CNPDIAparms {CNPDIA}R Documentation

Functions to retrieve parameters, porosity, depth and sediment grid, irrigation and bioturbaion, for the CNPDIA and MPBDIA model.

Description

CNPDIAparms, CNPDIAdepth, CNPDIAdx retrieve the parameters, sediment depths and layer thicknesses of CNPDIA model solutions.

CNPDIAbiot, CNPDIApor, CNPDIAirr retrieve the bioturbation, porosity, and irrigation profiles of CNPDIA model solutions.

MPBDIAparms retrieves the parameters of the MPBDIA model

Usage

  CNPDIAparms(out = NULL, as.vector = FALSE, which = NULL)
  MPBDIAparms(out = NULL, as.vector = FALSE, which = NULL)
  CNPDIAdepth(out = NULL)
  CNPDIAgrid(out = NULL)
  CNPDIAdx(out = NULL)
  CNPDIApor(out)
  CNPDIAbiot(out)
  CNPDIAirr(out)

Arguments

out

an output object returned by CNPDIAsolve, MPBDIAsolve, or CNPDIAdyna, MPBDIAdyna. If NULL, CNPDIAparms or MPBDIAparms 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 variables/parameters to return.

Details

For the CNPDIA model, the parameters and their meaning are the following (with default values):

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


# defaults
  defparms  <- CNPDIAparms(as.vector = TRUE)
  defparms

# a run to work with  
  defsteady <- CNPDIAsolve()
  defdyn    <- CNPDIAdyna()

  out <- CNPDIAdyna(parms = list(Cflux = 1000), CfluxForc = list(amp = 0.8))

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

[Package CNPDIA version 1.0 Index]