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Extract metabolism model parameters

Source: R/metab_model_interface.R, R/metab_Kmodel.R, R/metab_bayes.R, and 2 more
get_params.Rd

A function in the metab_model_interface. Returns estimates of the parameters describing the rates and/or shapes of GPP, ER, or reaeration.

Usage

get_params(
  metab_model,
  date_start = NA,
  date_end = NA,
  uncertainty = c("sd", "ci", "none"),
  messages = TRUE,
  fixed = c("none", "columns", "stars"),
  ...,
  attach.units = deprecated()
)

# S3 method for class 'metab_Kmodel'
get_params(
  metab_model,
  date_start = NA,
  date_end = NA,
  uncertainty = c("sd", "ci", "none"),
  messages = TRUE,
  fixed = c("none", "columns", "stars"),
  ...,
  attach.units = deprecated(),
  use_saved = TRUE
)

# S3 method for class 'metab_bayes'
get_params(
  metab_model,
  date_start = NA,
  date_end = NA,
  uncertainty = "ci",
  messages = TRUE,
  ...,
  attach.units = deprecated()
)

# S3 method for class 'metab_model'
get_params(
  metab_model,
  date_start = NA,
  date_end = NA,
  uncertainty = c("sd", "ci", "none"),
  messages = TRUE,
  fixed = c("none", "columns", "stars"),
  ...,
  attach.units = deprecated()
)

# S3 method for class 'metab_sim'
get_params(
  metab_model,
  date_start = NA,
  date_end = NA,
  uncertainty = c("sd", "ci", "none"),
  messages = TRUE,
  fixed = c("none", "columns", "stars"),
  ...,
  attach.units = deprecated()
)

Arguments

metab_model

A metabolism model that implements the metab_model_interface.

date_start

A Date or an object coercible with as.Date(). The first date (inclusive) for which to report parameters. If NA, no filtering is done.

date_end

A Date or an object coercible with as.Date(). The last date (inclusive) for which to report parameters. If NA, no filtering is done.

uncertainty

A string. Should columns for parameter uncertainty be excluded ("none"), reported as standard deviations ("sd"), or reported as lower and upper bounds of a 95 percent confidence interval ("ci")? When available (e.g., for Bayesian models), if "ci" then the central value will be the median (50th quantile) and the ranges will be the 2.5th and 97.5th quantiles. If "sd" then the central value will be the mean.

messages

A logical. Should warning and error messages from the fitting procedure be included in the output?

fixed

A string. Should values pulled from data_daily (i.e., fixed rather than fitted) be treated identically ("none"), paired with logical columns ending in .fixed ("columns"), or converted to character and marked with a leading asterisk ("stars")?

...

Other arguments passed to class-specific implementations of get_params().

attach.units

Deprecated. A logical indicating whether to attach units to the output.

use_saved

A logical. Is it OK to use predictions that were saved with the model?

Value

A data frame of the parameters needed to predict GPP, ER, D, and DO, with one row per date.

Methods (by class)

  • get_params(metab_Kmodel): Make daily re-predictions of K600.daily based on the across-days model of K600.daily versus predictors. Only returns estimates for K600.daily, not any of the other daily parameters

  • get_params(metab_bayes): Does a little formatting to convert from Stan output to streamMetabolizer parameter names; otherwise the same as get_params.metab_model

  • get_params(metab_model): This implementation is shared by many model types

  • get_params(metab_sim): Generates new simulated values for daily parameters if they were described with evaluatable expressions in specs(), or returns the fixed values for daily parameters if they were set in data_daily

See also

predict_metab() for daily average rates of GPP and ER.

Other metab_model_interface: get_data(), get_data_daily(), get_fit(), get_fitting_time(), get_info(), get_param_names(), get_specs(), get_version(), predict_DO(), predict_metab()

Examples

dat <- data_metab("3", day_start = 12, day_end = 36)
mm <- metab_night(specs(mm_name("night")), data = dat)
get_params(mm)
#>         date  ER.daily ER.daily.sd K600.daily K600.daily.sd warnings errors
#> 1 2012-09-18 -2.122498  0.11670762   26.17191      1.337894                
#> 2 2012-09-19 -2.927715  0.15616944   34.09664      1.692708                
#> 3 2012-09-20 -2.125522  0.09201041   29.65021      1.184019                
get_params(mm, date_start = get_fit(mm)$date[2])
#>         date  ER.daily ER.daily.sd K600.daily K600.daily.sd warnings errors
#> 1 2012-09-19 -2.927715  0.15616944   34.09664      1.692708                
#> 2 2012-09-20 -2.125522  0.09201041   29.65021      1.184019