diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2014-05-09 12:20:00 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2014-05-09 14:23:34 +0200 |
| commit | 824b3e1d4cbf1d4b5ca8dfb492c4a5b20e9de7d3 (patch) | |
| tree | dc7b08f1085970bf53310d07ceae5efb68778696 /R/mkinfit.R | |
| parent | 74f43ad7dcdff91f406bfa1e68e084ed85000035 (diff) | |
Set upper and lower boundx for untransformed fractions
Diffstat (limited to 'R/mkinfit.R')
| -rw-r--r-- | R/mkinfit.R | 19 |
1 files changed, 16 insertions, 3 deletions
diff --git a/R/mkinfit.R b/R/mkinfit.R index f44c67d7..ab1977d1 100644 --- a/R/mkinfit.R +++ b/R/mkinfit.R @@ -209,7 +209,8 @@ mkinfit <- function(mkinmod, observed, }
lower <- rep(-Inf, length(c(state.ini.optim, parms.optim)))
- names(lower) <- c(names(state.ini.optim), names(parms.optim))
+ upper <- rep(Inf, length(c(state.ini.optim, parms.optim)))
+ names(lower) <- names(upper) <- c(names(state.ini.optim), names(parms.optim))
if (!transform_rates) {
index_k <- grep("^k_", names(lower))
lower[index_k] <- 0
@@ -217,8 +218,18 @@ mkinfit <- function(mkinmod, observed, lower[other_rate_parms] <- 0
}
+ if (!transform_fractions) {
+ index_f <- grep("^f_", names(upper))
+ lower[index_f] <- 0
+ upper[index_f] <- 1
+ other_fraction_parms <- intersect(c("g"), names(upper))
+ lower[other_fraction_parms] <- 0
+ upper[other_fraction_parms] <- 1
+ }
+
fit <- modFit(cost, c(state.ini.optim, parms.optim),
- method = method.modFit, control = control.modFit, lower = lower, ...)
+ method = method.modFit, control = control.modFit,
+ lower = lower, upper = upper, ...)
# Reiterate the fit until convergence of the variance components (IRLS)
# if requested by the user
@@ -243,7 +254,7 @@ 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, lower = lower, ...)
+ control = control.modFit, lower = lower, upper = upper, ...)
reweight.diff = sum((sqrt(fit$var_ms_unweighted) - sigma.old)^2)
if (!quiet) {
cat("Iteration", n.iter, "yields variance estimates:\n")
@@ -275,6 +286,8 @@ mkinfit <- function(mkinmod, observed, fit$start$type = c(rep("state", length(state.ini.optim)),
rep("deparm", length(parms.optim)))
fit$start$transformed = c(state.ini.optim, parms.optim)
+ fit$start$lower_bound = lower
+ fit$start$upper_bound = upper
fit$fixed <- data.frame(value = c(state.ini.fixed,
backtransform_odeparms(parms.fixed, mod_vars,
|