updated documentation

ropensci-archive · Feb 20, 2014 · bf5f669 · bf5f669
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -4,59 +4,13 @@ Description: A programmatic interface to the
     project.
 Title: Interface to Mendeley API methods
 Version: 1.2
-License: MIT
+License: CC0
 Author: Carl Boettiger, Karthik Ram, Duncan Temple Lang
 Maintainer: Carl Boettiger <cboettig@gmail.com>
 Depends:
-    RJSONIO,
-    RCurl (>= 1.6),
-    ROAuth (>= 0.92.0),
     plyr,
-    methods
-Imports:
     RJSONIO,
-    ROAuth (>= 0.92.0),
+    ROAuth (>= 0.92.0)
+Imports:
     methods,
     RCurl (>= 1.6)
-Collate:
-    'authored.R'
-    'authors.R'
-    'categories.R'
-    'details.R'
-    'groups.R'
-    'papers.R'
-    'public_groups_details.R'
-    'public_groups_documents.R'
-    'public_groups_overview.R'
-    'public_groups_people.R'
-    'publications.R'
-    'related.R'
-    'search.R'
-    'subcategories.R'
-    'tagged.R'
-    'tags.R'
-    'utilities.R'
-    'user_add_doc_folder.r'
-    'user_addContact.r'
-    'user_author_stats.r'
-    'user_authored_pubs.r'
-    'user_contacts.r'
-    'user_create_folder.r'
-    'user_create_group.r'
-    'user_delete_document.r'
-    'user_delete_folder.r'
-    'user_docInfo.r'
-    'user_folder_documents.r'
-    'user_folders.r'
-    'user_group_doc_details.r'
-    'user_group_documents.r'
-    'user_group_people.r'
-    'user_groups.r'
-    'user_library.r'
-    'user_mendeley_auth.r'
-    'user_profile.r'
-    'user_pub_stats.r'
-    'user_tag_stats.r'
-    'user_delete_group.r'
-    'RMendeley.R'
-    'startup.r'
diff --git a/NAMESPACE b/NAMESPACE
@@ -53,3 +53,6 @@ exportClasses(MendeleyID)
 exportClasses(MendeleySimpleDocumentID)
 import(RCurl)
 import(RJSONIO)
+import(ROAuth)
+import(methods)
+import(plyr)
diff --git a/NEWS b/NEWS
@@ -1,7 +1,7 @@
 RMendeley 1.2
 ================
 
-* Lincense moved from BSD to MIT
+* Lincense moved from BSD to CC0 (public domain declaration)
 
 RMendeley 1.1
 ================

diff --git a/R/authored.R b/R/authored.R
@@ -14,6 +14,9 @@
 #' b$documents
 #' a$total_results
 #' }
+#' @import methods
+#' @import ROAuth
+#' @import plyr
 #' @export
 authored <- function(query,  page = NA, numItems = 100L, year=NA, key = getOption("MendeleyKey", stop("need an API key for Mendeley")), curl=getCurlHandle(), ...)
 {

diff --git a/R/user_groups.r b/R/user_groups.r
@@ -22,18 +22,18 @@ if (!is(mc, "MendeleyCredentials"))
 }
 
 
-#' getGroupID
+#' getGroupID function
 #'
-#'Retrieves Mendeley Group ID from a Mendeley Group Name
 #' @param mc OAuth object of class MendeleyCredentials
 #' @param group Group Name
 #' @param ... additional (optional) parameters
-#' @param curl curl handle
-#' @export
+#' @param curl the curl handle
+#' @return group id
 #' @examples \dontrun{
 #' getGroupID(mc, "Future of Science")
-#'}
-getGroupID <- function(mc = NULL, group = NULL,..., curl = getCurlHandle()) {
+#' }
+#' @export
+getGroupID <- function(mc = NULL, group = NULL, ..., curl = getCurlHandle()){
 name <- NA
  if (!is(mc, "MendeleyCredentials"))
         stop("Invalid or missing Mendeley credentials. ?mendeley_auth for more information.",

diff --git a/demo/00Index b/demo/00Index
@@ -1,2 +1,7 @@
 authEg    examples of using Open Authentication with RMendeley to access users own secure files
 erdos     example of using RMendeley to calculate one's Erdos number to a given author
+mendeley  examples using RMendeley
+user_create_document example of creating a document
+user_download_file example of downloading a file
+user_upload_file example of uploading a file
+
diff --git a/demo/mendeley.R b/demo/mendeley.R
@@ -13,23 +13,23 @@
 #
 #
 #Create new document (user_create_document.r)
-# • Upload file (user_upload_file.r)
-# • Add document to folder (user_add_doc_folder.r)
+# Upload file (user_upload_file.r)
+# Add document to folder (user_add_doc_folder.r)
 
