twoStation_DOlogprob: Log posterior probability for the DO curve given empirical...
In mtalluto/NSmetabolism: N-Station Stream Metabolism Modelling

Description Usage Arguments Details Value

Log posterior probability for the DO curve given empirical data

1	twoStation_DOlogprob(params, data, prior = list(), ...)

`params`	A named vector of model parameters; see details
`data`	A list of model data, see details
`prior`	A list of prior hyperparameters; see details
`...`	Additional parameters to be passed to `DO_predict()`

params must be a vector. The indices of the vector must map to model parameters as follows; (where parameters with length two are fit per site):

1:2 – logP1 $(W min g^-1 O_2)$ – inverse of the slope of a photosynthesis–irradiance curve at low light intensity
3:4 – logP2 $(m^2 min g^-1 O_2)$ – inverse maximum photosynthesis rate; can be zero to assume GPP is linear with light intensity instead of saturating
5:6 – logk600 – coefficient of gas exchange for a gas with a Schmidt number of 600
7:8 – logER24_20 – daily ecosystem respiration rate, standardized at 20 degrees C
9 – logsd – log(Error standard deviation)

data is a list of length 2 (one per site); each item is a list of (constant) data items, including the following:

DO 2-column data frame; first column is dissolved oxygen, second is time of observation
PAR 2-column data frame; first column is light, second is time of observation
temp 2-column data frame; first column is temperature, second is time of observation
P pressure, in atmospheres
z Depth, in meters

prior is a list of hyperparameters for the priors on parameters listed under params. All priors are normal. Thus, each list item should be named (following the names from params), and each item should be a vector of length two giving the mean and standard deviation of the prior for that parameter. Note that each parameter is optional (as is the entire list); missing items will get a minimally informative normal(0,10) distribution.

The unnormalized log probability of the model given the data

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