print citations to a file

.Rbuildignore

@@ -15,4 +15,6 @@ tmp/
 revdep/
 ^codemeta\.json$
 ^tic.R$
-^.pre-commit-config.yaml$
+^.pre-commit-config.yaml$
+^.*\.Rproj$
+^\.Rproj\.user$

.gitignore

@@ -18,3 +18,7 @@ revdep/
 README.html
 README_files/
 figure/
+.Rproj.user
+*.Rproj
+
+cit*.t*xt

DESCRIPTION

@@ -49,7 +49,7 @@ VignetteBuilder:
     knitr
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.1.99.9001
+RoxygenNote: 7.0.0
 X-schema.org-isPartOf: https://ropensci.org
 X-schema.org-keywords: metadata, ropensci, phylogenetics,
     independant-contrasts, biodiversity

NAMESPACE

@@ -1,6 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(`[`,otl_ott_id)
+S3method("[",otl_ott_id)
 S3method(candidate_for_synth,study_meta)
 S3method(flags,match_names)
 S3method(flags,taxon_info)
@@ -63,6 +63,7 @@ S3method(unique_name,tol_summary)
 S3method(update,match_names)
 export(candidate_for_synth)
 export(flags)
+export(get_citations)
 export(get_publication)
 export(get_study)
 export(get_study_meta)

R/base.R

@@ -208,3 +208,19 @@ check_label_format <- function(x) {
     return(FALSE)
   }
 }
+
+# res is an output from .tol_induced_subtree or .tol_subtree
+# returns a list with tree and study ids supporting a subtree
+studies_from_otl <- function(res){
+  if (is.list(res)) {
+    if (!is.null(res$supporting_studies)) {
+        studies <- res$supporting_studies
+    }
+    else {
+        stop("Cannot find supporting studies")
+    }
+  }
+  study_ids <- sapply(stringr::str_split(studies, "@"), '[', 1)
+  trees <- sapply(stringr::str_split(studies, "@"), '[', 2)
+  return(list(study_ids = study_ids, trees = trees))
+}

R/studies-methods.R

@@ -87,3 +87,11 @@ candidate_for_synth.study_meta <- function(sm) {
 get_study_year.study_meta <- function(sm) {
   sm[["nexml"]][["^ot:studyYear"]]
 }
+
+##' Get citations for a set of study ids
+##' @export
+##' @param study_ids is a vector of study ids
+get_citations <- function(study_ids){
+  citations <- sapply(study_ids, function(x) get_publication.study_meta(get_study_meta(study_id = x)))
+  return(citations)
+}

R/tol.R

@@ -427,6 +427,8 @@ tol_subtree <- function(ott_id = NULL, node_id = NULL, label_format = NULL,
 ##'     (the default).
 ##' @param file If specified, the function will write the subtree to a file in
 ##'     newick format.
+##' @param file_citations If specified, the function will write citations from
+##'        supporting source trees to a txt file. It will automatically add the "txt" extension.
 ##' @param ... additional arguments to customize the API call (see
 ##'     \code{\link{rotl}} for more information).
 ##'
@@ -455,11 +457,28 @@ tol_subtree <- function(ott_id = NULL, node_id = NULL, label_format = NULL,
 ##' }
 ##' @export
 tol_induced_subtree <- function(ott_ids = NULL, node_ids = NULL, label_format = NULL,
-                                file, ...) {
+                                file, file_citations, ...) {
   res <- .tol_induced_subtree(
     ott_ids = ott_ids, node_ids = node_ids,
     label_format = label_format, ...
   )
+  # print citations
+  if (!missing(file_citations)) {
+    filecit <- paste0(file_citations, ".txt")
+    citations <- get_citations(studies_from_otl(res)$study_ids)
+    unlink(filecit)
+    cat(paste(citations, collapse = '\n\n'), file = filecit)
+    message(paste0("Citations were written to ", filecit, " in dir ", getwd()))
+  }
+  #   else {
+  #   # enhance: if file is not provided write to tmp dir
+  #   # tmpdir <- "temporary file dir"
+  #   # message(paste("'citations.txt' file has been written to dir", tmpdir))
+  #   filecit <- "citations.txt"
+  #   enhance: print to screen at leats part of citations, so users know that they're there.
+  # }
+
+
   if (!missing(file)) {
     unlink(file)
     cat(res$newick, file = file)