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Return the data types that may be used by metab_models using the metab_model_interface.

Source: R/mm_data.R
mm_data.Rd

Produces a unitted data.frame with the column names, units, and data format to be used by metab_models that comply strictly with the metab_model_interface. These are the columns that may be included:

  • solar.time date-time values in mean solar time (see calc_solar_time and/or convert_UTC_to_solartime), in POSIXct format with a tzone attribute of 'UTC'. May be approximated by local, non-daylight-savings clock time (still with nominal UTC timezone but with clock noons close to solar noon), but mean solar time is better for matching model time windows to the diel cycle of light availability. Throughout this package, variables named "solar.time" are mean solar time, "app.solar.time" means apparent solar time, and "any.solar.time" means either.

  • DO.obs dissolved oxygen concentration observations, \(mg O[2] L^{-1}\)

  • DO.sat dissolved oxygen concentrations if the water were at equilibrium saturation \(mg O[2] L^{-1}\). Calculate using calc_DO_sat

  • depth stream depth, \(m\).

  • temp.water water temperature, \(degC\).

  • light photosynthetically active radiation, \(\mu mol\ m^{-2} s^{-1}\)

  • date dates of interest in Date format

  • err.obs.sigma SD of observation error to use in simulating data

  • err.obs.phi autocorrelation of observation error to use in simulating data

  • err.proc.sigma SD of process error to use in simulating data

  • err.proc.phi autocorrelation of process error to use in simulating data

  • DO.obs dissolved oxygen concentration observations, \(mg O[2] L^{-1}\)

  • GPP daily estimates of GPP, \(g O[2] m^-2 d^-1\)

  • ER daily estimates of ER, \(g O[2] m^-2 d^-1\)

  • K600 daily estimates of K600, \(d^-1\)

  • GPP.init daily initial values of GPP, \(g O[2] m^-2 d^-1\), for use in maximum likelihood estimation

  • ER.init daily initial values of ER, \(g O[2] m^-2 d^-1\), for use in maximum likelihood estimation

  • K600.init daily initial values of K600, \(d^-1\), for use in maximum likelihood estimation

  • discharge.daily daily mean river discharge, \(m^3 s^-1\)

  • velocity.daily daily mean river flow velocity, \(m s^-1\)

Usage

mm_data(..., optional = "none")

Arguments

...

column names to select, as passed to select

optional

one or more character strings listing the columns, if any, that may be excluded. If 'all', the entire data.frame may be omitted. If 'none', the entire data.frame must be included as prototyped. If specific column names are given, those columns may be omitted entirely or passed to metab() as all NAs.

Value

data data.frame with columns as in the description

Details

Most models will require a subset of these data columns. Specialized models may deviate from this format, but this is discouraged.

Examples

# all possible columns
mm_data()
#>            solar.time    DO.obs    DO.sat depth temp.water          light
#> U                     mgO2 L^-1 mgO2 L^-1     m       degC umol m^-2 s^-1
#> 1 2050-03-14 15:10:00      10.1      14.2   0.5       21.8          300.9
#>   discharge velocity       date  DO.mod.1 err.obs.sigma err.obs.phi
#> U  m^3 s^-1   m s^-1            mgO2 L^-1     mgO2 L^-1            
#> 1         9        2 2050-03-14       7.5          0.01           0
#>   err.proc.sigma err.proc.phi     GPP.daily          Pmax              alpha
#> U  gO2 d^-1 m^-2              gO2 d^-1 m^-2 gO2 d^-1 m^-2 gO2 s d^-1 umol^-1
#> 1              5            0             5            10              1e-04
#>        ER.daily          ER20 K600.daily K600.daily.lower K600.daily.upper
#> U gO2 d^-1 m^-2 gO2 d^-1 m^-2       d^-1             d^-1             d^-1
#> 1           -10           -10         10              4.5             15.6
#>   init.GPP.daily     init.Pmax         init.alpha init.ER.daily     init.ER20
#> U  gO2 d^-1 m^-2 gO2 d^-1 m^-2 gO2 s d^-1 umol^-1 gO2 d^-1 m^-2 gO2 d^-1 m^-2
#> 1              5            10              1e-04           -10           -10
#>   init.K600.daily discharge.daily velocity.daily           GPP     GPP.lower
#> U            d^-1        m^3 s^-1         m s^-1 gO2 d^-1 m^-2 gO2 d^-1 m^-2
#> 1              10               9              2             5             4
#>       GPP.upper            ER      ER.lower      ER.upper             D
#> U gO2 d^-1 m^-2 gO2 d^-1 m^-2 gO2 d^-1 m^-2 gO2 d^-1 m^-2 gO2 d^-1 m^-3
#> 1             6            -5            -6            -4             5
#>         D.lower       D.upper
#> U gO2 d^-1 m^-3 gO2 d^-1 m^-3
#> 1             5             5

# columns typical of instantaneous data
mm_data(solar.time, DO.obs, DO.sat, depth, temp.water, light)
#>            solar.time    DO.obs    DO.sat depth temp.water          light
#> U                     mgO2 L^-1 mgO2 L^-1     m       degC umol m^-2 s^-1
#> 1 2050-03-14 15:10:00      10.1      14.2   0.5       21.8          300.9

# columns typical of daily data
mm_data(date, K600.daily, discharge.daily, velocity.daily)
#>         date K600.daily discharge.daily velocity.daily
#> U                  d^-1        m^3 s^-1         m s^-1
#> 1 2050-03-14         10               9              2