diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/endpoints.R | 14 | ||||
| -rw-r--r-- | R/mkinfit.R | 14 | ||||
| -rw-r--r-- | R/mkinmod.R | 1 |
3 files changed, 27 insertions, 2 deletions
diff --git a/R/endpoints.R b/R/endpoints.R index 163dc8d..c9a6a51 100644 --- a/R/endpoints.R +++ b/R/endpoints.R @@ -11,6 +11,20 @@ endpoints <- function(fit, pseudoDT50 = FALSE) { ep$SFORB <- vector()
for (obs_var in obs_vars) {
type = names(fit$mkinmod$map[[obs_var]])[1]
+
+ # Get formation fractions if directly fitted, and calculate remaining fraction to sink
+ f_names = grep(paste("f", obs_var, sep = "_"), names(parms.all), value=TRUE)
+ f_values = parms.all[f_names]
+ f_to_sink = 1 - sum(f_values)
+ names(f_to_sink) = ifelse(type == "SFORB",
+ paste(obs_var, "free", "sink", sep = "_"),
+ paste(obs_var, "sink", sep = "_"))
+ for (f_name in f_names) {
+ ep$ff[[sub("f_", "", sub("_to_", "_", f_name))]] = f_values[[f_name]]
+ }
+ ep$ff = append(ep$ff, f_to_sink)
+
+ # Get the rest
if (type == "SFO") {
k_names = grep(paste("k", obs_var, sep="_"), names(parms.all), value=TRUE)
k_tot = sum(parms.all[k_names])
diff --git a/R/mkinfit.R b/R/mkinfit.R index b80be97..cf018f0 100644 --- a/R/mkinfit.R +++ b/R/mkinfit.R @@ -28,6 +28,8 @@ mkinfit <- function(mkinmod, observed, fixed_parms = NULL,
fixed_initials = names(mkinmod$diffs)[-1],
solution_type = "auto",
+ method.modFit = "Marq",
+ control.modFit = list(),
plot = FALSE, quiet = FALSE,
err = NULL, weight = "none", scaleVar = FALSE,
atol = 1e-8, rtol = 1e-10, n.outtimes = 100,
@@ -45,6 +47,13 @@ mkinfit <- function(mkinmod, observed, # Define starting values for parameters where not specified by the user
if (parms.ini[[1]] == "auto") parms.ini = vector()
+
+ # Prevent inital parameter specifications that are not in the model
+ wrongpar.names <- setdiff(names(parms.ini), mkinmod$parms)
+ if (length(wrongpar.names) > 0) {
+ stop("Initial parameter(s) ", paste(wrongpar.names, collapse = ", "), " not used in the model")
+ }
+
defaultpar.names <- setdiff(mkinmod$parms, names(parms.ini))
for (parmname in defaultpar.names) {
# Default values for rate constants, depending on the parameterisation
@@ -168,7 +177,7 @@ mkinfit <- function(mkinmod, observed, }
return(mC)
}
- fit <- modFit(cost, c(state.ini.optim, parms.optim), ...)
+ fit <- modFit(cost, c(state.ini.optim, parms.optim), method = method.modFit, control = control.modFit, ...)
# We need to return some more data for summary and plotting
fit$solution_type <- solution_type
@@ -203,6 +212,7 @@ mkinfit <- function(mkinmod, observed, fit$data <- data[order(data$variable, data$time), ]
fit$atol <- atol
fit$rtol <- rtol
+
# Return all backtransformed parameters for summary
fit$bparms.optim <- bparms.optim
fit$bparms.fixed <- bparms.fixed
@@ -239,7 +249,7 @@ summary.mkinfit <- function(object, data = TRUE, distimes = TRUE, alpha = 0.05, dimnames(param) <- list(pnames, c("Estimate", "Std. Error", "Lower", "Upper"))
blci <- buci <- numeric()
- # Only use lower end of CI for one parameter at a time
+ # Only transform boundaries of CI for one parameter at a time
for (pname in pnames) {
par.lower <- par.upper <- object$par
par.lower[pname] <- param[pname, "Lower"]
diff --git a/R/mkinmod.R b/R/mkinmod.R index adfd9ea..09deea4 100644 --- a/R/mkinmod.R +++ b/R/mkinmod.R @@ -26,6 +26,7 @@ mkinmod <- function(..., use_of_ff = "min") # 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 (grepl("_to_", obs_var)) stop("Sorry, names of observed variables can not contain _to_")
}
if (!use_of_ff %in% c("min", "max"))
|