-# • Add Contacts (user_add_contacts.r)
+# Add Contacts (user_add_contacts.r)
 #
-# # • Download file (user_download_file.r)
+# Download file (user_download_file.r)
 #
-# • Create folder (user_create_folder.r)
-# • Delete folder (user_delete_folder.r)
-# • Delete document from folder (user_delete_folder_doc.r)
+# Create folder (user_create_folder.r)
+# Delete folder (user_delete_folder.r)
+# Delete document from folder (user_delete_folder_doc.r)
 #
-# • Create group (user_create_group.r)
-# • Delete group (user_delete_group.r) # Is there delete in addition to get and post?
+# Create group (user_create_group.r)
+# Delete group (user_delete_group.r) # Is there delete in addition to get and post?
 #
 #
 # Test
-# • Delete document (user_delete_document.r)
+# Delete document (user_delete_document.r)
 #
 
 library(ROAuth)

diff --git a/man/Folders.Rd b/man/Folders.Rd
@@ -2,7 +2,7 @@
 \alias{Folders}
 \title{Folders - retuns a list of your Mendeley folders with sizes.}
 \usage{
-  Folders(mc = NULL, ..., curl = getCurlHandle())
+Folders(mc = NULL, ..., curl = getCurlHandle())
 }
 \arguments{
   \item{mc}{Your Mendeley ROAuth credential.}
@@ -15,18 +15,18 @@
   tools mostly).}
 }
 \value{
-  list
+list
 }
 \description{
-  Folders - retuns a list of your Mendeley folders with
-  sizes.
+Folders - retuns a list of your Mendeley folders with
+sizes.
 }
 \examples{
 \dontrun{
 Folders(mc)
 }
 }
 \author{
-  Karthik Ram \email{karthik.ram@gmail.com}
+Karthik Ram \email{karthik.ram@gmail.com}
 }
 
diff --git a/man/MendeleyCredentials-class.Rd b/man/MendeleyCredentials-class.Rd
@@ -1,13 +1,14 @@
+\docType{class}
 \name{MendeleyCredentials-class}
 \alias{MendeleyCredentials-class}
 \title{An S4 class that stores Mendeley credentials}
 \description{
-  An S4 class that stores Mendeley credentials
+An S4 class that stores Mendeley credentials
 
-  An S4 class that stores Mendeley credentials
+An S4 class that stores Mendeley credentials
 
-  An S4 class that stores MendeleyID
+An S4 class that stores MendeleyID
 
-  An S4 class that stores MendeleyDocumentID
+An S4 class that stores MendeleyDocumentID
 }
 
diff --git a/man/MendeleyDocumentID-class.Rd b/man/MendeleyDocumentID-class.Rd
@@ -2,6 +2,6 @@
 \alias{MendeleyDocumentID-class}
 \title{An S4 class that stores Mendeley credentials}
 \description{
-  An S4 class that stores Mendeley credentials
+An S4 class that stores Mendeley credentials
 }
 
diff --git a/man/MendeleyFolderID-class.Rd b/man/MendeleyFolderID-class.Rd
@@ -1,9 +1,10 @@
+\docType{class}
 \name{MendeleyFolderID-class}
 \alias{MendeleyFolderID-class}
 \title{An S4 class that stores MendeleyFolderID}
 \description{
-  An S4 class that stores MendeleyFolderID
+An S4 class that stores MendeleyFolderID
 
-  An S4 class that stores MendeleyFolderId
+An S4 class that stores MendeleyFolderId
 }
 
diff --git a/man/MendeleyGroupID-class.Rd b/man/MendeleyGroupID-class.Rd
@@ -1,9 +1,10 @@
+\docType{class}
 \name{MendeleyGroupID-class}
 \alias{MendeleyGroupID-class}
 \title{An S4 class that stores MendeleyGroupID}
 \description{
-  An S4 class that stores MendeleyGroupID
+An S4 class that stores MendeleyGroupID
 
-  An S4 class that stores MendeleyGroupID
+An S4 class that stores MendeleyGroupID
 }
 
diff --git a/man/MendeleyID-class.Rd b/man/MendeleyID-class.Rd
@@ -1,7 +1,8 @@
+\docType{class}
 \name{MendeleyID-class}
 \alias{MendeleyID-class}
 \title{An S4 class that stores MendeleyID}
 \description{
-  An S4 class that stores MendeleyID
+An S4 class that stores MendeleyID
 }
 
diff --git a/man/MendeleySimpleDocumentID-class.Rd b/man/MendeleySimpleDocumentID-class.Rd
@@ -2,6 +2,6 @@
 \alias{MendeleySimpleDocumentID-class}
 \title{An S4 class that stores Mendeley credentials}
 \description{
-  An S4 class that stores Mendeley credentials
+An S4 class that stores Mendeley credentials
 }
 
