add warning

rsetienne · May 23, 2024 · 6db49a5 · 6db49a5
1 parent e17710d
commit 6db49a5
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Showing 2 changed files with 3 additions and 9 deletions.
diff --git a/R/secsse_loglik.R b/R/secsse_loglik.R
@@ -60,15 +60,6 @@ master_loglik <- function(parameter,
                            num_unique_traits = num_modeled_traits,
                            traitStates = traitStates)
   }
-
-  for (i in 1:nrow(states)) {
-    v <- sum(states[i, ])
-    if (!is.na(v)) {
-      if (v == 0) {
-        cat("states entry zero: ", i, states[i, ], "\n")
-      }
-    }
-  }
 
   RcppParallel::setThreadOptions(numThreads = num_threads)
   calcul <- calc_ll_cpp(rhs = if (using_cla) "ode_cla" else "ode_standard",

diff --git a/R/secsse_prep.R b/R/secsse_prep.R
@@ -145,6 +145,9 @@ create_q_matrix <- function(state_names,
                             diff.conceal = FALSE) {
 
   total_num_states <- length(state_names)
+  if (total_num_states != num_concealed_states) {
+    stop("number of concealed states has to be equal to the number of observed states")
+  }
   trans_matrix <- matrix(0, ncol = total_num_states,
                          nrow = total_num_states)