update version nr

Author: thijsjanzen

DESCRIPTION

@@ -2,7 +2,7 @@ Package: secsse
 Type: Package
 Title: Several Examined and Concealed States-Dependent Speciation and
  Extinction
-Version: 3.6.0
+Version: 3.6.1
 License: GPL (>= 3) | file LICENSE
 Authors@R: c(
  person(given = "Leonel",

NEWS.md

@@ -1,10 +1,18 @@
+# 3.6.1
+- added support for having a different number of concealed states compared to
+the number of observed states when creating a q_matrix using `q_doubletrans`.
+
 # 3.6.0
 - changed the default integration method to "odeint::runge_kutta_cash_karp54",
 although a bit slower, this method is more numerically stable.
 - fixed lack of sorting of numeric traits in the function `q_doubletrans`
-- fixed an error in preparing the state matrices when NAs were present in the traits
-- ML and LL functions now optionally also return the root state, which in turn can be used to in `secsse_sim` as a starting point at the root / crown of the tree.
-- updated simulations to sample species using a binary search, instead of using stochastic acceptance
+- fixed an error in preparing the state matrices when NAs were present in the
+traits
+- ML and LL functions now optionally also return the root state, which in turn
+can be used to in `secsse_sim` as a starting point at the root / crown of the
+tree.
+- updated simulations to sample species using a binary search, instead of using
+stochastic acceptance
 - better documentation of output of ML and LL functions.
 # 3.5.0
 Version 3.5.0 uses a separate calculation for 1 - E, e.g. one minus the local

R/secsse_prep.R

@@ -145,9 +145,7 @@ 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)
 
@@ -161,9 +159,11 @@ create_q_matrix <- function(state_names,
 
   diag(trans_matrix) <- NA
 
-  trans_matrix <- secsse::q_doubletrans(traits = state_names,
-                                        masterBlock = trans_matrix,
-                                        diff.conceal = diff.conceal)
+  trans_matrix <- 
+    secsse::q_doubletrans(traits = state_names,
+                          masterBlock = trans_matrix,
+                          diff.conceal = diff.conceal,
+                          num_concealed_states = num_concealed_states)
 
   all_state_names <- get_state_names(state_names, num_concealed_states)
   colnames(trans_matrix) <- all_state_names