FESDIAvars: Functions to retrieve variables for the PHDIA and FESDIA...

In FESDIA: Diagenetic model including Fe, S and CH4 dynamics

Description

FESDIA0D, FESDIA1D, FESDIAsvar retrieve the (0-dimensional or 1-dimensional) output variables or state variables of FESDIA model solutions. When called with out not specified, will return the names of these variables and their units.

PHDIA0D, PHDIA1D, PHDIAsvar retrieve the (0-dimensional or 1-dimensional) output variables or state variables of PHDIA model solutions. When called with out not specified, will return the names of these variables and their units.

FESDIAextract extracts model output variables of any dimension.

FESDIApH estimates the pH profile(s) from FESDIA model solutions.

Usage

  FESDIA0D(out, as.vector = FALSE, which = NULL) 
  FESDIA1D(out, which = NULL) 
  FESDIAsvar(out, which = NULL) 
  
  PHDIA0D(out, as.vector = FALSE, which = NULL) 
  PHDIA1D(out, which = NULL) 
  PHDIAsvar(out, which = NULL) 
  
  FESDIAextract(out, which = NULL) 
  FESDIApH(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 variables to return.

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 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

# =====================
# defaults
# =====================

  FESDIAsvar()
  head(FESDIA0D())
  FESDIA1D()
  
# =====================
# variables of runs  
# =====================

# defaults
  defsteady <- FESDIAsolve()
  defdyn    <- FESDIAdyna()

# altered steady-state run
  out  <- FESDIAsolve(parms = list(Cflux = 10))
  dyna <- FESDIAdyna(parms = list(Cflux = 10), CfluxForc = list(amp = 1))

# 0-D outputs
  cbind(steady.default = FESDIA0D(defsteady, as.vector = TRUE), 
        dyna.default   = FESDIA0D(defdyn, as.vector = TRUE), 
        out            = FESDIA0D(out,  as.vector = TRUE),
        dyna           = FESDIA0D(dyna, as.vector = TRUE))

# 1-D outputs
  head(FESDIA1D(out))
  head(FESDIA1D(defdyn, which = c("O2", "TOC")))

# and the pH
  mf <- par (mfrow = c(1,2))
  plot(x = FESDIApH(out), y = FESDIAdepth(dyna), ylim = c(10,0), type = "l")

  image2D(FESDIApH(dyna), y = FESDIAdepth(dyna), ylim = c(10,0))


  par(mfrow = mf)

FESDIA documentation built on April 22, 2021, 3 p.m.