diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/mkinfit.R | 13 | ||||
| -rw-r--r-- | R/transform_odeparms.R | 4 |
2 files changed, 13 insertions, 4 deletions
diff --git a/R/mkinfit.R b/R/mkinfit.R index a623146..16b4ff3 100644 --- a/R/mkinfit.R +++ b/R/mkinfit.R @@ -208,8 +208,17 @@ mkinfit <- function(mkinmod, observed, return(mC)
}
+ lower <- rep(-Inf, length(c(state.ini.optim, parms.optim)))
+ names(lower) <- c(names(state.ini.optim), names(parms.optim))
+ if (!transform_rates) {
+ index_k <- grep("^k_", names(lower))
+ lower[index_k] <- 0
+ other_rate_parms <- intersect(c("alpha", "beta", "k1", "k2"), names(lower))
+ lower[other_rate_parms] <- 0
+ }
+
fit <- modFit(cost, c(state.ini.optim, parms.optim),
- method = method.modFit, control = control.modFit, ...)
+ method = method.modFit, control = control.modFit, lower = lower, ...)
# Reiterate the fit until convergence of the variance components (IRLS)
# if requested by the user
@@ -234,7 +243,7 @@ mkinfit <- function(mkinmod, observed, sigma.old <- sqrt(fit$var_ms_unweighted)
observed[err] <- sqrt(fit$var_ms_unweighted)[as.character(observed$name)]
fit <- modFit(cost, fit$par, method = method.modFit,
- control = control.modFit, ...)
+ control = control.modFit, lower = lower, ...)
reweight.diff = sum((sqrt(fit$var_ms_unweighted) - sigma.old)^2)
if (!quiet) {
cat("Iteration", n.iter, "yields variance estimates:\n")
diff --git a/R/transform_odeparms.R b/R/transform_odeparms.R index 31200c7..24de074 100644 --- a/R/transform_odeparms.R +++ b/R/transform_odeparms.R @@ -44,8 +44,8 @@ transform_odeparms <- function(parms, mod_vars, }
}
- # Transform parameters also for FOMC, DFOP and HS models if requested
- for (pname in c("alpha", "beta", "k1", "k2", "tb")) {
+ # Transform rate and fraction parameters also for FOMC, DFOP and HS models if requested
+ for (pname in c("alpha", "beta", "k1", "k2")) {
if (!is.na(parms[pname])) {
transparms[pname] <- ifelse(transform_rates, log(parms[pname]), parms[pname])
transparms[pname] <- ifelse(transform_rates, log(parms[pname]), parms[pname])
|