diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-11 05:15:19 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-11 05:18:32 +0200 |
| commit | 234c9059a95e104917e488a6ddd2313234a96cdc (patch) | |
| tree | f6e54098f79d94578434ef727b62f7cc5d5e79b7 /R/mkinfit.R | |
| parent | d113cd79b178fdc91aecb894707ed356129dfb75 (diff) | |
Avoid merge() and data.frame() in cost function
also for deSolve and eigenvalue based solutions. This noticeably increases
performance for these methods, see test.log and benchmark vignette.
Diffstat (limited to 'R/mkinfit.R')
| -rw-r--r-- | R/mkinfit.R | 8 |
1 files changed, 2 insertions, 6 deletions
diff --git a/R/mkinfit.R b/R/mkinfit.R index e1089673..f6691b1b 100644 --- a/R/mkinfit.R +++ b/R/mkinfit.R @@ -592,12 +592,8 @@ mkinfit <- function(mkinmod, observed, method.ode = method.ode, atol = atol, rtol = rtol, ...) - out_long <- mkin_wide_to_long(out, time = "time") - - out_merged <- merge(observed[c("name", "time")], out_long) - out_merged$name <- ordered(out_merged$name, levels = obs_vars) - out_merged <- out_merged[order(out_merged$name, out_merged$time), ] - observed$predicted <- out_merged$value + observed_index <- cbind(as.character(observed$time), as.character(observed$name)) + observed$predicted <- out[observed_index] } # Define standard deviation for each observation |