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Predict metabolism from a fitted model.

Source: R/metab_model_interface.R, R/metab_bayes.R, R/metab_model.predict_metab.R
predict_metab.Rd

A function in the metab_model_interface. Returns predictions (estimates) of GPP, ER, and K600.

Usage

predict_metab(
  metab_model,
  date_start = NA,
  date_end = NA,
  day_start = get_specs(metab_model)$day_start,
  day_end = min(day_start + 24, get_specs(metab_model)$day_end),
  ...,
  attach.units = deprecated(),
  use_saved = TRUE
)

# S3 method for metab_bayes
predict_metab(
  metab_model,
  date_start = NA,
  date_end = NA,
  ...,
  attach.units = deprecated()
)

# S3 method for metab_model
predict_metab(
  metab_model,
  date_start = NA,
  date_end = NA,
  day_start = get_specs(metab_model)$day_start,
  day_end = min(day_start + 24, get_specs(metab_model)$day_end),
  ...,
  attach.units = deprecated(),
  use_saved = TRUE
)

Arguments

metab_model

A metabolism model, implementing the metab_model_interface, to use in predicting metabolism

date_start

Date or a class convertible with as.Date. The first date (inclusive) for which to report metabolism predictions. If NA, no filtering is done.

date_end

Date or a class convertible with as.Date. The last date (inclusive) for which to report metabolism predictions. If NA, no filtering is done.

day_start

start time (inclusive) of a day's data in number of hours from the midnight that begins the date. For example, day_start=-1.5 indicates that data describing 2006-06-26 begin at 2006-06-25 22:30, or at the first observation time that occurs after that time if day_start doesn't fall exactly on an observation time. For daily metabolism predictions, day_end - day_start should probably equal 24 so that each day's estimate is representative of a 24-hour period.

day_end

end time (exclusive) of a day's data in number of hours from the midnight that begins the date. For example, day_end=30 indicates that data describing 2006-06-26 end at the last observation time that occurs before 2006-06-27 06:00. For daily metabolism predictions, day_end - day_start should probably equal 24 so that each day's estimate is representative of a 24-hour period.

...

Other arguments passed to class-specific implementations of predict_metab

attach.units

(deprecated, effectively FALSE in future) logical. Should units be attached to the output?

use_saved

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

Value

A data.frame of daily metabolism estimates. Columns include:

GPP

numeric estimate of Gross Primary Production, positive when realistic, \(g O_2 m^{-2} d^{-1}\)

ER

numeric estimate of Ecosystem Respiration, negative when realistic, \(g O_2 m^{-2} d^{-1}\)

K600

numeric estimate of the reaeration rate \(d^{-1}\)

Methods (by class)

  • metab_bayes: Pulls daily metabolism estimates out of the Stan model results; looks for GPP or GPP_daily and for ER or ER_daily among the params_out (see specs), which means you can save just one (or both) of those sets of daily parameters when running the Stan model. Saving fewer parameters can help models run faster and use less RAM.

  • metab_model: This implementation is shared by many model types

See also

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

Examples

dat <- data_metab('3', day_start=12, day_end=36)
mm <- metab_night(specs(mm_name('night')), data=dat)
predict_metab(mm)
#>         date GPP GPP.lower GPP.upper        ER  ER.lower  ER.upper msgs.fit
#> 1 2012-09-18   0        NA        NA -2.122498 -2.351240 -1.893755         
#> 2 2012-09-19   0        NA        NA -2.927715 -3.233801 -2.621628         
#> 3 2012-09-20   0        NA        NA -2.125522 -2.305859 -1.945185         
#>   warnings errors
#> 1                
#> 2                
#> 3                
predict_metab(mm, date_start=get_fit(mm)$date[2])
#>         date GPP GPP.lower GPP.upper        ER  ER.lower  ER.upper msgs.fit
#> 1 2012-09-19   0        NA        NA -2.927715 -3.233801 -2.621628         
#> 2 2012-09-20   0        NA        NA -2.125522 -2.305859 -1.945185         
#>   warnings errors
#> 1                
#> 2