Merge 0aca74f into 3d7b50f

CONTRIBUTING.md

@@ -16,7 +16,7 @@ is intended to be a general-purpose wrapper for the `Eutils` API. Functions that
 make use of `rentrez` to perform more specific tasks should be added to existing
 packages, or form the basis of new ones. 
 
-###Perferred way to contribute code
+###Preferred way to contribute code
 
 * Fork this repo to your Github account
 * Clone your version on your account down to your machine from your account, e.g,. `git clone https://github.com/<yourgithubusername>/rentrez.git`
@@ -33,5 +33,5 @@ Please note that this project is released with a [Contributor Code of
 Conduct](CONDUCT.md). By participating in this project you agree to abide by its
 terms.
 
- Thanks for contibuting!
+ Thanks for contributing!
 

NEWS

@@ -8,19 +8,19 @@ Version 0.4
 ------------------------
  * entrez_summary now fetches 'version 2.0' esummary records from NCBI
      * This change may break some scripts. In particular, the names of some
-       elements in esummary records have changed. Broken scripts shold produce a
+       elements in esummary records have changed. Broken scripts should produce a
        helpful error message, and using entrez_summary(..., version="1.0")
        should fix it. More details are given in the help to entrez_summary. 
      * When version 2.0 records are requested entrez_summary fetches the json
        record.
  * New helper functions for einfo Eutil
-    * entrez_dbs() lists avaliable databases.
+    * entrez_dbs() lists available databases.
     * entrez_db_summary() gets summary information about a given database.  
     * entrez_db_links() lists databases against which a given db's records might
       be cross referenced.
-    * entrez_db_searchable() lists search terms avaliable for a given database.
+    * entrez_db_searchable() lists search terms available for a given database.
  * Nicer print functions for search and summary objects
- * New dependancy on jsonlite for handling json records.
+ * New dependency on jsonlite for handling json records.
  * Bunch of bugs squashed and typos cleaned up
 
 Version 0.3.1
@@ -41,8 +41,8 @@ Version 0.2.4
 
 Version 0.2.3
 ---------------------------------
-    * Edited license/description to meet CRAN requiremens
-    * Added sentence to description to summarise the package
+    * Edited license/description to meet CRAN requirements
+    * Added sentence to description to summarize the package
 
 
 Version 0.2.2

R/base.r

@@ -3,7 +3,7 @@
 #
 #  http://cran.r-project.org/web/packages/httr/vignettes/api-packages.html
 #
-#and also conforming to the NBCI's requirements about rate limiting and 
+#and also conforming to the NBCI's requirements about rate limiting and
 #adding identifiers to each request:
 #
 # http://www.ncbi.nlm.nih.gov/books/NBK25497/#chapter2.Usage_Guidelines_and_Requirements
@@ -16,24 +16,25 @@
 entrez_email <- function() 'david.winter@gmail.com'
 entrez_tool <- function() 'rentrez'
 
-#Create a URL for the EUtils API. 
+#Create a URL for the EUtils API.
 #
 # This function is used by all the API-querying functions in rentrez to build
 # the appropriate url. Required arguments for each rentrez are handled in each
 # function. Those arguments that either ID(s) or are WebEnv cookie can be set
 # by passing a string or two argument names to `make_entrez_query`
 #
 #
-# efetch_url <- make_entrez_query("efetch", require_one_of=c("id", "WebEnv"), 
+# efetch_url <- make_entrez_query("efetch", require_one_of=c("id", "WebEnv"),
 #                                 id=c(23310964,23310965), db="pubmed",
 #                                 rettype="xml")
 #
 
 
 make_entrez_query <- function(util, config, interface=".fcgi?", ...){
+    ##this fxn assembles the uri make query and return the result as text
     args <- list(..., email=entrez_email(), tool=entrez_tool())
     if("id" %in% names(args)){
-        args$id <- paste(args$id, collapse=",")      
+        args$id <- paste(args$id, collapse=",")
     }
     uri <- paste0("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/", util, interface)
     response <- httr::GET(uri, query=args, config= config)
@@ -42,13 +43,13 @@ make_entrez_query <- function(util, config, interface=".fcgi?", ...){
 }
 
