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Predict dissolved oxygen from a fitted model

Source: R/metab_model_interface.R, R/metab_Kmodel.R, R/metab_model.predict_DO.R, and 2 more
predict_DO.Rd

A function in the metab_model_interface. Returns predictions of dissolved oxygen.

Usage

predict_DO(
  metab_model,
  date_start = NA,
  date_end = NA,
  ...,
  attach.units = deprecated(),
  use_saved = TRUE
)

# S3 method for class 'metab_Kmodel'
predict_DO(metab_model, date_start = NA, date_end = NA, ..., use_saved = TRUE)

# S3 method for class 'metab_model'
predict_DO(
  metab_model,
  date_start = NA,
  date_end = NA,
  ...,
  attach.units = deprecated(),
  use_saved = TRUE
)

# S3 method for class 'metab_night'
predict_DO(metab_model, date_start = NA, date_end = NA, ..., use_saved = TRUE)

# S3 method for class 'metab_sim'
predict_DO(metab_model, date_start = NA, date_end = NA, ...)

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 DO 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 DO predictions. If NA, no filtering is done.

...

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

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 dissolved oxygen predictions at the temporal resolution of the input data.

Methods (by class)

  • predict_DO(metab_Kmodel): Throws an error because models of type 'Kmodel' can't predict DO. metab_Kmodel predicts K at daily timesteps and usually knows nothing about GPP or ER. So it's not possible to predict DO from this model. Try passing the output to metab_mle and THEN predicting DO.

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

  • predict_DO(metab_night): Generate nighttime dissolved oxygen predictions from a nighttime regression model. metab_night only fits ER and K, and only for the darkness hours, so predictions are only generated for those hours.

  • predict_DO(metab_sim): Simulate values for DO.obs (with process and observation error), DO.mod (with process error only), and DO.pure (with no error). The errors are randomly generated on every new call to predict_DO.

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_metab()

Examples

dat <- data_metab("3", day_start = 12, day_end = 36)
mm <- metab_night(specs(mm_name("night")), data = dat)
preds <- predict_DO(mm, date_start = get_fit(mm)$date[3])
head(preds)
#> # A tibble: 6 × 8
#>   date       solar.time          DO.obs DO.sat depth temp.water light DO.mod
#>   <date>     <dttm>               <dbl>  <dbl> <dbl>      <dbl> <dbl>  <dbl>
#> 1 2012-09-20 2012-09-20 17:55:58   8.07   7.77  0.16       9.76     0   8.07
#> 2 2012-09-20 2012-09-20 18:00:58   8.06   7.78  0.16       9.69     0   8.00
#> 3 2012-09-20 2012-09-20 18:05:58   8      7.80  0.16       9.61     0   7.93
#> 4 2012-09-20 2012-09-20 18:10:58   7.94   7.81  0.16       9.54     0   7.88
#> 5 2012-09-20 2012-09-20 18:15:58   7.91   7.83  0.16       9.46     0   7.83
#> 6 2012-09-20 2012-09-20 18:20:58   7.87   7.84  0.16       9.38     0   7.78