McCall 2,4,5-T dataset, lower bound for transform_rates=FALSE

1 files changed, 11 insertions, 2 deletions

diff --git a/R/mkinfit.R b/R/mkinfit.R
index a623146e..16b4ff3c 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")