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snirh.lab

Overview

Convert laboratory data into the official SNIRH (Portuguese Information System for Water Resources) format - https://snirh.apambiente.pt/. The snirh.lab package validates monitoring stations, standardizes parameters and units, and generates compliant files for submission to SNIRH.

Key Features

  • ✅ Automatic validation against SNIRH database
  • ✅ Station status checking (existence and active status)
  • ✅ Surface water and biota matrices support
  • ✅ Clear, informative error messages
  • ✅ Step-by-step progress tracking
  • ✅ Detailed validation reports

Installation

From CRAN 

install.packages("snirh.lab")

Development version from GitHub 

# Install pak if needed
install.packages("pak")

# Then install from GitHub
pak::pak("lpereira-ue/snirh.lab")

Dependencies 

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

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

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

Main Functions

Core Functions

Quick Start

Basic Conversion 

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")
print(result)

Station Validation 

# 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]

Browse Available Stations 

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

List Parameters 

# 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)])

Error Handling

Invalid Station Example 

# 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"))

Note: If a station exists but is inactive, you’ll get: - “Station(s) not active in SNIRH database: STATION_ID (STATUS)” - “Only stations with status ‘ATIVA’ can receive data”

Working Offline

No Internet Connection 

# 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)

Getting Help 

# 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")

Best Practices

  • ✅ Always validate stations first for production workflows
  • ✅ Handle errors gracefully in automated systems
  • ✅ Keep the package updated for latest SNIRH compatibility
  • ✅ Test with small datasets before processing large files

Validation Coverage

The package performs comprehensive validation:

  • ✅ Column structure and naming
  • ✅ Station existence and status
  • ✅ Duplicate detection
  • ✅ Parameter conversion availability
  • ✅ Value format validation
  • ✅ Unit conversion accuracy
  • ✅ Output format compliance

This ensures high-quality data submission to SNIRH with minimal manual intervention.

Citation

To cite snirh.lab in publications, please use:

citation("snirh.lab")