diff options
Diffstat (limited to 'R/mkinmod.R')
| -rw-r--r-- | R/mkinmod.R | 20 |
1 files changed, 13 insertions, 7 deletions
diff --git a/R/mkinmod.R b/R/mkinmod.R index 491b3d0a..2805ef54 100644 --- a/R/mkinmod.R +++ b/R/mkinmod.R @@ -1,4 +1,4 @@ -# Copyright (C) 2010-2015 Johannes Ranke {{{
+# Copyright (C) 2010-2015,2019 Johannes Ranke {{{
# Contact: jranke@uni-bremen.de
# This file is part of the R package mkin
@@ -42,8 +42,8 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verb parms <- vector()
# }}}
- # Do not return a coefficient matrix mat when FOMC, IORE, DFOP or HS is used for the parent {{{
- if(spec[[1]]$type %in% c("FOMC", "IORE", "DFOP", "HS")) {
+ # Do not return a coefficient matrix mat when FOMC, IORE, DFOP, HS or logistic is used for the parent {{{
+ if(spec[[1]]$type %in% c("FOMC", "IORE", "DFOP", "HS", "logistic")) {
mat = FALSE
} else mat = TRUE
#}}}
@@ -57,10 +57,10 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verb # 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", "IORE", "DFOP", "HS", "SFORB")) stop(
- "Available types are SFO, FOMC, IORE, DFOP, HS and SFORB only")
- if(spec[[varname]]$type %in% c("FOMC", "DFOP", "HS") & match(varname, obs_vars) != 1) {
- stop(paste("Types FOMC, DFOP and HS are only implemented for the first compartment,",
+ if(!spec[[varname]]$type %in% c("SFO", "FOMC", "IORE", "DFOP", "HS", "SFORB", "logistic")) stop(
+ "Available types are SFO, FOMC, IORE, DFOP, HS, SFORB and logistic only")
+ if(spec[[varname]]$type %in% c("FOMC", "DFOP", "HS", "logistic") & match(varname, obs_vars) != 1) {
+ stop(paste("Types FOMC, DFOP, HS and logistic are only implemented for the first compartment,",
"which is assumed to be the source compartment"))
}
#}}}
@@ -71,6 +71,7 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verb IORE = varname,
DFOP = varname,
HS = varname,
+ logistic = varname,
SFORB = paste(varname, c("free", "bound"), sep = "_")
)
map[[varname]] <- new_boxes
@@ -141,6 +142,11 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verb decline_term <- paste(HS_decline, "*", box_1)
parms <- c(parms, "k1", "k2", "tb")
} #}}}
+ if(spec[[varname]]$type == "logistic") { # {{{ Add logistic decline term
+ # From p. 67 of the FOCUS kinetics report (2014)
+ decline_term <- paste("(k0 * kmax)/(k0 + (kmax - k0) * exp(-r * time)) *", box_1)
+ parms <- c(parms, "kmax", "k0", "r")
+ } #}}}
# Add origin decline term to box 1 (usually the only box, unless type is SFORB)#{{{
diffs[[box_1]] <- paste(diffs[[box_1]], "-", decline_term)#}}}
if(spec[[varname]]$type == "SFORB") { # {{{ Add SFORB reversible binding terms
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