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Basic Bayesian metabolism model fitting function

Source: R/metab_bayes.R
metab_bayes.Rd

Fits a Bayesian model to estimate GPP and ER from input data on DO, temperature, light, etc. See mm_name to choose a Bayesian model and specs for relevant options for the specs argument.

Usage

metab_bayes(
  specs = specs(mm_name("bayes")),
  data = mm_data(solar.time, DO.obs, DO.sat, depth, temp.water, light, discharge,
    optional = "discharge"),
  data_daily = mm_data(date, discharge.daily, optional = "all"),
  info = NULL
)

Arguments

specs

a list of model specifications and parameters for a model. Although this may be specified manually (it's just a list), it is easier and safer to use specs to generate the list, because the set of required parameters and their defaults depends on the model given in the model_name argument to specs. The help file for specs lists the necessary parameters, describes them in detail, and gives default values.

data

data.frame (not a tbl_df) of input data at the temporal resolution of raw observations (unit-value). Columns must have the same names, units, and format as the default. The solar.time column must also have a timezone code ('tzone' attribute) of 'UTC'. See the 'Formatting data' section below for a full description.

data_daily

data.frame containing inputs with a daily timestep. See the 'Formatting data_daily' section below for a full description.

info

any information, in any format, that you would like to store within the metab_model object

Value

A metab_bayes object containing the fitted model. This object can be inspected with the functions in the metab_model_interface and also get_mcmc.

Details

As of summer and fall 2016, a new compilation of any Stan model gives deprecation warnings including typedef 'size_type' locally defined but not used [-Wunused-local-typedefs], typedef 'index_range' locally defined but not used [-Wunused-local-typedefs], typedef 'index' locally defined but not used [-Wunused-local-typedefs], and 'void stan::math::set_zero_all_adjoints()' defined but not used [-Wunused-function]. THESE ARE OKAY. Subsequent runs of the compiled Stan model will be quieter, and the model will work.

See also

Other metab_model: metab_Kmodel, metab_mle, metab_night, metab_sim

Author

Alison Appling, Bob Hall

Examples

if (FALSE) {
dat <- data_metab('3', res='30')
# fast-ish model version, but still too slow to auto-run in examples
mm <- metab_bayes(data=dat,
  specs(mm_name('bayes', err_proc_iid=FALSE),
    n_cores=3, n_chains=3, burnin_steps=300, saved_steps=100))
mm
get_fitting_time(mm)
predict_metab(mm)
plot_DO_preds(predict_DO(mm))

# error and warning messages are printed with the mm object if present
dat <- data_metab('3', res='30', flaws=c('missing middle'))
mm <- metab(specs(mm_name('bayes', err_proc_iid=FALSE),
  n_cores=3, n_chains=3, burnin_steps=300, saved_steps=100, verbose=FALSE),
  data=dat)
predict_metab(mm)

# view the Stan model file as stored on your system
file.edit(get_specs(mm)$model_path)
}