update phytools article

waldronlab · Sep 21, 2023 · b107266 · b107266
1 parent ea8e9d0
commit b107266
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Showing 2 changed files with 10 additions and 2 deletions.
diff --git a/inst/scripts/phagorn.R b/inst/scripts/phagorn.R
@@ -42,6 +42,14 @@ system.time(
 )
 
 
+system.time(
+    {
+        ## This one takes too long
+        fit <- pml(mpa_tree, myData)
+        fit <- optim.pml(fit, model = NULL, control = pml.control(trace=0))
+    }
+)
+
 anc_pars_data <- vector('list', length(anc_pars))
 for (i in seq_along(anc_pars_data)) {
     anc_pars_data[[i]] <- as.data.frame(unname(anc_pars[[i]]))

diff --git a/vignettes/articles/phytools.Rmd b/vignettes/articles/phytools.Rmd
@@ -168,7 +168,7 @@ mean(names(phys_data_list) %in% get_all_nodes)
 How many tips included in the mpa tree
 
 ```{r}
-mpa_tip_data <- ltp(x = 'tips') |> 
+mpa_tip_data <- mpa(x = 'tips') |> 
     modify(as.character) |> 
     as_tibble()
 mean(mpa_tip_data$taxid %in% sub('^\\w__', '', phys_data_ready$NCBI_ID))
@@ -305,7 +305,7 @@ table(tip$Evidence)
 
 
 ```{r}
-mpa_tree <- ltp()
+mpa_tree <- mpa()
 m1 <- tip |> 
     select(tip_label, Attribute, Score) |> 
     filter(!is.na(Attribute)) |>