Bug fixes

pbastide · Feb 27, 2024 · 80741de · 80741de
1 parent b69f4e1
commit 80741de
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/R/phylogeneticCorrelations.R b/R/phylogeneticCorrelations.R
@@ -320,6 +320,7 @@ get_consensus_tree_OUfixedRoot <- function(phy, all_phyfit, measurement_error, t
   }
 
   get_lambda_error_OU <- function(phyfit) {
+    if (is.na(phyfit$optpar)) return(NA)
     tree_model <- phylolm::transf.branch.lengths(phy, "OUfixedRoot",
                                                  parameters = list(alpha = phyfit$optpar))$tree
     tilde_t <- tree_height(tree_model) / (2 * phyfit$optpar)

diff --git a/R/phylolmFit.R b/R/phylolmFit.R
@@ -139,7 +139,7 @@ phylolmFit <- function(object, design = NULL, phy, col_species = NULL,
 
   } else {
     ## one phylo model per gene
-    C_tree_params <- get_chol_tree(y_data,  design, phy, 1, model, measurement_error, REML, ddf_method, ...)
+    C_tree_params <- get_chol_tree(y_data,  design, phy, NULL, model, measurement_error, REML, ddf_method, ...)
     C_tree <- C_tree_params$C_tree
 
     ddf_fits <- C_tree_params$ddf
@@ -271,7 +271,7 @@ get_chol_tree <- function(y_data, design, phy, phy_ind = NULL, model, measuremen
       C_tree_chol_and_params <- format_list(C_tree_chol_and_params)
     }
   } else {
-    if (!length(unique(phy_ind)) == 1) stop("Can only have one tree in the non BM case.")
+    if (!is.null(phy_ind)) stop("Can only have one tree in the non BM case.")
     C_tree_chol_and_params <- apply(y_data, 1,
                                     get_C_tree, design, phy, model, measurement_error, REML, ddf_method, ...)
     C_tree_chol_and_params <- format_list(C_tree_chol_and_params)