diff options
Diffstat (limited to 'R/mkinfit.R')
| -rw-r--r-- | R/mkinfit.R | 13 |
1 files changed, 10 insertions, 3 deletions
diff --git a/R/mkinfit.R b/R/mkinfit.R index 59598631..7a465c2b 100644 --- a/R/mkinfit.R +++ b/R/mkinfit.R @@ -43,7 +43,7 @@ mkinfit <- function(mkinmod, observed, {
# Check mkinmod and generate a model for the variable whith the highest value
# if a suitable string is given
- parent_models_available = c("SFO", "FOMC", "DFOP", "HS", "SFORB")
+ parent_models_available = c("SFO", "FOMC", "DFOP", "HS", "SFORB", "IORE")
if (class(mkinmod) != "mkinmod") {
presumed_parent_name = observed[which.max(observed$value), "name"]
if (mkinmod[[1]] %in% parent_models_available) {
@@ -60,7 +60,10 @@ mkinfit <- function(mkinmod, observed, method.modFit = match.arg(method.modFit)
if (maxit.modFit != "auto") {
if (method.modFit == "Marq") control.modFit$maxiter = maxit.modFit
- if (method.modFit == "Port") control.modFit$iter.max = maxit.modFit
+ if (method.modFit == "Port") {
+ control.modFit$iter.max = maxit.modFit
+ control.modFit$eval.max = maxit.modFit
+ }
if (method.modFit %in% c("SANN", "Nelder-Mead", "BFGS", "CG", "L-BFGS-B")) {
control.modFit$maxit = maxit.modFit
}
@@ -116,13 +119,15 @@ mkinfit <- function(mkinmod, observed, defaultpar.names <- setdiff(mkinmod$parms, names(parms.ini))
for (parmname in defaultpar.names) {
# Default values for rate constants, depending on the parameterisation
- if (substr(parmname, 1, 2) == "k_") {
+ if (grepl("^k", parmname)) {
parms.ini[parmname] = 0.1 + k_salt
k_salt = k_salt + 1e-4
}
# Default values for rate constants for reversible binding
if (grepl("free_bound$", parmname)) parms.ini[parmname] = 0.1
if (grepl("bound_free$", parmname)) parms.ini[parmname] = 0.02
+ # Default values for IORE exponents
+ if (grepl("^N", parmname)) parms.ini[parmname] = 1
# Default values for the FOMC, DFOP and HS models
if (parmname == "alpha") parms.ini[parmname] = 1
if (parmname == "beta") parms.ini[parmname] = 10
@@ -306,6 +311,8 @@ mkinfit <- function(mkinmod, observed, if (!transform_rates) {
index_k <- grep("^k_", names(lower))
lower[index_k] <- 0
+ index_k.iore <- grep("^k.iore_", names(lower))
+ lower[index_k.iore] <- 0
other_rate_parms <- intersect(c("alpha", "beta", "k1", "k2", "tb"), names(lower))
lower[other_rate_parms] <- 0
}
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