R/OnepModel14.R

In SoilR: Models of Soil Organic Matter Decomposition

#' Implementation of a one-pool C14 model
#' 
#' This function creates a model for one pool. It is a wrapper for the more
#' general function \code{\link{GeneralModel_14}}.
#' 
#' 
#' @param 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
#' \code{\link{C14Atm_NH}} is 1900-2010.
#' @param k A scalar with the decomposition rate of the pool.
#' @param C0 A scalar containing the initial amount of carbon in the pool.
#' @param F0_Delta14C A scalar containing the initial amount of the radiocarbon
#' fraction in the pool in Delta_14C format.
#' @param In A scalar or a data.frame object specifying the amount of litter
#' inputs by time.
#' @param xi A scalar or a data.frame specifying the external (environmental
#' and/or edaphic) effects on decomposition rates.
#' @param inputFc A Data Frame object consisting of a function describing the
#' fraction of C_14 in per mille. The first column will be assumed to contain
#' the times.
#' @param 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.
#' @param lag A (positive) scalar representing a time lag for radiocarbon to
#' enter the system.
#' @param solver A function that solves the system of ODEs. This can be
#' \code{\link{euler}} or \code{\link{deSolve.lsoda.wrapper}} or any other user
#' provided function with the same interface.
#' @param pass if TRUE Forces the constructor to create the model even if it is
#' invalid
#' @seealso There are other \code{\link{predefinedModels}} and also more
#' general functions like \code{\link{Model_14}}.
#' @examples
#' years=seq(1901,2009,by=0.5)
#' LitterInput=700 
#' 
#' Ex=OnepModel14(t=years,k=1/10,C0=500, F0=0,In=LitterInput, inputFc=C14Atm_NH)
#' C14t=getF14(Ex)
#' 
#' plot(C14Atm_NH,type="l",xlab="Year",ylab="Delta 14C (per mil)",xlim=c(1940,2010)) 
#' lines(years, C14t[,1], col=4)
#' legend(
#' "topright",
#' c("Delta 14C Atmosphere", "Delta 14C in SOM"),
#' lty=c(1,1),
#' col=c(1,4),
#' lwd=c(1,1),
#' bty="n"
#' )
OnepModel14<- function 
  (  t, 
     k, 
     C0,	
     F0_Delta14C,  
     In,     
     xi=1,   
     inputFc, 
     lambda=-0.0001209681, 
     lag=0, 
     solver=deSolve.lsoda.wrapper, 
     pass=FALSE  
  )	
  { 
    t_start=min(t)
    t_stop=max(t)
    if(length(k)!=1) stop("k must be a scalar (length == 1)")
    if(length(C0)!=1) stop("initial conditions must be of length = 1")
    if(length(F0_Delta14C)!=1) stop("initial 14C fraction must be of length = 1")
    C0=c(C0)
    F0_Delta14C=c(F0_Delta14C)
    if(length(In)==1) inputFluxes=BoundInFluxes(
                                      function(t){matrix(nrow=1,ncol=1,In)},
                                      t_start,
                                      t_stop
                                      )
    if(inherits(In, "data.frame")){
      x=In[,1]  
      y=In[,2]  
      inputFlux=function(t0){as.numeric(spline(x,y,xout=t0)[2])}
      inputFluxes=BoundInFluxes(
                      function(t){matrix(nrow=1,ncol=1,inputFlux(t),0)},
                      t_start,
                      t_stop
                      )   
    }
    if(length(xi)==1) fX=function(t){xi}
    if(inherits(xi, "data.frame")){
      X=xi[,1]
      Y=xi[,2]
      fX=function(t){as.numeric(spline(X,Y,xout=t)[2])}
    }
    A=-abs(matrix(k,1,1))
    At=BoundLinDecompOp(
           function(t){
             fX(t)*A
           },
           t_start,
           t_stop
           ) 
    inputFc=BoundFc(inputFc,lag=lag,format="Delta14C")
    mod=GeneralModel_14(
      t,
      At,
      ivList=C0,
      initialValF=ConstFc(F0_Delta14C,"Delta14C"),
      inputFluxes=inputFluxes,
      inputFc,
      Fc=NULL,
      di=lambda,
      pass=pass
    )
  }