Minor code cleanups

R/api_keys.r

@@ -22,4 +22,3 @@ set_entrez_key <- function(key){
 is_entrez_key_set <- function(){
     !identical(Sys.getenv('ENTREZ_KEY'), "")
 }
-

R/base.r

@@ -20,7 +20,7 @@ entrez_tool <- function() 'rentrez'
 #
 # This function is used by all the API-querying functions in rentrez to build
 # the appropriate url. Required arguments for each endpoint are handled by
-# specific funcitons. All of these functions can use the id_or_webenv() function
+# specific functions. All of these functions can use the id_or_webenv() function
 # (below) to ensure that at least on of these arguments are provided and the
 # sleep_time() function to set the approrate time to wait between requests.
 #
@@ -156,7 +156,7 @@ parse_response <- function(x, type=NULL){
     return(res)
 }
 
-#contsructor for web history objects
+#constructor for web history objects
 web_history <- function(WebEnv, QueryKey){
     res <- list(WebEnv=WebEnv, QueryKey=QueryKey)
     class(res) <- list("web_history", "list")
@@ -169,8 +169,6 @@ print.web_history <- function(x, ...){
         ", WebEnv = ", substr(x$WebEnv, 1, 12), "...", ")\n",sep="")    
 }
 
-
-
 add_class <- function(x, new_class){
     class(x) <- c(new_class, class(x))
     x

R/entrez_fetch.r

@@ -66,7 +66,7 @@ entrez_fetch <- function(db, id=NULL, web_history=NULL, rettype, retmode="", par
     if(parsed){
         #At the moment, this is just a long-winded way to call
         #XML::xmlTreeParse, but we already use this approach to parse
-        #esummaries,and this is more flexible if NCBI starts sharing more
+        #esummaries, and this is more flexible if NCBI starts sharing more
         #records in JSON.
         return(parse_response(records, rettype))
     }

R/entrez_info.r

@@ -1,7 +1,7 @@
 #' Get information about EUtils databases
 #'
 #' Gather information about EUtils generally, or a given Eutils database.
-#'Note: The most common uses-cases for the einfo util are finding the list of
+#' Note: The most common uses-cases for the einfo util are finding the list of
 #' search fields available for a given database or the other NCBI databases to
 #' which records in a given database might be linked. Both these use cases
 #' are implemented in higher-level functions that return just this information

R/entrez_link.r

@@ -1,11 +1,10 @@
 #' Get links to datasets related to records from an NCBI database
 #'
-#' Discover records related to a set of unique identifiers from
-#' an NCBI database. The object returned by this function depends on the value
-#' set for the \code{cmd} argument. Printing the returned object lists the names
-#' , and provides a brief description, of the elements included in the object.
+#' Discover records related to a set of unique identifiers from an NCBI
+#' database. The object returned by this function depends on the value set for
+#' the \code{cmd} argument. Printing the returned object lists the names, and
+#' provides a brief description, of the elements included in the object.
 #'
-#'@export
 #'@param db character Name of the database to search for links (or use "all" to 
 #' search all databases available for \code{db}. \code{entrez_db_links} allows you
 #' to discover databases that might have linked information (see examples).
@@ -53,9 +52,7 @@
 #'  res <- entrez_link(dbfrom="pubmed", db="", cmd="llinks", id=pubmed_search$ids)
 #'  linkout_urls(res)
 #'}
-#'
-
-
+#'@export
 entrez_link <- function(dbfrom, web_history=NULL, id=NULL, db=NULL, cmd='neighbor', by_id=FALSE, config=NULL, ...){
     identifiers <- id_or_webenv()
     args <- c(list("elink", db=db, dbfrom=dbfrom, cmd=cmd, config=config, by_id=by_id, ...), identifiers)
@@ -202,7 +199,6 @@ parse_linkouts <- function(x){
 
 
 #' @export
-
 print.elink_list <- function(x, ...){
     payload <- attr(x[[1]], "content")
     cat("List of", length(x), "elink objects,each containing\n", payload)
@@ -214,7 +210,6 @@ print.elink <- function(x, ...){
     cat("elink object with contents:\n", payload, "\n",sep="")
 }
 
-
 #' @export
 print.linkout <- function(x,...){
     cat("Linkout from", x$Provider$Name, "\n $Url:", substr(x$Url, 1, 26), "...\n")

R/entrez_post.r

@@ -38,4 +38,3 @@ entrez_post <- function(db, id=NULL, web_history=NULL, config=NULL, ...){
     return(result)
 }
 
-

R/entrez_search.r

@@ -79,7 +79,6 @@ entrez_search <- function(db, term, config=NULL, retmode="xml", use_history=FALS
     parse_esearch(parsed, history=use_history)
 }
 
-
 parse_esearch <- function(x, history) UseMethod("parse_esearch")
 
 parse_esearch.XMLInternalDocument <- function(x, history){
@@ -125,6 +124,3 @@ print.esearch <- function(x, ...){
                 "web_history object)\n Search term (as translated): "  , display_term, "\n")
     cat(msg)
 }
-
-
- c("//IdList/Id", "/eSearchResult/Count", "/eSearchResult/RetMax", "/eSearchResult/QueryTranslation")

R/entrez_summary.r

@@ -140,16 +140,14 @@ parse_esummary.list <- function(x, version, always_return_list){
     res
 }
 
-# Prase a summary XML 
+# Parse a summary XML 
 #
 # Logic goes like this
 # 1. Define functions parse_esumm_* to handle all data types
 # 2. For each node detect type, parse accordingly
 # 3. wrap it all up in function parse_summary that 
 #
 
-#
-#@export
 parse_esummary.XMLInternalDocument  <- function(x, version, always_return_list){
     check_xml_errors(x)
     #Version 2.0 records have no type information (int, list etc) so we