GaudinskiModel14: Implementation of a the six-pool C14 model proposed by...

In SoilR: Models of Soil Organic Matter Decomposition

Implementation of a the six-pool C14 model proposed by Gaudinski et al. 2000

Description

This function creates a model as described in Gaudinski et al. 2000. It is a wrapper for the more general functions GeneralModel_14 that can handle an arbitrary number of pools.

Usage

GaudinskiModel14(
  t,
  ks = c(kr = 1/1.5, koi = 1/1.5, koeal = 1/4, koeah = 1/80, kA1 = 1/3, kA2 = 1/75, kM =
    1/110),
  C0 = c(FR0 = 390, C10 = 220, C20 = 390, C30 = 1370, C40 = 90, C50 = 1800, C60 = 560),
  F0_Delta14C = rep(0, 7),
  LI = 150,
  RI = 255,
  xi = 1,
  inputFc,
  lambda = -0.0001209681,
  lag = 0,
  solver = deSolve.lsoda.wrapper,
  pass = FALSE
)

Arguments

t	A vector containing the points in time where the solution is sought. It must be specified within the same period for which the Delta 14 C of the atmosphere is provided. The default period in the provided dataset C14Atm_NH is 1900-2010.
ks	A vector of length 7 containing the decomposition rates for the 6 soil pools plus the fine-root pool.
C0	A vector of length 7 containing the initial amount of carbon for the 6 pools plus the fine-root pool.
F0_Delta14C	A vector of length 7 containing the initial amount of the radiocarbon fraction for the 7 pools as Delta14C values in per mil.
LI	A scalar or a data.frame object specifying the amount of litter inputs by time.
RI	A scalar or a data.frame object specifying the amount of root inputs by time.
xi	A scalar or a data.frame specifying the external (environmental and/or edaphic) effects on decomposition rates.
inputFc	A Data Frame object containing values of atmospheric Delta14C per time. First column must be time values, second column must be Delta14C values in per mil.
lambda	Radioactive decay constant. By default lambda=-0.0001209681 y^-1 . This has the side effect that all your time related data are treated as if the time unit was year.
lag	A positive integer representing a time lag for radiocarbon to enter the system.
solver	A function that solves the system of ODEs. An alternative to the default is euler or any other user provided function with the same interface.
pass	if TRUE Forces the constructor to create the model even if it is invalid

Value

A Model Object that can be further queried

References

Gaudinski JB, Trumbore SE, Davidson EA, Zheng S (2000) Soil carbon cycling in a temperate forest: radiocarbon-based estimates of residence times, sequestration rates and partitioning fluxes. Biogeochemistry 51: 33-69

See Also

There are other predefinedModels and also more general functions like Model.

Examples

years=seq(1901,2010,by=0.5)

Ex=GaudinskiModel14(
t=years,
ks=c(kr=1/3, koi=1/1.5, koeal=1/4, koeah=1/80, kA1=1/3, kA2=1/75, kM=1/110),
inputFc=C14Atm_NH
)
R14m=getF14R(Ex)
C14m=getF14C(Ex)

plot(
C14Atm_NH,
type="l",
xlab="Year",
ylab=expression(paste(Delta^14,"C (per mille)")),
xlim=c(1940,2010)
) 
lines(years,C14m,col=4)
points(HarvardForest14CO2[1:11,1],HarvardForest14CO2[1:11,2],pch=19,cex=0.5)
points(HarvardForest14CO2[12:173,1],HarvardForest14CO2[12:173,2],pch=19,col=2,cex=0.5)
points(HarvardForest14CO2[158,1],HarvardForest14CO2[158,2],pch=19,cex=0.5)
lines(years,R14m,col=2)
legend(
"topright",
c("Delta 14C Atmosphere",
"Delta 14C SOM", 
"Delta 14C Respired"
),
lty=c(1,1,1), 
col=c(1,4,2),
bty="n"
)
## We now show how to bypass soilR s parameter sanity check if nacessary 
## (e.g in for parameter estimation ) in functions
## which might call it with unreasonable parameters
years=seq(1800,2010,by=0.5)
Ex=GaudinskiModel14(
t=years,
ks=c(kr=1/3,koi=1/1.5,koeal=1/4,koeah=1/80,kA1=1/3,kA2=1/75,kM=1/110),
inputFc=C14Atm_NH,
pass=TRUE
)

SoilR documentation built on Oct. 13, 2023, 5:06 p.m.