refactor function names in R/tree.R

NAMESPACE

@@ -25,11 +25,13 @@ export(cleanup_species)
 export(combine_files)
 export(combine_full)
 export(combine_ipr)
+export(convertAlignment2Trees)
+export(convertFA2Tree)
 export(convert_aln2fa)
-export(convert_fa2tre)
 export(count_bycol)
 export(count_to_sunburst)
 export(count_to_treemap)
+export(createFA2Tree)
 export(create_all_col_params)
 export(create_lineage_lookup)
 export(create_one_col_params)
@@ -42,9 +44,7 @@ export(find_top_acc)
 export(format_job_args)
 export(gc_undirected_network)
 export(generate_all_aln2fa)
-export(generate_fa2tre)
 export(generate_msa)
-export(generate_trees)
 export(get_accnums_from_fasta_file)
 export(get_job_message)
 export(get_proc_medians)

R/tree.R

@@ -1,6 +1,6 @@
 ## Generating Phylogenetic Trees from Alignment Fasta files
 ## Includes the following functions:
-## generate_trees, convert_fa2tre, generate_fa2tre
+## convertAlignment2Trees, convertFA2Tree, createFA2Tree
 ## Modified: Jan, 2020
 ## Janani Ravi (@jananiravi), Molecular Ecologist (@molecologist)
 
@@ -35,7 +35,7 @@
 ## Approach 0 | FastTree2.0
 ###########################
 ## !! FastTree will only work if there are unique sequence names!!
-#' convert_fa2tre
+#' convertFA2Tree
 #'
 #' @param fa_path
 #' @param tre_path
@@ -45,7 +45,7 @@
 #' @export
 #'
 #' @examples
-convert_fa2tre <- function(fa_path = here("data/alns/pspa_snf7.fa"),
+convertFA2Tree <- function(fa_path = here("data/alns/pspa_snf7.fa"),
     tre_path = here("data/alns/pspa_snf7.tre"),
     fasttree_path = here("src/FastTree")) {
     # fa_path=here("data/alns/pspa_snf7.fa")
@@ -67,7 +67,7 @@ convert_fa2tre <- function(fa_path = here("data/alns/pspa_snf7.fa"),
     #              here("src/FastTree.c"), "-lm", collapse=" "))
 }
 ## Generate Trees for ALL fasta files in "data/alns"
-#' generate_trees
+#' convertAlignment2Trees
 #'
 #' @description
 #' Generate Trees for ALL fasta files in "data/alns"
@@ -82,7 +82,7 @@ convert_fa2tre <- function(fa_path = here("data/alns/pspa_snf7.fa"),
 #' @export
 #'
 #' @examples
-generate_trees <- function(aln_path = here("data/alns/")) {
+convertAlignment2Trees <- function(aln_path = here("data/alns/")) {
     # finding all fasta alignment files
     fa_filenames <- list.files(path = aln_path, pattern = "*.fa")
     fa_paths <- paste0(aln_path, fa_filenames)
@@ -96,15 +96,15 @@ generate_trees <- function(aln_path = here("data/alns/")) {
         tre_path = paste0(aln_path, variable, ".tre")
     )
     pmap(
-        .l = fa2tre_args, .f = convert_fa2tre,
+        .l = fa2tre_args, .f = convertFA2Tree,
         fasttree_path = here("src/FastTree")
     )
 }
 
 ##############################
 ## REFS: 1-4
 ############
-#' generate_fa2tre
+#' createFA2Tree
 #'
 #' @author Janani Ravi, MolEcologist
 #' @keywords phylogenetic tree, alignment, fasta
@@ -134,7 +134,7 @@ generate_trees <- function(aln_path = here("data/alns/")) {
 #' \dontrun{
 #' generate_aln2tree("pspa_snf7.fa")
 #' }
-generate_fa2tre <- function(fa_file = "data/alns/pspa_snf7.fa",
+createFA2Tree <- function(fa_file = "data/alns/pspa_snf7.fa",
     out_file = "data/alns/pspa_snf7.tre") {
     ## SAMPLE ARGS
     # fa_file="data/alns/pspa_snf7.fa"