Description Usage Arguments Value Author(s) See Also Examples
This function runs the ordinary least squares metabolism model on the supplied gas concentration and other supporting data. This is a common approach that allows for the concurrent estimation of metabolism paramters from a timeseries.
1 |
do.obs |
Vector of dissolved 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 |
... |
additional arguments; currently "datetime" is the only recognized argument passed through |
A data.frame with columns corresponding to components of metabolism
numeric estimate of Gross Primary Production, mg O2 / L / d
numeric estimate of Respiration, mg O2 / L / d
numeric estimate of Net Ecosystem production, mg O2 / L / d
Luke A Winslow, Ryan Batt, GLEON Fellows
metab, metab.bookkeep, metab.mle, metab.kalman, metab.bayesian,
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | library(rLakeAnalyzer)
doobs = load.ts(system.file('extdata',
'sparkling.doobs', package="LakeMetabolizer"))
wtr = load.ts(system.file('extdata',
'sparkling.wtr', package="LakeMetabolizer"))
wnd = load.ts(system.file('extdata',
'sparkling.wnd', package="LakeMetabolizer"))
irr = load.ts(system.file('extdata',
'sparkling.par', package="LakeMetabolizer"))
#Subset a day
mod.date = as.POSIXct('2009-07-08')
doobs = doobs[trunc(doobs$datetime, 'day') == mod.date, ]
wtr = wtr[trunc(wtr$datetime, 'day') == mod.date, ]
wnd = wnd[trunc(wnd$datetime, 'day') == mod.date, ]
irr = irr[trunc(irr$datetime, 'day') == mod.date, ]
z.mix = ts.thermo.depth(wtr)
k600 = k.cole.base(wnd[,2])
k.gas = k600.2.kGAS.base(k600, wtr[,3], 'O2')
do.sat = o2.at.sat.base(wtr[,3], altitude=300)
metab.ols(doobs[,2], do.sat, k.gas, z.mix[,2], irr[,2], wtr[,3])
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