Require branch lengths in 'tree' argument

R/coev_fit.R

@@ -13,7 +13,8 @@
 #' @param id A character of length one identifying the variable in the data that
 #'   links rows to tips on the phylogeny. Must refer to a valid column name in
 #'   the data. The id column must exactly match the tip labels in the phylogeny.
-#' @param tree A phylogenetic tree object of class \code{phylo}.
+#' @param tree A phylogenetic tree object of class \code{phylo}. The tree must
+#'   include branch lengths.
 #' @param effects_mat (optional) A boolean matrix with row and column names
 #'   exactly matching the variables declared for the model. If not specified,
 #'   all cross-lagged effects will be estimated in the model. If specified, the

R/coev_helpers.R

@@ -154,6 +154,10 @@ run_checks <- function(data, variables, id, tree, effects_mat,
   if (!methods::is(tree, "phylo")) {
     stop2("Argument 'tree' must be an phylogenetic tree object of class phylo.")
   }
+  # stop if tree does not have branch length information
+  if (is.null(tree$edge.length)) {
+    stop2("Argument 'tree' does not include branch lengths.")
+  }
   # stop if id in data does not match tree tip labels exactly
   if (!identical(sort(unique(data[,id])), sort(tree$tip.label))) {
     stop2("The id variable in the data does not match tree tip labels exactly.")

R/coev_make_stancode.R

@@ -13,7 +13,8 @@
 #' @param id A character of length one identifying the variable in the data that
 #'   links rows to tips on the phylogeny. Must refer to a valid column name in
 #'   the data. The id column must exactly match the tip labels in the phylogeny.
-#' @param tree A phylogenetic tree object of class \code{phylo}.
+#' @param tree A phylogenetic tree object of class \code{phylo}. The tree must
+#'   include branch lengths.
 #' @param effects_mat (optional) A boolean matrix with row and column names
 #'   exactly matching the variables declared for the model. If not specified,
 #'   all cross-lagged effects will be estimated in the model. If specified, the

R/coev_make_standata.R

@@ -13,7 +13,8 @@
 #' @param id A character of length one identifying the variable in the data that
 #'   links rows to tips on the phylogeny. Must refer to a valid column name in
 #'   the data. The id column must exactly match the tip labels in the phylogeny.
-#' @param tree A phylogenetic tree object of class \code{phylo}.
+#' @param tree A phylogenetic tree object of class \code{phylo}. The tree must
+#'   include branch lengths.
 #' @param effects_mat (optional) A boolean matrix with row and column names
 #'   exactly matching the variables declared for the model. If not specified,
 #'   all cross-lagged effects will be estimated in the model. If specified, the

tests/testthat/test-coev_fit.R

@@ -232,6 +232,18 @@ test_that("coev_fit() produces expected errors", {
     ),
     "Argument 'tree' must be an phylogenetic tree object of class phylo."
   )
+  expect_error(
+    coev_fit(
+      data = d,
+      variables = list(
+        x = "bernoulli_logit",
+        y = "ordered_logistic"
+      ),
+      id = "id",
+      tree = ape::rtree(n, br = NULL)
+    ),
+    "Argument 'tree' does not include branch lengths."
+  )
   expect_error(
     {
       d2 <- d

tests/testthat/test-coev_make_stancode.R

@@ -232,6 +232,18 @@ test_that("coev_make_stancode() produces expected errors", {
     ),
     "Argument 'tree' must be an phylogenetic tree object of class phylo."
   )
+  expect_error(
+    coev_make_stancode(
+      data = d,
+      variables = list(
+        x = "bernoulli_logit",
+        y = "ordered_logistic"
+      ),
+      id = "id",
+      tree = ape::rtree(n, br = NULL)
+    ),
+    "Argument 'tree' does not include branch lengths."
+  )
   expect_error(
     {
       d2 <- d

tests/testthat/test-coev_make_standata.R

@@ -232,6 +232,18 @@ test_that("coev_make_standata() produces expected errors", {
     ),
     "Argument 'tree' must be an phylogenetic tree object of class phylo."
   )
+  expect_error(
+    coev_make_standata(
+      data = d,
+      variables = list(
+        x = "bernoulli_logit",
+        y = "ordered_logistic"
+      ),
+      id = "id",
+      tree = ape::rtree(n, br = NULL)
+    ),
+    "Argument 'tree' does not include branch lengths."
+  )
   expect_error(
     {
       d2 <- d