 ##
-# Check for that we have either the ID or the web-history functions are 
+# Check for that we have either the ID or the web-history functions are
 # specified for those functions that need one.
 ##
 
 id_or_webenv <- function(){
-    args <- sys.frame(sys.parent())
-    msg <- "Must specify either (not both) 'id' or web history arguments 'WebEnv' and 'query_key'" 
+    args <- sys.frame(sys.parent()) ##get the eviroment of using the parent call frame number
+    msg <- "Must specify either (not both) 'id' or web history arguments 'WebEnv' and 'query_key'"
     if(!is.null(args$id)){
         if(!is.null(args$web_history)){
             stop(msg, call.=FALSE)
@@ -89,7 +90,7 @@ check_xml_errors <- function(x){
 
 
 parse_response <- function(x, type=NULL){
-    res <- switch(type, 
+    res <- switch(type,
             "json" = fromJSON(x),
             "xml"  = xmlTreeParse(x, useInternalNodes=TRUE),
             "text" = x, #citmatch uses plain old plain text
@@ -108,7 +109,7 @@ web_history <- function(WebEnv, QueryKey){
 #'@export
 print.web_history <- function(x, ...){
     cat("Web history object (QueryKey = ", x$QueryKey,
-        ", WebEnv = ", substr(x$WebEnv, 1, 12), "...", ")\n",sep="")    
+        ", WebEnv = ", substr(x$WebEnv, 1, 12), "...", ")\n",sep="")
 }
 
 

R/entrez_info.r

@@ -100,9 +100,10 @@ entrez_db_summary <- function(db, config=NULL){
 entrez_db_links <- function(db, config=NULL){
     rec <- entrez_info(db, config)
     unparsed <- xpathApply(rec, "//Link", xmlChildren)
-    res <- lapply(unparsed, lapply, xmlValue)
+    res <- lapply(unparsed, lapply, xmlValue) ##this line applies xmlvalue fun to the list element of a list
+                                              ##and return a list of list
     res <- lapply(res, add_class, new_class='eInfoEntry')
-    names(res) <- sapply(res, "[[", "DbTo")
+    names(res) <- sapply(res, "[[", "DbTo") ##this line get the 4th elemnt of each element(also a list) in res
     class(res) <- c("eInfoLink", "eInfoList", "list")
     attr(res, 'db') <- xmlValue(rec["/eInfoResult/DbInfo/DbName"][[1]])
     res
@@ -115,9 +116,9 @@ entrez_db_links <- function(db, config=NULL){
 #' search fields to include in the \code{term} argument of that function.
 #'@param config config vector passed to \code{httr::GET}
 #'@param db character, name of database to get search field from
-#'@return An eInfoSearch object (subclassed from list) summarizing linked-databases. 
+#'@return An eInfoSearch object (subclassed from list) summarizing linked-databases.
 #' Can be coerced to a data-frame with \code{as.data.frame}. Printing the object
-#' shows only the names of each available search field. 
+#' shows only the names of each available search field.
 #'@seealso \code{\link{entrez_search}}
 #'@family einfo
 #'@examples
@@ -134,7 +135,7 @@ entrez_db_links <- function(db, config=NULL){
 
 entrez_db_searchable <- function(db, config=NULL){
     rec <- entrez_info(db, config)
-    unparsed <- xpathApply(rec, 
+    unparsed <- xpathApply(rec,
                            "/eInfoResult/DbInfo/FieldList/Field",
                            xmlChildren)
     res <- lapply(unparsed, lapply, xmlValue)
@@ -160,7 +161,7 @@ as.data.frame.eInfoList <- function(x, ...){
 print.eInfoSearch <- function(x, ...){
     cat("Searchable fields for database '", attr(x, "db"), "'\n", sep="")
     for (term in x){
-        cat(" ", term$Name, "\t", term$Description, "\n")  
+        cat(" ", term$Name, "\t", term$Description, "\n")
     }
 }
 

