R/UnBoundNonLinDecompOp_by_PoolNames.R

In SoilR: Models of Soil Organic Matter Decomposition

# #' A flux and pool name based representation of a possibly nonlinear and nonautonomous 
# #' Compartmental Matrix 
# #' 
# #' @param internal_fluxes \code{\link{InternalFluxList_by_PoolName}}
# #' @param out_fluxes \code{\link{OutFluxList_by_PoolName}}
# #' @param timeSymbol 
# setMethod(
#     f="UnBoundNonLinDecompOp_by_PoolNames",
#     signature=c(
#       internal_fluxes='InternalFluxList_by_PoolName'
#       ,out_fluxes='OutFluxList_by_PoolName'
#       ,timeSymbol='character'
#     ),
#     definition=function(
#       internal_fluxes
#       ,out_fluxes
#       ,timeSymbol
#       ) {
#           new(
#               'UnBoundNonLinDecompOp_by_PoolNames'
#               ,internal_fluxes=internal_fluxes
#               ,out_fluxes=out_fluxes
#               ,timeSymbol=timeSymbol
#           )
#       }
# )
# 
# #' Compartmental Matrix as function of the state vector and time
# #' 
# #' @param object An object of the class \code{UnBoundNonLinDecompOp_by_PoolNames} which is a representation equivalent to the compartmental matrix
# #' but independent of the order of state variables (pools) which therefore 
# #' can be translated to any such ordering. 
# #' @param timeSymbol The name of the argument representing time in the functions defining the fluxes in \code{object}
# #' @param state_variable_names The vector of the names of the state variables.
# #' The argument object is a representation of the compartmental system as #' lists of fluxes (internal fluxes and out-fluxes) as functions of the state variables and time. This method translates it to a matrix based formulation specific to a given ordering of the state variables.
# #' It is assumed (and checked) that the names formal arguments of the flux functions in \code{object} are a subset of the names of \code{state_variable_names} 
# #' The method is used internally to translate the more intuitive (and more general) flux based description to the matrix based description required by the ode solvers. 
# setMethod(
#     f="getCompartmentalMatrixFunc"
#     ,signature=signature(
#         object="UnBoundNonLinDecompOp_by_PoolNames"
#         ,timeSymbol='character'
#         ,state_variable_names='character'
#     )
#     ,definition=function(
#         object
#         ,timeSymbol
#         ,state_variable_names
#         ){ 
#         o_by_Index=UnBoundNonLinDecompOp(
#             state_variable_names=state_variable_names
#             ,timeSymbol=timeSymbol
#             ,operator=object
#         )
#         
#         o_by_Index@matFunc 
#     }
# )
# 
# #' convert to Indexed version
# setMethod(
#     f="UnBoundNonLinDecompOp",
#     signature=c(
#        matFunc="missing"
#       ,internal_fluxes='missing'
#       ,out_fluxes='missing'
#       ,numberOfPools='missing'
#       ,state_variable_names="character"
#       ,timeSymbol="character"
#       ,operator="UnBoundNonLinDecompOp_by_PoolNames"
#     ),
#     definition=function(state_variable_names,timeSymbol,operator){
#       internal_fluxes_by_index=by_PoolIndex(
#         obj         =   operator@internal_fluxes
#         ,poolNames  =   state_variable_names
#         ,timeSymbol =   timeSymbol
#       )
# 
#       out_fluxes_by_index=by_PoolIndex(
#         operator@out_fluxes
#         ,poolNames  =   state_variable_names
#         ,timeSymbol =   timeSymbol)
#       op_by_ind<-UnBoundNonLinDecompOp(
#         internal_fluxes =   internal_fluxes_by_index
#         ,out_fluxes     =   out_fluxes_by_index
#         ,numberOfPools  =   length(state_variable_names)
#       )
#     }
# )