diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/ilr.R | 7 | ||||
| -rw-r--r-- | R/mkinfit.R | 6 | ||||
| -rw-r--r-- | R/mkinmod.R | 6 | ||||
| -rw-r--r-- | R/mkinpredict.R | 4 |
4 files changed, 20 insertions, 3 deletions
@@ -40,5 +40,12 @@ invilr<-function(x) { for (i in 1:D) { z[i] <- exp(y[i])/sum(exp(y)) } + + # Work around a numerical problem with NaN values returned by the above + # Only works if there is only one NaN value: replace it with 1 + # if the sum of the other components is < 1e-10 + if (sum(is.na(z)) == 1 && sum(z[!is.na(z)]) < 1e-10) + z = ifelse(is.na(z), 1, z) + return(z) } diff --git a/R/mkinfit.R b/R/mkinfit.R index 37eee330..cf58a7d2 100644 --- a/R/mkinfit.R +++ b/R/mkinfit.R @@ -111,6 +111,9 @@ mkinfit <- function(mkinmod, observed, {
assign("calls", calls+1, inherits=TRUE) # Increase the model solution counter
+ # Trace parameter values if quiet is off
+ if(!quiet) cat(P, "\n")
+
# Time points at which observed data are available
# Make sure we include time 0, so initial values for state variables are for time 0
outtimes = sort(unique(c(observed$time,
@@ -305,7 +308,8 @@ mkinfit <- function(mkinmod, observed, data$variable <- ordered(data$variable, levels = obs_vars)
fit$data <- data[order(data$variable, data$time), ]
fit$atol <- atol
- fit$parms.all <- parms.all
+ fit$parms.all <- parms.all # Return all backtransformed parameters for summary
+ fit$odeparms.final <- parms.all[mkinmod$parms] # Return ode parameters for further fitting
class(fit) <- c("mkinfit", "modFit")
return(fit)
diff --git a/R/mkinmod.R b/R/mkinmod.R index 54b3b5f4..41dbefa8 100644 --- a/R/mkinmod.R +++ b/R/mkinmod.R @@ -92,7 +92,7 @@ mkinmod <- function(..., use_of_ff = "min") parms <- c(parms, k_compound_sink)
decline_term <- paste(k_compound_sink, "*", box_1)
} else { # otherwise no decline term needed here
- decline_term = ""
+ decline_term = "0"
}
} else {
k_compound <- paste("k", box_1, sep="_")
@@ -128,6 +128,10 @@ mkinmod <- function(..., use_of_ff = "min") reversible_binding_term_2 <- paste("+", k_free_bound, "*", box_1, "-",
k_bound_free, "*", box_2)
} else { # Use formation fractions also for the free compartment
+ stop("The maximum use of formation fractions is not supported for SFORB models")
+ # The problems were: Calculation of dissipation times did not work in this case
+ # and the coefficient matrix is not generated correctly by the code present
+ # in this file in this case
f_free_bound <- paste("f", varname, "free", "bound", sep="_")
k_bound_free <- paste("k", varname, "bound", "free", sep="_")
parms <- c(parms, f_free_bound, k_bound_free)
diff --git a/R/mkinpredict.R b/R/mkinpredict.R index 49166f30..2b7e51d5 100644 --- a/R/mkinpredict.R +++ b/R/mkinpredict.R @@ -17,7 +17,9 @@ mkinpredict <- function(mkinmod, odeparms, odeini, outtimes, solution_type = "de o <- switch(parent.type, SFO = SFO.solution(outtimes, evalparse(parent.name), - evalparse(paste("k", parent.name, sep="_"))), + ifelse(mkinmod$use_of_ff == "min", + evalparse(paste("k", parent.name, "sink", sep="_")), + evalparse(paste("k", parent.name, sep="_")))), FOMC = FOMC.solution(outtimes, evalparse(parent.name), evalparse("alpha"), evalparse("beta")), |