Nothing
#' automatic title
#'
#' @param .Object no manual documentation
#' @param starttime no manual documentation
#' @param endtime no manual documentation
#' @param numberOfPools no manual documentation
#' @param alpha no manual documentation
#' @param f no manual documentation
#' @param lag no manual documentation
#' @autocomment These comments were created by the auto_comment_roclet by
#' inspection of the code. You can use the "update_auto_comment_roclet" to
#' automatically adapt them to changes in the source code. This will remove
#' `@param` tags for parameters that are no longer present in the source code
#' and add `@param` tags with a default description for yet undocumented
#' parameters. If you remove this `@autocomment` tag your comments will no
#' longer be touched by the "update_autocomment_roclet".
setMethod(
f="initialize",
signature="TransportDecompositionOperator",
definition=function(
.Object,
starttime=numeric(),
endtime=numeric(),
numberOfPools=1,
alpha=list(),
f=function(t,O){t},
lag=0
){
.Object@starttime=starttime
.Object@endtime=endtime
.Object@numberOfPools=numberOfPools
.Object@alpha=alpha
.Object@f=f
return(.Object)
}
)
#fromToSplitter=function(){"_to_"}
getRecipient=function(stri){
as.numeric(unlist(strsplit(stri,split=fromToSplitter()))[[2]])
}
getSender=function(stri){
as.numeric(unlist(strsplit(stri,split=fromToSplitter()))[[1]])
}
#' automatic title
#'
#' @param object no manual documentation
#' @autocomment These comments were created by the auto_comment_roclet by
#' inspection of the code. You can use the "update_auto_comment_roclet" to
#' automatically adapt them to changes in the source code. This will remove
#' `@param` tags for parameters that are no longer present in the source code
#' and add `@param` tags with a default description for yet undocumented
#' parameters. If you remove this `@autocomment` tag your comments will no
#' longer be touched by the "update_autocomment_roclet".
setMethod(
f= "getDotOut",
signature(object="TransportDecompositionOperator"),
definition=function(object){
return(object@f)
}
)
#' automatic title
#'
#' @param object no manual documentation
#' @autocomment These comments were created by the auto_comment_roclet by
#' inspection of the code. You can use the "update_auto_comment_roclet" to
#' automatically adapt them to changes in the source code. This will remove
#' `@param` tags for parameters that are no longer present in the source code
#' and add `@param` tags with a default description for yet undocumented
#' parameters. If you remove this `@autocomment` tag your comments will no
#' longer be touched by the "update_autocomment_roclet".
setMethod(
f= "getCompartmentalMatrixFunc",
signature(object="TransportDecompositionOperator"),
definition=function(object){
NFunc<-function(C,t){
outFluxVectorFunc=object@f
outFluxVec=outFluxVectorFunc(C,t)
n_vec=as.numeric(outFluxVec/C)
Nmat <- diag(n_vec)
Nmat
}
TFunc=getTransferMatrixFunc(object)
BFunc<-function(C,t){
T <- TFunc(C,t)
N <- NFunc(C,t)
B <- T%*%N
B
}
return(BFunc)
}
)
#' automatic title
#'
#' @param object no manual documentation
#' @param i no manual documentation
#' @autocomment These comments were created by the auto_comment_roclet by
#' inspection of the code. You can use the "update_auto_comment_roclet" to
#' automatically adapt them to changes in the source code. This will remove
#' `@param` tags for parameters that are no longer present in the source code
#' and add `@param` tags with a default description for yet undocumented
#' parameters. If you remove this `@autocomment` tag your comments will no
#' longer be touched by the "update_autocomment_roclet".
setMethod(
f= "getOutputReceivers",
signature(object="TransportDecompositionOperator",i="numeric"),
definition=function(object,i){
keys <- names(object@alpha)
pattern <- paste("^",i,sep="");
mask <- grepl(pattern,keys)
js=unlist(lapply(keys[mask],getRecipient))
return(js)
}
)
#setMethod(
# f= "getTransferMatrix",
# signature(object="TransportDecompositionOperator"),
# definition=function(object){
# # fixme mm
# # add a deprecation warning in the generic
# return(getTransferMatrixFunc(object))
# }
#)
#' automatic title
#'
#' @param object no manual documentation
#' @autocomment These comments were created by the auto_comment_roclet by
#' inspection of the code. You can use the "update_auto_comment_roclet" to
#' automatically adapt them to changes in the source code. This will remove
#' `@param` tags for parameters that are no longer present in the source code
#' and add `@param` tags with a default description for yet undocumented
#' parameters. If you remove this `@autocomment` tag your comments will no
#' longer be touched by the "update_autocomment_roclet".
setMethod(
f= "getTransferMatrixFunc",
signature(object="TransportDecompositionOperator"),
definition=function(object){
alpha=object@alpha
np=object@numberOfPools
m=matrix(nrow=np,ncol=np,0)
for (i in 1:np){m[i,i]=-1}
keys=names(alpha)
Tr=function(C,t){
for (key in keys){
m[getRecipient(key),getSender(key)]=alpha[[key]](C,t)
}
return(m)
}
return(Tr)
}
)
#' automatic title
#'
#' @param object no manual documentation
#' @autocomment These comments were created by the auto_comment_roclet by
#' inspection of the code. You can use the "update_auto_comment_roclet" to
#' automatically adapt them to changes in the source code. This will remove
#' `@param` tags for parameters that are no longer present in the source code
#' and add `@param` tags with a default description for yet undocumented
#' parameters. If you remove this `@autocomment` tag your comments will no
#' longer be touched by the "update_autocomment_roclet".
setMethod(
f= "getTransferCoefficients",
signature(object="TransportDecompositionOperator"),
definition=function(object){
return(object@alpha)
}
)
#' automatic title
#'
#' @param object no manual documentation
#' @autocomment These comments were created by the auto_comment_roclet by
#' inspection of the code. You can use the "update_auto_comment_roclet" to
#' automatically adapt them to changes in the source code. This will remove
#' `@param` tags for parameters that are no longer present in the source code
#' and add `@param` tags with a default description for yet undocumented
#' parameters. If you remove this `@autocomment` tag your comments will no
#' longer be touched by the "update_autocomment_roclet".
setMethod(
f= "getNumberOfPools",
signature(object="TransportDecompositionOperator"),
definition=function(object){
return(object@numberOfPools)
}
)
#' automatic title
#'
#' @param object no manual documentation
#' @autocomment These comments were created by the auto_comment_roclet by
#' inspection of the code. You can use the "update_auto_comment_roclet" to
#' automatically adapt them to changes in the source code. This will remove
#' `@param` tags for parameters that are no longer present in the source code
#' and add `@param` tags with a default description for yet undocumented
#' parameters. If you remove this `@autocomment` tag your comments will no
#' longer be touched by the "update_autocomment_roclet".
setMethod(
f="getFunctionDefinition",
signature(object="TransportDecompositionOperator"),
definition=function(object){
return(object@f)
}
)
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