FESDIAparms {FESDIA}R Documentation

Functions to retrieve parameters, porosity, depth and sediment grid, irrigation and bioturbation, for the FESDIA and PHDIA models

Description

PHDIAparms, FESDIAparms retrieve the parameters PHDIA and FESDIA model solutions.

FESDIAdepth, FESDIAdx retrieve the sediment depths and layer thicknesses of PHDIA or FESDIA model solutions.

FESDIAbiot, FESDIApor, FESDIAirr retrieve the bioturbation, porosity, and irrigation profiles of PHDIA and FESDIA model solutions.

Usage

  FESDIAparms(out = NULL, as.vector = FALSE, which = NULL)
  PHDIAparms(out = NULL, as.vector = FALSE, which = NULL)
  
  FESDIAdepth(out = NULL)
  FESDIAgrid(out = NULL)
  FESDIAbiot(out)
  FESDIApor(out)
  FESDIAirr(out)

Arguments

out

an output object returned by FESDIAsolve or FESDIAdyna. If NULL, FESDOIAparms will return the default (parameter) values.

as.vector

if TRUE will return the parameter vector, else a data.frame that also contains the units.

which

if not NULL, a vector with names of the parameters to return.

Details

The parameters and their meaning are the following (with default values):

Value

FESDIA0D and FESDIA1D return the output variables of the solution as a vector or data.frame. For dynamic runs, the output is averaged over the mean of the run.

FESDIA1D always returns the sediment depth and the porosity as the first two columns.

Author(s)

Karline Soetaert

References

Soetaert K, PMJ Herman and JJ Middelburg, 1996a. A model of early diagenetic processes from the shelf to abyssal depths. Geochimica Cosmochimica Acta, 60(6):1019-1040.

Soetaert K, PMJ Herman and JJ Middelburg, 1996b. Dynamic response of deep-sea sediments to seasonal variation: a model. Limnol. Oceanogr. 41(8): 1651-1668.

Examples


# default parameters
  defparms  <- FESDIAparms(as.vector = TRUE)
  defparms
  
# Some runs to work with  
  defsteady <- FESDIAsolve()
  defdyn    <- FESDIAdyna()

# altered steady-state run
  out <- FESDIAdyna(parms = list(Cflux = 10), CfluxForc = list(amp = 1))
  cbind(default = defparms, out = FESDIAparms(out))
  
# grid used for outputs

  pm <- par(mfrow = c(2, 2))
  plot(FESDIApor(out), FESDIAdepth(out), ylim = c(10,0), 
       type = "l", ylab = "cm", xlab = "-", main = "porosity")
  plot(FESDIAbiot(out), FESDIAdepth(out), ylim = c(10,0), 
       type = "l", ylab = "cm", xlab = "cm2/d", main = "bioturbation")
  image(out, which = "NH3", grid = FESDIAdepth(out), ylim = c(10,0), 
        main = "NH3", mfrow = NULL, legend = TRUE, ylab = "cm")
  matplot.1D(out, which = "NH3", xyswap = TRUE, grid = FESDIAdepth(out), 
        type = "l", col = "grey", ylim = c(10,0), mfrow = NULL, 
        ylab = "cm", xlab = "mmol/m3")      
        
  par(mfrow = pm)


[Package FESDIA version 1.0 Index]