README.Rmd

@@ -11,7 +11,7 @@ knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>"
 )
-knitr::opts_knit$set(upload.fun = knitr::imgur_upload, base.url = NULL)  
+knitr::opts_knit$set(upload.fun = knitr::imgur_upload, base.url = NULL)
 
 ```
 
@@ -45,12 +45,12 @@ or [by filing an issue](https://github.com/ropensci/rentrez/issues)
 
 ##The EUtils API
 
-Each of the functions exportd by `rentrez` is documented, and this README and
-the pakage vignette provide examples of how to use the functions together as part
+Each of the functions exported by `rentrez` is documented, and this README and
+the package vignette provide examples of how to use the functions together as part
 of a workflow. The API itself is [well-documented](http://www.ncbi.nlm.nih.gov/books/NBK25500/).
-Be sure to read the official documenation to get the most out of API. In particular, be aware of the NCBI's usage
+Be sure to read the official documentation to get the most out of API. In particular, be aware of the NCBI's usage
 policies and try to limit very large requests to off peak (USA) times (`rentrez`
-takes care of limiting the number of requests per second, and seeting the
+takes care of limiting the number of requests per second, and setting the
 appropriate entrez tool name in each request).
 
 See [getting information about NCBI databases](#getting-information-about-ncbi-databases)
@@ -95,7 +95,7 @@ In this case we'll get the protein sequences as genbank files, using '
 hox_proteins <- entrez_fetch(db="protein", id=hox_data$pubmed_protein, rettype="gb")
 ```
 
-###Retreiving datasets associated a particular organism.
+###Retrieving datasets associated a particular organism.
 
 I like spiders. So let's say I want to learn a little more about New Zealand's
 endemic "black widow" the katipo. Specifically, in the past the katipo has
@@ -160,7 +160,7 @@ configuration options.
 
 Any `rentrez` function that interacts with the Eutils api will
 pass the value of the argument `config` along to `httr`'s  `GET` function. For
-instance, if you acess the internet through a proxy you use the `httr` function
+instance, if you access the internet through a proxy you use the `httr` function
 `use_proxy()` to provide connection details to an entrez call:
 
 ```r
@@ -204,7 +204,7 @@ snail_coi <- entrez_fetch(db="nuccore", WebEnv=cookie, query_key=qk, rettype="fa
 
 ###Getting information about NCBI databases
 
-Most of the exmples above required some background information about what
+Most of the examples above required some background information about what
 databases NCBI has to offer, and how they can be searched. `rentrez` provides
 a set of functions with names starting `entrez_db` that help you to discover
 this information in an interactive session.
@@ -216,14 +216,14 @@ First up, `entrez_dbs()` gives you a list of database names
 entrez_dbs()
 ```
 
-Some of the names are a little opaque, so you can get some more descriptve
+Some of the names are a little opaque, so you can get some more descriptive
 information about each with `entrez_db_summary()`
 
 ```{r summary}
 entrez_db_summary("cdd")
 ```
 
