Improve multistart documentation, bugfix

- Split out llhist and parhist documentation
- Add example code for multistart
- Create a multistart vignette, because the example code fails when run
by pkgdown
- Fix multistart for the case of mkin transformations in the saem fit

1 files changed, 23 insertions, 0 deletions

diff --git a/vignettes/web_only/multistart.R b/vignettes/web_only/multistart.R
new file mode 100644
index 00000000..a860757d
--- /dev/null
+++ b/vignettes/web_only/multistart.R
@@ -0,0 +1,23 @@
+## -----------------------------------------------------------------------------
+library(mkin)
+dmta_ds <- lapply(1:7, function(i) {
+  ds_i <- dimethenamid_2018$ds[[i]]$data
+  ds_i[ds_i$name == "DMTAP", "name"] <-  "DMTA"
+  ds_i$time <- ds_i$time * dimethenamid_2018$f_time_norm[i]
+  ds_i
+})
+names(dmta_ds) <- sapply(dimethenamid_2018$ds, function(ds) ds$title)
+dmta_ds[["Elliot"]] <- rbind(dmta_ds[["Elliot 1"]], dmta_ds[["Elliot 2"]])
+dmta_ds[["Elliot 1"]] <- dmta_ds[["Elliot 2"]] <- NULL
+
+## -----------------------------------------------------------------------------
+f_mmkin <- mmkin("DFOP", dmta_ds, error_model = "tc", cores = 7, quiet = TRUE)
+f_saem_full <- saem(f_mmkin)
+f_saem_full_multi <- multistart(f_saem_full, n = 16, cores = 16)
+parhist(f_saem_full_multi, lpos = "bottomright")
+
+## -----------------------------------------------------------------------------
+f_saem_reduced <- update(f_saem_full, covariance.model = diag(c(1, 1, 0, 1)))
+f_saem_reduced_multi <- multistart(f_saem_reduced, n = 16, cores = 16)
+parhist(f_saem_reduced_multi, lpos = "bottomright")
+