Bugfix, model shorthand, state.ini[[1]] from observed data

- The bug occurred when using transform_rates=FALSE for FOMC, DFOP or HS
- Make it possible to use mkinfit("SFO", ...)
- Take initial mean value at time zero for the variable with the highest
  value in the observed data
- Update of vignette/FOCUS_L
- Improve the Makefile to build single vignettes

1 files changed, 15 insertions, 7 deletions

diff --git a/R/transform_odeparms.R b/R/transform_odeparms.R
index 912a5c0a..f518ae32 100644
--- a/R/transform_odeparms.R
+++ b/R/transform_odeparms.R
@@ -69,7 +69,11 @@ transform_odeparms <- function(parms, mkinmod,
   # and HS parameter tb if transformation of rates is requested

   for (pname in c("alpha", "beta", "k1", "k2", "tb")) {

     if (!is.na(parms[pname])) {

-      transparms[paste0("log_", pname)] <- ifelse(transform_rates, log(parms[pname]), parms[pname])

+      if (transform_rates) {

+        transparms[paste0("log_", pname)] <- log(parms[pname])

+      } else {

+        transparms[pname] <- parms[pname]

+      }

     } 

   }

   if (!is.na(parms["g"])) {

@@ -130,12 +134,16 @@ backtransform_odeparms <- function(transparms, mkinmod,
 

   # Transform parameters also for FOMC, DFOP and HS models

   for (pname in c("alpha", "beta", "k1", "k2", "tb")) {

-    pname_trans = paste0("log_", pname)

-    if (!is.na(transparms[pname_trans])) {

-      parms[pname] <- ifelse(transform_rates, 

-                             exp(transparms[pname_trans]), 

-                             transparms[pname])

-    } 

+    if (transform_rates) {

+      pname_trans = paste0("log_", pname)

+      if (!is.na(transparms[pname_trans])) {

+        parms[pname] <- exp(transparms[pname_trans])

+      }

+    } else {

+      if (!is.na(transparms[pname])) {

+        parms[pname] <- transparms[pname]

+      }

+    }

   }

   if (!is.na(transparms["g_ilr"])) {

     g_ilr <- transparms["g_ilr"]