R: Metabolism model based on a bayesian parameter estimation...
metab.bayesian
R Documentation
Metabolism model based on a bayesian parameter estimation framework
Description
This function runs the bayesian metabolism model on the supplied
gas concentration and other supporting data. This allows for both estimates of
metabolism along with uncertainty around the parameters.
Vector of dissovled oxygen concentration observations, mg L^-1
do.sat
Vector of dissolved oxygen saturation values based on water temperature. Calculate using o2.at.sat
k.gas
Vector of kGAS values calculated from any of the gas flux models
(e.g., k.cole) and converted to kGAS using k600.2.kGAS
z.mix
Vector of mixed-layer depths in meters. To calculate, see ts.meta.depths
irr
Vector of photosynthetically active radiation in micro mols / m^2 / s
wtr
Vector of water temperatures in degrees C. Used in scaling respiration with temperature
priors
Parameter priors supplied as a named numeric vector (example: c("gppMu"=0, "gppSig2"=1E5, "rMu"=0, "rSig2"=1E5, "kSig2"=NA))
...
additional arguments; currently "datetime" is the only recognized argument passed through ...
Value
A list of length 4 with components:
model
the jags model, including posterior draws (see jags)
params
parameter estimates of interest from model (medians)
metab.sd
standard deviation of metabolism estimates
metab
daily metabolism estimates as a data.frame with columns corresponding to
GPP
numeric estimate of Gross Primary Production, mg O2 / L / d
R
numeric estimate of Respiration, mg O2 / L / d
NEP
numeric estimate of Net Ecosystem production, mg O2 / L / d
Author(s)
Ryan Batt, Luke A. Winslow
References
Holtgrieve, Gordon W., Daniel E. Schindler, Trevor a. Branch, and Z. Teresa A'mar.
2010. Simultaneous Quantification of Aquatic Ecosystem Metabolism and Reaeration
Using a Bayesian Statistical Model of Oxygen Dynamics.
Limnology and Oceanography 55 (3): 1047-1062. doi:10.4319/lo.2010.55.3.1047.
http://www.aslo.org/lo/toc/vol_55/issue_3/1047.html.