Merge pull request #17 from JRaviLab/16-bug-molevolvr-dep-phangornreadaa

fixes #16
JRaviLab · Sep 20, 2024 · 94369a2 · 94369a2
2 parents 9e6d0e5 + 52855df
commit 94369a2
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -210,7 +210,7 @@ importFrom(phangorn,plotBS)
 importFrom(phangorn,pml)
 importFrom(phangorn,pml.control)
 importFrom(phangorn,pratchet)
-importFrom(phangorn,read.aa)
+importFrom(phangorn,read.phyDat)
 importFrom(phangorn,upgma)
 importFrom(plotly,plot_ly)
 importFrom(purrr,as_vector)

diff --git a/R/tree.R b/R/tree.R
@@ -116,7 +116,7 @@ generate_trees <- function(aln_path = here("data/alns/")) {
 #' @param out_file
 #'
 #' @importFrom ape write.tree
-#' @importFrom phangorn bootstrap.pml dist.ml NJ modelTest phyDat plotBS pml pml.control pratchet optim.parsimony optim.pml read.aa upgma
+#' @importFrom phangorn bootstrap.pml dist.ml NJ modelTest phyDat plotBS pml pml.control pratchet optim.parsimony optim.pml read.phyDat upgma
 #' @importFrom seqinr dist.alignment read.alignment
 #' @importFrom stats logLik
 #'
@@ -156,7 +156,7 @@ generate_fa2tre <- function(fa_file = "data/alns/pspa_snf7.fa",
     ###########################
     ## Alignment file formats and conversion
     # read in sequence data, convert to phyDat
-    prot_fa <- read.aa(fa_file, format = "fasta")
+    prot_fa <- read.phyDat(fa_file, format = "fasta", type = "AA")
     prot_phyDat <- phyDat(prot_fa, type = "AA", levels = NULL)
     prot10 <- subset(prot_phyDat, 1:10)
     prot10_phyDat <- phyDat(prot10, type = "AA", levels = NULL)