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Model layers

Source: R/cfp_layers_map.R
cfp_layers_map.Rd

A function to create a cfp_layers_map object that defines the layers of both fg_flux() and pro_flux() models.

Usage

cfp_layers_map(x, ...)

# S3 method for class 'cfp_dat'
cfp_layers_map(x, ...)

# S3 method for class 'data.frame'
cfp_layers_map(
  x,
  id_cols,
  gas = NULL,
  lowlim = NULL,
  highlim = NULL,
  layer_couple = 0,
  ...
)

Arguments

x

(data.frame) That defines the layers for which the production or flux is modeled. Note that some parameters can also be provided directly to the function call instead (see Details).

  • id_cols the relevant id_cols (see below)

  • gas, the gas that is modelled.

  • upper, lower the upper and lower boundaries of each layer

  • lowlim, highlim as the lower and upper limits of the production rate to be modeled in \(\mu~mol~m^{-3}\)

  • the parameter layer_couple, that indicates how strongly the layer should be linked to the one below it (0 for no coupling)

...

not used

id_cols

Column names in data.frame that uniquely identify each profile.

gas

(character vector) of gas names to be added to x which is then repeated for each gas.

lowlim

(numeric vector) the same length as gas with the lower limit of possible production allowed in pro_flux() models.

highlim

(numeric vector) the same length as gas with the upper limit of possible production allowed in pro_flux() models.

layer_couple

[Experimental] (numeric_vector) A vector the same length as gas that indicates how strongly the layer should be linked to the one below it (0 for no coupling, the default).

Value

A cfp_layered_profile() data.frame with the columns described above as well as layer and pmap columns that identify each layer with an integer (ascending from bottom to top).

Add lowlim and highlim for multiple gases

Sometimes it is practical to model different gases with different limits. For example, it is a reasonable assumption that CO2 is not consumed in relevant amounts in most soils, whereas CH4 may be both produced or consumed. Therefore we may want to limit production rates of CO2 to only positive values, whereas allowing for negative CH4 production rates (i.e. consumption) as well.

To make this setup easy, you can provide a gas vector to the function together with highlim and lowlim vectors of the same length. The provided layers_map data.frame will then be replicated for each gas with the respective values of the production limits provided.

See also

Other data formats: cfp_dat(), cfp_gasdata(), cfp_layered_profile(), cfp_profile(), cfp_soilphys()

Examples

cfp_layers_map(
   ConFluxPro::layers_map,
   gas = "CO2",
   lowlim = 0,
   highlim = 1000,
   id_cols = "site")
#> 
#> added 'gas' to id_cols
#> 
#> A cfp_layers_map object 
#> id_cols: site gas 
#> 2  unique profiles 
#> 
#>     site upper lower gas lowlim highlim layer_couple layer pmap
#> 1 site_a     0  -100 CO2      0    1000            0     1    1
#> 2 site_b     0  -100 CO2      0    1000            0     1    1
#> 3 site_a     5     0 CO2      0    1000            0     2    2
#> 4 site_b     7     0 CO2      0    1000            0     2    2

### add multiple gases at once
cfp_layers_map(
   ConFluxPro::layers_map,
   id_cols = "site",
   gas = c("CO2", "CH4"),
   lowlim = c(0, -1000),
   highlim = c(1000, 1000))
#> 
#> added 'gas' to id_cols
#> 
#> A cfp_layers_map object 
#> id_cols: site gas 
#> 4  unique profiles 
#> 
#>     site upper lower gas lowlim highlim layer_couple layer pmap
#> 1 site_a     0  -100 CO2      0    1000            0     1    1
#> 2 site_b     0  -100 CO2      0    1000            0     1    1
#> 3 site_a     0  -100 CH4  -1000    1000            0     1    1
#> 4 site_b     0  -100 CH4  -1000    1000            0     1    1
#> 5 site_a     5     0 CO2      0    1000            0     2    2
#> 6 site_a     5     0 CH4  -1000    1000            0     2    2
#> 7 site_b     7     0 CO2      0    1000            0     2    2
#> 8 site_b     7     0 CH4  -1000    1000            0     2    2

### Extract from an existing cfp_dat
cfp_layers_map(ConFluxPro::base_dat)
#> 
#> A cfp_layers_map object 
#> id_cols: site gas 
#> 2  unique profiles 
#> 
#>     site upper lower gas lowlim highlim layer_couple layer pmap
#> 1 site_a     0  -100 CO2      0    1000            0     1    1
#> 2 site_b     0  -100 CO2      0    1000            0     1    1
#> 3 site_a     5     0 CO2      0    1000            0     2    2
#> 4 site_b     7     0 CO2      0    1000            0     2    2