snirh.lab

install.packages("snirh.lab")

# install.packages("devtools")
devtools::install_github("lpereira-ue/snirh.lab")

# Core requirements
install.packages(c("data.table", "cli"))

# For station validation
install.packages("sf")

# For better internet connectivity checks (optional)
install.packages("curl")

library(snirh.lab)
library(data.table)

# Prepare your data
lab_data <- data.table(
  snirh_entity = "LAB001",
  station_name = "Rio Douro - Crestuma",
  station_id = "01F/01", # Must be valid SNIRH station
  sampling_date = as.POSIXct("2024-01-15 10:30:00"),
  parameter = "pH - Campo",
  unit = "Escala Sorensen",
  value = "7.2"
)

# Convert with automatic station validation
result <- convert_to_snirh(lab_data, "surface.water")

# Check if your stations are valid and active
my_stations <- c("01F/01", "25G/07", "16H/03")
station_check <- check_station_status(my_stations, "surface.water")
print(station_check)

# Only proceed with active stations
active_stations <- station_check[active == TRUE, station_id]
filtered_data <- lab_data[station_id %in% active_stations]

# Get all active surface water stations
active_stations <- get_snirh_stations("surface.water", active_only = TRUE)
print(paste("Available stations:", nrow(active_stations)))

# Find stations in your region (example with spatial filtering)
if (requireNamespace("sf", quietly = TRUE)) {
  library(sf)
  stations_sf <- get_snirh_stations("surface.water")
  # Add your spatial filtering logic here
}

# List all water quality parameters
water_params <- list_snirh_parameters("water")
print(head(water_params))

# Get detailed conversion information
detailed_params <- list_snirh_parameters("water", include_conversion_info = TRUE)
print(detailed_params[1:5, .(param_lab, unit_lab, param_snirh, unit_snirh, factor)])

# This will fail with clear error message
bad_data <- data.table(
  snirh_entity = "LAB001",
  station_name = "Invalid Station",
  station_id = "INVALID_ID",
  sampling_date = as.POSIXct("2024-01-15 10:30:00"),
  parameter = "pH - Campo",
  unit = "Escala Sorensen",
  value = "7.2"
)

# Will produce error: "Station ID(s) not found in SNIRH database: INVALID_ID"
try(convert_to_snirh(bad_data, "surface.water"))

# Will produce: "Internet connection required for station validation"
# Solution: Check connection or use validate_stations = FALSE
result <- convert_to_snirh(lab_data, "surface.water", validate_stations = FALSE)

# For testing or when working offline
result <- convert_to_snirh(lab_data, "surface.water", validate_stations = FALSE)

# For slow connections
result <- convert_to_snirh(lab_data, "surface.water", timeout = 60)

# Process multiple files with error handling
process_lab_files <- function(file_paths) {
  results <- list()
  
  for (file_path in file_paths) {
    tryCatch({
      # Read your data
      lab_data <- read_your_data_function(file_path)
      
      # Check stations first
      unique_stations <- unique(lab_data$station_id)
      station_status <- check_station_status(unique_stations, "surface.water")
      
      # Filter to active stations only
      active_stations <- station_status[active == TRUE, station_id]
      filtered_data <- lab_data[station_id %in% active_stations]
      
      if (nrow(filtered_data) > 0) {
        # Convert filtered data
        result <- convert_to_snirh(filtered_data, "surface.water")
        results[[file_path]] <- result
        cat("✅ Successfully processed:", file_path, "\n")
      } else {
        cat("⚠️ No active stations in:", file_path, "\n")
      }
      
    }, error = function(e) {
      cat("❌ Error processing:", file_path, "-", e$message, "\n")
    })
  }
  
  return(results)
}

# View package help
help(package = "snirh.lab")

# Function-specific help
?convert_to_snirh
?get_snirh_stations
?check_station_status

# List all available parameters
list_snirh_parameters("all")

citation("snirh.lab")