metabLoss_v4: Metab Loss, Version 4 Estimating Metabolism from DO data....

In MFEh2o/MFEUtilities: Utility functions for the MFE Database

Metab Loss, Version 4 Estimating Metabolism from DO data. This function calculates the likelihoods; use in conjunction with an optimization routine to minimize NLL. Use this for one day's data at a time. Created by CTS, 29 January 2009. Version 4 created August 2009.

Description

Metab Loss, Version 4 Estimating Metabolism from DO data. This function calculates the likelihoods; use in conjunction with an optimization routine to minimize NLL. Use this for one day's data at a time. Created by CTS, 29 January 2009. Version 4 created August 2009.

Usage

metabLoss_v4(parsIn, dataIn)

Arguments

parsIn	A vector of parameters. First element is iota (primary productivity per unit of PAR; units are (mg L-1 timeStep-1) / (mmol m-2 s-1)). Second element is rho (nighttime respiration; units are (mg L-1 (timeStep)-1)). Third element is DOInit (initial DOHat value; units are mg L-1). TimeStep is the number of minutes between observations. parsIn is given in log units.
dataIn	A data frame, which includes the following columns: DOObs: DO (mg/L); DOSat: DO at saturation (mg/L); irr: irradiance (PAR) (mmol m-2 s-1) >>>> note that GLEON data may actually be in umol; check; kO2: piston velocity for O2, m (timeStep)-1; zMix: depth of the mixed layer (m); fluxDummy: 0 if zMix is above DO sensor depth (prevents atm flux); 1 otherwise.

Value

NLL, which is a scalar (I think? -KG)

MFEh2o/MFEUtilities documentation built on May 6, 2023, 1:33 p.m.