neonMetabolizer is an in-development R package that is intended to pull National Ecological Observatory Network (NEON) data and model two-station stream metabolism. This package is not a NEON or U.S. Geological Survey (USGS) product and is not supported, maintained, or endorsed by these agencies.
NEONmetabolizer relies on @NEONScience's NEON-utilities, localPressureDO, and reaRate packages. NEON-metabolizer also uses some functions from @USGS-R's streamMetabolizer package.
request_NEON()- Pulls and formats water quality, temperature, PAR, nitrate, discharge, water chemistry, aquatic plant counts, and barometric pressure data products during the time period of choice into a single time-series dataframe
- Pulls SF6 data to calculate K600 reaeration rates and the relationship between measured K and measured stream discharge
clean_NEON()- Takes products returned from
request_NEON()and checks for obviously erronious sensor data (i.e. things like discharge < 0), equal 15-minute breaks throughout the time series, and the amount of missing data - Any missing data is filled using an ARIMA model (check out the documentation for
auto.arima()for more info) - K600 and travel time between sensor stations are extrapolated for each time point using the relationship between field measurements and discharge
- Column names and formatting are changed to jive with
streamMetabolizer's requirements for metabolism modeling
- Takes products returned from
- Model metabolism
- Functions for this step are in active development - see notes below!
This package is not a product of NEON or USGS, and is not supported, maintained, or endorsed by these agencies.