diff options
Diffstat (limited to 'R/mkinmod.R')
| -rw-r--r-- | R/mkinmod.R | 54 |
1 files changed, 38 insertions, 16 deletions
diff --git a/R/mkinmod.R b/R/mkinmod.R index eb290719..8b86303f 100644 --- a/R/mkinmod.R +++ b/R/mkinmod.R @@ -1,4 +1,4 @@ -# Copyright (C) 2010-2013 Johannes Ranke {{{
+# Copyright (C) 2010-2014 Johannes Ranke {{{
# Contact: jranke@uni-bremen.de
# This file is part of the R package mkin
@@ -33,38 +33,39 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL) stop("The use of formation fractions 'use_of_ff' can only be 'min' or 'max'")
# The returned model will be a list of character vectors, containing {{{
- # differential equations, parameter names and a mapping from model variables
- # to observed variables. If possible, a matrix representation of the
- # differential equations is included
+ # differential equations (if supported), parameter names and a mapping from
+ # model variables to observed variables. If possible, a matrix representation
+ # of the differential equations is included
parms <- vector()
- diffs <- vector()
- map <- list()
# }}}
- # Do not return a coefficient matrix mat when FOMC, DFOP or HS are used for
- # the parent compound {{{
- if(spec[[1]]$type %in% c("FOMC", "DFOP", "HS")) {
+ # Do not return a coefficient matrix mat when FOMC, IORE, DFOP or HS is used for the parent {{{
+ if(spec[[1]]$type %in% c("FOMC", "IORE", "DFOP", "HS")) {
mat = FALSE
} else mat = TRUE
#}}}
# Establish a list of differential equations as well as a map from observed {{{
# compartments to differential equations
+ diffs <- vector()
+ map <- list()
for (varname in obs_vars)
{
# Check the type component of the compartment specification {{{
if(is.null(spec[[varname]]$type)) stop(
"Every part of the model specification must be a list containing a type component")
- if(!spec[[varname]]$type %in% c("SFO", "FOMC", "DFOP", "HS", "SFORB")) stop(
- "Available types are SFO, FOMC, DFOP, HS and SFORB only")
+ if(!spec[[varname]]$type %in% c("SFO", "FOMC", "IORE", "DFOP", "HS", "SFORB")) stop(
+ "Available types are SFO, FOMC, IORE, DFOP, HS and SFORB only")
if(spec[[varname]]$type %in% c("FOMC", "DFOP", "HS") & match(varname, obs_vars) != 1) {
stop(paste("Types FOMC, DFOP and HS are only implemented for the first compartment,",
"which is assumed to be the source compartment"))
- } #}}}
+ }
+ #}}}
# New (sub)compartments (boxes) needed for the model type {{{
new_boxes <- switch(spec[[varname]]$type,
SFO = varname,
FOMC = varname,
+ IORE = varname,
DFOP = varname,
HS = varname,
SFORB = paste(varname, c("free", "bound"), sep = "_")
@@ -85,20 +86,40 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL) # Turn on sink if this is not explicitly excluded by the user by
# specifying sink=FALSE
if(is.null(spec[[varname]]$sink)) spec[[varname]]$sink <- TRUE
- if(spec[[varname]]$type %in% c("SFO", "SFORB")) { # {{{ Add SFO or SFORB decline term
+ if(spec[[varname]]$type %in% c("SFO", "IORE", "SFORB")) { # {{{ Add decline term
if (use_of_ff == "min") { # Minimum use of formation fractions
if(spec[[varname]]$sink) {
- # If sink is required, add first-order sink term
+ if(spec[[varname]]$type == "IORE" && length(spec[[varname]]$to) > 0) {
+ stop("Transformation reactions from compounds modelled with IORE\n",
+ "are only supported with formation fractions (use_of_ff = 'max')")
+ }
+ # If sink is required, add first-order/IORE sink term
k_compound_sink <- paste("k", box_1, "sink", sep = "_")
+ if(spec[[varname]]$type == "IORE") {
+ k_compound_sink <- paste("k.iore", box_1, "sink", sep = "_")
+ }
parms <- c(parms, k_compound_sink)
decline_term <- paste(k_compound_sink, "*", box_1)
+ if(spec[[varname]]$type == "IORE") {
+ N <- paste("N", box_1, sep = "_")
+ parms <- c(parms, N)
+ decline_term <- paste0(decline_term, "^", N)
+ }
} else { # otherwise no decline term needed here
decline_term = "0"
}
} else {
k_compound <- paste("k", box_1, sep = "_")
+ if(spec[[varname]]$type == "IORE") {
+ k_compound <- paste("k.iore", box_1, sep = "_")
+ }
parms <- c(parms, k_compound)
decline_term <- paste(k_compound, "*", box_1)
+ if(spec[[varname]]$type == "IORE") {
+ N <- paste("N", box_1, sep = "_")
+ parms <- c(parms, N)
+ decline_term <- paste0(decline_term, "^", N)
+ }
}
} #}}}
if(spec[[varname]]$type == "FOMC") { # {{{ Add FOMC decline term
@@ -157,9 +178,10 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL) for (target in to) {
target_box <- switch(spec[[target]]$type,
SFO = target,
+ IORE = target,
SFORB = paste(target, "free", sep = "_"))
- if (use_of_ff == "min" && spec[[varname]]$type %in% c("SFO",
- "SFORB")) {
+ if (use_of_ff == "min" && spec[[varname]]$type %in% c("SFO", "SFORB"))
+ {
k_from_to <- paste("k", origin_box, target_box, sep = "_")
parms <- c(parms, k_from_to)
diffs[[origin_box]] <- paste(diffs[[origin_box]], "-",
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