Skip to contents

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 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 class 'metab_bayes'
predict_metab(
  metab_model,
  date_start = NA,
  date_end = NA,
  ...,
  attach.units = deprecated()
)

# S3 method for class '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 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 metabolism predictions. 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 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.

...

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

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 with one row per date and columns that include:

  • GPP: Gross primary production, which is positive when realistic, in gO₂ m⁻² d⁻¹.

  • ER: Ecosystem respiration, which is negative when realistic, in gO₂ m⁻² d⁻¹.

  • K600: The reaeration rate, in d⁻¹.

Methods (by class)

  • predict_metab(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.

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

See also

Other metab_model_interface: get_data(), get_data_daily(), get_fit(), get_fitting_time(), 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)
#> # A tibble: 3 × 10
#>   date         GPP GPP.lower GPP.upper    ER ER.lower ER.upper msgs.fit warnings
#>   <date>     <dbl> <lgl>     <lgl>     <dbl>    <dbl>    <dbl> <chr>    <chr>   
#> 1 2012-09-18     0 NA        NA        -2.12    -2.35    -1.89 "      … ""      
#> 2 2012-09-19     0 NA        NA        -2.93    -3.23    -2.62 "      … ""      
#> 3 2012-09-20     0 NA        NA        -2.13    -2.31    -1.95 "      … ""      
#> # ℹ 1 more variable: errors <chr>
predict_metab(mm, date_start = get_fit(mm)$date[2])
#> # A tibble: 2 × 10
#>   date         GPP GPP.lower GPP.upper    ER ER.lower ER.upper msgs.fit warnings
#>   <date>     <dbl> <lgl>     <lgl>     <dbl>    <dbl>    <dbl> <chr>    <chr>   
#> 1 2012-09-19     0 NA        NA        -2.93    -3.23    -2.62 "      … ""      
#> 2 2012-09-20     0 NA        NA        -2.13    -2.31    -1.95 "      … ""      
#> # ℹ 1 more variable: errors <chr>