Merge pull request #34 from tece-lab/develop

Restrict values passed from initial optimisation to relaxed-rate model
tece-lab · Oct 20, 2023 · 9670906 · 9670906
2 parents 99fc626 + 016bba0
commit 9670906
Show file tree

Hide file tree

Showing 2 changed files with 7 additions and 2 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: DAISIEutils
 Title: Utility Functions for the DAISIE Package
-Date: 2023-05-03
+Date: 2023-10-08
 Version: 1.6.1
 Authors@R: c(
     person(given = "Pedro",

diff --git a/R/run_daisie_ml.R b/R/run_daisie_ml.R
@@ -104,7 +104,12 @@ run_daisie_ml <- function(daisie_data,
     initparsopt[1:5] <- unlist(lik_res)[1:5]
 
     # prevent infinite parameter estimates given as initial parameters
-    initparsopt[is.infinite(initparsopt)] <- 1e5
+    initparsopt[initparsopt > 1e3] <- 1e3
+
+    # prevent initial parameters being greater than upper parameter limit
+    pick <- which(c("cladogenesis", "extinction", "carrying_capacity",
+                    "immigration", "anagenesis") == cs_version$relaxed_par)
+    initparsopt[initparsopt[pick] > par_upper_bound] <- par_upper_bound / 2
   }
 
   ##### ML Optimization ####