receiver = as.factor(detectionObj$ReceiverFull),
Latitude = as.double(detectionObj$deploy_lat),
Longitude = as.double(detectionObj$deploy_long),
Sensor.Value = as.integer(detectionObj$sensorvalue),
Sensor.Unit = as.factor(detectionObj$sensorunit)
)
tagMetadata <- dplyr::left_join(tagMetadata, releaseData, by = "Tag.ID")
animal_sex <- tagMetadata$Sex
animal_sex[animal_sex == "NULL"] <- NA
tagMetadata <- tagMetadata %>% dplyr::mutate(
Sex = as.factor(as.character(animal_sex))
)
stations <- unique(dplyr::tibble(
Station.Name = as.factor(detectionObj$station),
Receiver = as.factor(detectionObj$ReceiverFull),
Installation = as.factor(NA),
Receiver.Project = as.factor(detectionObj$collectioncode),
Deployment.Date = detectionObj$deploy_date_time,
Recovery.Date = detectionObj$recover_date_time,
Station.Latitude = as.double(detectionObj$deploy_lat),
Station.Longitude = as.double(detectionObj$deploy_long),
Receiver.Status = as.factor(NA)
))
att_obj <- list(
Tag.Detections = detections,
Tag.Metadata = tagMetadata,
Station.Information = stations
)
class(att_obj) <- "ATT"
# Note that sf::st_crs() uses class name 'crs' but this is changed to 'CRS'
# because VTrack/ATT are using sp::CRS()
if (inherits(crs, "crs")) {
attr(att_obj, "CRS") <- crs
} else {
message(
"Geographic projection for detection positions not recognised, ",
"reverting to WGS84 global coordinate reference system."
)
attr(att_obj, "CRS") <- eval(formals()$crs)
}
return(att_obj)
}
# Simple query to WoRMS based on the common name and returns the sci name
query_worms_common <- function(commonName,
silent = FALSE) {
url <- utils::URLencode(
sprintf(
"https://www.marinespecies.org/rest/AphiaRecordsByVernacular/%s",
commonName
)
)
sapply(
url,
FUN = function(x) {
tryCatch(
{
if (!silent) print(x)
payload <- jsonlite::fromJSON(x)
sciname <- list(payload$scientificname)
},
error = function(e) {
print(geterrmessage())
stop(sprintf(
"Error in querying WoRMS, %s was probably not found.",
utils::URLdecode(gsub(".*/", "", x))
))
}
)
return(sciname)
},
USE.NAMES = FALSE
)
}
convert_sex <- function(sex) {
sapply(sex,
FUN = function(.) {
if (toupper(.) %in% c("F", "FEMALE")) {
return("FEMALE")
}
if (toupper(.) %in% c("M", "MALE")) {
return("MALE")
}
return(.)
},
USE.NAMES = FALSE
)
}