diff options
Diffstat (limited to 'R/transform_odeparms.R')
| -rw-r--r-- | R/transform_odeparms.R | 70 |
1 files changed, 48 insertions, 22 deletions
diff --git a/R/transform_odeparms.R b/R/transform_odeparms.R index 4b8bfd1..8b39874 100644 --- a/R/transform_odeparms.R +++ b/R/transform_odeparms.R @@ -1,46 +1,72 @@ -transform_odeparms <- function(odeparms, mod_vars) {
- # Transform rate constants and formation fractions
- transparms <- odeparms
- # Exponential transformation for rate constants
- index_k <- grep("^k_", names(odeparms))
+transform_odeparms <- function(parms, mod_vars) {
+ # Set up container for transformed parameters
+ transparms <- parms
+
+ # Log transformation for rate constants
+ index_k <- grep("^k_", names(transparms))
if (length(index_k) > 0) {
- transparms[index_k] <- exp(odeparms[index_k])
+ transparms[index_k] <- log(parms[index_k])
}
- # Go through state variables and apply inverse isotropic logratio transformation
+ # Go through state variables and apply isotropic logratio transformation
for (box in mod_vars) {
- indices_f <- grep(paste("^f", box, sep = "_"), names(odeparms))
- f_names <- grep(paste("^f", box, sep = "_"), names(odeparms), value = TRUE)
+ indices_f <- grep(paste("^f", box, sep = "_"), names(parms))
+ f_names <- grep(paste("^f", box, sep = "_"), names(parms), value = TRUE)
n_paths <- length(indices_f)
if (n_paths > 0) {
- f <- invilr(odeparms[indices_f])[1:n_paths] # We do not need the last component
- names(f) <- f_names
- transparms[indices_f] <- f
+ f <- parms[indices_f]
+ trans_f <- ilr(c(f, 1 - sum(f)))
+ names(trans_f) <- f_names
+ transparms[indices_f] <- trans_f
}
}
+
+ # Transform parameters also for FOMC, DFOP and HS models
+ for (pname in c("alpha", "beta", "k1", "k2", "tb")) {
+ if (!is.na(parms[pname])) {
+ transparms[pname] <- log(parms[pname])
+ }
+ }
+ if (!is.na(parms["g"])) {
+ g <- parms["g"]
+ transparms["g"] <- ilr(c(g, 1- g))
+ }
+
return(transparms)
}
backtransform_odeparms <- function(transparms, mod_vars) {
- # Transform rate constants and formation fractions
- odeparms <- transparms
- # Log transformation for rate constants
- index_k <- grep("^k_", names(transparms))
+ # Set up container for backtransformed parameters
+ parms <- transparms
+
+ # Exponential transformation for rate constants
+ index_k <- grep("^k_", names(parms))
if (length(index_k) > 0) {
- odeparms[index_k] <- log(transparms[index_k])
+ parms[index_k] <- exp(transparms[index_k])
}
- # Go through state variables and apply isotropic logratio transformation
+ # Go through state variables and apply inverse isotropic logratio transformation
for (box in mod_vars) {
indices_f <- grep(paste("^f", box, sep = "_"), names(transparms))
f_names <- grep(paste("^f", box, sep = "_"), names(transparms), value = TRUE)
n_paths <- length(indices_f)
if (n_paths > 0) {
- trans_f <- transparms[indices_f]
- f <- ilr(c(trans_f, 1 - sum(trans_f)))
+ f <- invilr(transparms[indices_f])[1:n_paths] # We do not need the last component
names(f) <- f_names
- odeparms[indices_f] <- f
+ parms[indices_f] <- f
}
}
- return(odeparms)
+
+ # Transform parameters also for DFOP and HS models
+ for (pname in c("alpha", "beta", "k1", "k2", "tb")) {
+ if (!is.na(transparms[pname])) {
+ parms[pname] <- exp(transparms[pname])
+ }
+ }
+ if (!is.na(transparms["g"])) {
+ g <- transparms["g"]
+ parms["g"] <- invilr(g)[1]
+ }
+
+ return(parms)
}
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