diff options
Diffstat (limited to 'R/mkinmod.R')
| -rw-r--r-- | R/mkinmod.R | 24 |
1 files changed, 16 insertions, 8 deletions
diff --git a/R/mkinmod.R b/R/mkinmod.R index 5d8271a..adfd9ea 100644 --- a/R/mkinmod.R +++ b/R/mkinmod.R @@ -22,6 +22,12 @@ mkinmod <- function(..., use_of_ff = "min") {
spec <- list(...)
obs_vars <- names(spec)
+
+ # Check if any of the names of the observed variables contains any other
+ for (obs_var in obs_vars) {
+ if (length(grep(obs_var, obs_vars)) > 1) stop("Sorry, variable names can not contain each other")
+ }
+
if (!use_of_ff %in% c("min", "max"))
stop("The use of formation fractions 'use_of_ff' can only be 'min' or 'max'")
@@ -43,7 +49,7 @@ mkinmod <- function(..., use_of_ff = "min") "Only constant formation fractions over time are implemented.",
"Depending on the reason for the time dependence of degradation",
"this may be unrealistic. You may want to consider using the",
- "SFORB model",
+ "SFORB model",
sep="\n")
warning(message)
} else message <- "ok"
@@ -84,12 +90,11 @@ mkinmod <- function(..., use_of_ff = "min") {
# Get the name of the box(es) we are working on for the decline term(s)
box_1 = map[[varname]][[1]] # This is the only box unless type is SFORB
+ # 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]]$type %in% c("SFO", "SFORB")) { # {{{ Add SFO or SFORB decline term
if (use_of_ff == "min") { # Minimum use of formation fractions
- # Turn on sink if this is not explicitly excluded by the user by
- # specifying sink=FALSE
- if(is.null(spec[[varname]]$sink)) spec[[varname]]$sink <- TRUE
-
if(spec[[varname]]$sink) {
# If sink is required, add first-order sink term
k_compound_sink <- paste("k", box_1, "sink", sep="_")
@@ -103,7 +108,7 @@ mkinmod <- function(..., use_of_ff = "min") parms <- c(parms, k_compound)
decline_term <- paste(k_compound, "*", box_1)
}
- }#}}}
+ } #}}}
if(spec[[varname]]$type == "FOMC") { # {{{ Add FOMC decline term
# From p. 53 of the FOCUS kinetics report
decline_term <- paste("(alpha/beta) * ((time/beta) + 1)^-1 *", box_1)
@@ -132,7 +137,7 @@ mkinmod <- function(..., use_of_ff = "min") reversible_binding_term_2 <- paste("+", k_free_bound, "*", box_1, "-",
k_bound_free, "*", box_2)
} else { # Use formation fractions also for the free compartment
- stop("The maximum use of formation fractions is not supported for SFORB models")
+ stop("The maximum use of formation fractions is not supported for SFORB models")
# The problems were: Calculation of dissipation times did not work in this case
# and the coefficient matrix is not generated correctly by the code present
# in this file in this case
@@ -167,6 +172,9 @@ mkinmod <- function(..., use_of_ff = "min") diffs[[target_box]] <- paste(diffs[[target_box]], "+",
k_from_to, "*", origin_box)
} else {
+ if (!spec[[varname]]$sink) {
+ stop("Turning off the sink when using formation fractions is not supported")
+ }
fraction_to_target = paste("f", origin_box, "to", target, sep="_")
parms <- c(parms, fraction_to_target)
diffs[[target_box]] <- paste(diffs[[target_box]], "+",
@@ -240,4 +248,4 @@ mkinmod <- function(..., use_of_ff = "min") class(model) <- "mkinmod"
return(model)
}
-# vim: set foldmethod=marker:
+# vim: set foldmethod=marker ts=2 sw=2 expandtab:
|