-`entrez_db_searchable()` lets you discover the fields avalible for search terms
+`entrez_db_searchable()` lets you discover the fields available for search terms
 for a given database. You get back a named-list, with names are fields. Each
 element has additional information about each named search field (you can also
 use `as.data.frame` to create a dataframe, with one search-field per row):
@@ -259,7 +259,7 @@ papers_by_year <- function(years, search_term){
         }
 ```
 
-With that we can fetch the data for earch term and, by searching with no term,
+With that we can fetch the data for each term and, by searching with no term,
 find the total number of papers published in each year:
 
 

man/entrez_fetch.Rd

@@ -10,7 +10,7 @@ entrez_fetch(db, id = NULL, web_history = NULL, rettype, retmode = "text",
 \arguments{
 \item{db}{character Name of the database to use}
 
-\item{id}{vector with unique ID(s) for reacods in database \code{db}.}
+\item{id}{vector with unique ID(s) for records in database \code{db}.}
 
 \item{web_history}{A web_history object}
 
@@ -24,7 +24,7 @@ file. Only works with rettype="xml" at present}
 \item{config}{vector configuration options passed to httr::GET}
 
 \item{\dots}{character Additional terms to add to the request, see NCBI
-documentation linked to in referenes for a complete list}
+documentation linked to in references for a complete list}
 }
 \value{
 character string containing the file created

man/entrez_link.Rd

@@ -12,20 +12,20 @@ entrez_link(dbfrom, web_history = NULL, id = NULL, db = NULL,
 
 \item{web_history}{a web_history object}
 
-\item{id}{vector with unique ID(s) for reacods in database \code{db}.}
+\item{id}{vector with unique ID(s) for records in database \code{db}.}
 
 \item{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).}
 
-\item{cmd}{link function to use. Allowled values include
+\item{cmd}{link function to use. Allowed values include
 \itemize{
   \item neighbor (default). Returns a set of IDs in \code{db} linked to the
   input IDs in \code{dbfrom}.
   \item neighbor_score. As 'neighbor', but additionally returns similarity scores.
   \item neighbor_history. As 'neighbor', but returns web history objects.
   \item acheck. Returns a list of linked databases available from NCBI for a set of IDs.
-  \item ncheck. Checks for the existance of links within a single database.
+  \item ncheck. Checks for the existence of links within a single database.
   \item lcheck. Checks for external (i.e. outside NCBI) links.
   \item llinks. Returns a list of external links for each ID, excluding links
   provided by libraries.
@@ -38,7 +38,7 @@ to discover databases that might have linked information (see examples).}
 \item{config}{vector configuration options passed to httr::GET}
 
 \item{\dots}{character Additional terms to add to the request, see NCBI
-documentation linked to in referenes for a complete list}
+documentation linked to in references for a complete list}
 }
 \value{
 An elink object containing the data defined by the \code{cmd} argument

man/entrez_search.Rd

@@ -17,11 +17,11 @@ entrez_search(db, term, config = NULL, retmode = "xml",
 \item{retmode}{character One of json (default) or xml. This will make no
 difference in most cases.}
 
-\item{use_history}{locgical Return a web_history object for use in
+\item{use_history}{logical Return a web_history object for use in
 later calls to the NCBI}
 
 \item{\dots}{character Additional terms to add to the request, see NCBI
-documentation linked to in referenes for a complete list}
+documentation linked to in references for a complete list}
 }
 \value{
 ids integer Unique IDS returned by the search

man/entrez_summary.Rd

@@ -10,7 +10,7 @@ entrez_summary(db, id = NULL, web_history = NULL, version = c("2.0",
 \arguments{
 \item{db}{character Name of the database to search for}
 
-\item{id}{vector with unique ID(s) for reacods in database \code{db}.}
+\item{id}{vector with unique ID(s) for records in database \code{db}.}
 
 \item{web_history}{A web_history object}
 
@@ -22,7 +22,7 @@ when only one ID is provided.}
 \item{config}{vector configuration options passed to \code{httr::GET}}
 
 \item{\dots}{character Additional terms to add to the request, see NCBI
-documentation linked to in referenes for a complete list}
+documentation linked to in references for a complete list}
 }
 \value{
 A list of esummary records (if multiple IDs are passed and

staticdocs/entrez_fetch.html

@@ -60,7 +60,7 @@ <h2>Arguments</h2>
     <div class="Value">
       <h2>Value</h2>
 
-      <p>chracter string containing the file created</p>
+      <p>character string containing the file created</p>
 
     </div>
 
@@ -93,4 +93,4 @@ <h2 id="examples">Examples</h2>
       </footer>
     </div>
   </body>
-</html>
+</html>

staticdocs/entrez_global_query.html

@@ -35,7 +35,7 @@
 
       </header>
 
-      <h1>See how many hits there are for a given term across all NCBI Entrez databses</h1>
+      <h1>See how many hits there are for a given term across all NCBI Entrez databases</h1>
 
 <div class="row">
   <div class="span8">
@@ -51,14 +51,14 @@ <h2>Arguments</h2>
     <div class="Value">
       <h2>Value</h2>
 
-      <p>a named vector with counts for each a datbase</p>
+      <p>a named vector with counts for each a database</p>
 
     </div>
 
     <div class="Description">
       <h2>Description</h2>
 
-      <p>Contstructs a url with the given arguments, and downloads
+      <p>Constructs a url with the given arguments, and downloads
   xml record returned by that url. See the package-level
   documentation for general advice on using the EUtils
   functions.</p>
@@ -86,4 +86,4 @@ <h2 id="examples">Examples</h2>
       </footer>
     </div>
   </body>
-</html>
+</html>