onestation: Calibrate a single station metabolism model

In mtalluto/NSmetabolism: N-Station Stream Metabolism Modelling

Description

Calibrate a single station metabolism model

Usage

onestation(
  oxy,
  temp,
  light,
  pressure,
  depth,
  dt,
  nsamples = 1000,
  prior = list(),
  ...
)

Arguments

oxy	Dissolved oxygen time series (g/L)
temp	Water temperature time series (degrees); one per DO observation
light	Light, (lux or W/m^2); one per DO observation
pressure	Air pressure (hPa); single value or one per DO observation
depth	Water depth, in meters
dt	Time interval of observations (minutes)
nsamples	The number of posterior samples to return
prior	Priors for the function chosenl, see 'details'
...	Additional arguments to pass to the rstan

Details

Implements a one-station stream metaoblism model; much code from Fuß et al 2017.

This model requires that the observations consist of a single 24-hour period. Start time may be arbitrary, as long as an entire 24-hours is covered. No checking is done for this, it is up to the user to ensure this is correct.

For a prior, you may specify a named list, with each item a vector of parameters to use for the prior. Currently, the following parameters are supported:

• lp1: the log of the inverse of the slope of the photosynthesis-irradiance curve; default c(0, 9).

• lp2: the log of the saturation term of the photosynthesis-irradiance curve; default c(0, 9).

• k: gas transfer velocity, default c(0, 10)

• gpp: daily gross primary productivity, default c(0, 10)

• er: daily in-situ ecosystem respiration, default c(0, 10) (note first item must be <= 0)

Priors all use a half normal distribution.

Value

A fitted rstan model

References

Fuß, T. et al. (2017). Land use controls stream ecosystem metabolism by shifting dissolved organic matter and nutrient regimes. Freshw Biol 62:582–599.

mtalluto/NSmetabolism documentation built on May 3, 2021, 7:51 p.m.