diff --git a/man/RMendeley.Rd b/man/RMendeley.Rd
@@ -5,71 +5,70 @@
 \alias{package-RMendeley}
 \title{RMendeley - A programmatic interface to the Web Service methods provided by the Mendeley open science}
 \description{
-  This is version 1.0.0 of package RMendeley. User specific
-  API methods require obtaining access keys from
-  Mendeley.com. To do so, first sign up at the Mendeley
-  \href{http://apidocs.mendeley.com/}{developer site} and
-  obtain Mendeley API keys. Ideally you should store these
-  keys in your \code{.rprofile} but you may also specify
-  them inline when authenticating with
-  \code{\link{mendeley_auth}}.
+This is version 1.0.0 of package RMendeley. User specific
+API methods require obtaining access keys from
+Mendeley.com. To do so, first sign up at the Mendeley
+\href{http://apidocs.mendeley.com/}{developer site} and
+obtain Mendeley API keys. Ideally you should store these
+keys in your \code{.rprofile} but you may also specify them
+inline when authenticating with
+\code{\link{mendeley_auth}}.
 }
 \details{
-  To save your cosumer key/secret combo in your
-  \code{.rprofile}, add the following lines:
+To save your cosumer key/secret combo in your
+\code{.rprofile}, add the following lines:
 
-  \code{options(MendeleyKey = "YOUR_CONSUMER_KEY")}
+\code{options(MendeleyKey = "YOUR_CONSUMER_KEY")}
 
-  \code{options(MendeleyPrivateKey = "YOUR_PRIVATE_KEY")}
+\code{options(MendeleyPrivateKey = "YOUR_PRIVATE_KEY")}
 
-  Most functions now require users to authenticate first
-  using \code{\link{mendeley_auth}}. Once you had approved
-  \code{RMendeley} on the Mendeley website, return to the R
-  console and paste the PIN to complete authentication. You
-  may save this \code{MendeleyCredential} object for future
-  use and not repeat the authentication process for each
-  session.
+Most functions now require users to authenticate first
+using \code{\link{mendeley_auth}}. Once you had approved
+\code{RMendeley} on the Mendeley website, return to the R
+console and paste the PIN to complete authentication. You
+may save this \code{MendeleyCredential} object for future
+use and not repeat the authentication process for each
+session.
 
-  \strong{Profile methods} \itemize{ \item
-  \code{\link{contacts}} \item \code{\link{addContact}}
-  \item \code{\link{mendeley_profile}} }
+\strong{Profile methods} \itemize{ \item
+\code{\link{contacts}} \item \code{\link{addContact}} \item
+\code{\link{mendeley_profile}} }
 
-  \strong{Stats methods} \itemize{ \item
-  \code{\link{authorStats}} \item \code{\link{tagStats}}
-  \item \code{\link{pubStats}} }
+\strong{Stats methods} \itemize{ \item
+\code{\link{authorStats}} \item \code{\link{tagStats}}
+\item \code{\link{pubStats}} }
 
-  \strong{Document methods} \itemize{ \item
-  \code{\link{mendeley_library}} \item
-  \code{\link{authoredPubs}} \item \code{\link{docInfo}}
-  \item \code{createDoc} \emph{Not yet coded.} \item
-  \code{MendeleyUpload} \emph{Not yet coded.} \item
-  \code{MendeleyDownload} \emph{Not yet coded.} \item
-  \code{\link{deleteDocument}} }
+\strong{Document methods} \itemize{ \item
+\code{\link{mendeley_library}} \item
+\code{\link{authoredPubs}} \item \code{\link{docInfo}}
+\item \code{createDoc} \emph{Not yet coded.} \item
+\code{MendeleyUpload} \emph{Not yet coded.} \item
+\code{MendeleyDownload} \emph{Not yet coded.} \item
+\code{\link{deleteDocument}} }
 
-  \strong{Group methods} \itemize{ \item
-  \code{\link{myGroups}} \item \code{\link{groupPeople}}
-  \item \code{\link{groupDocs}} \item
-  \code{\link{groupDocInfo}} \item
-  \code{\link{createGroup}} \item \code{\link{deleteGroup}}
-  \item \code{\link{leaveGroup}} \item
-  \code{\link{unfollowGroup}} } \strong{Folder methods}
-  \itemize{ \item \code{\link{Folders}} \item
-  \code{\link{folderDocs}} \item \code{\link{addFolderDoc}}
-  \item \code{\link{createFolder}} \item
-  \code{\link{deleteFolder}} }
+\strong{Group methods} \itemize{ \item
+\code{\link{myGroups}} \item \code{\link{groupPeople}}
+\item \code{\link{groupDocs}} \item
+\code{\link{groupDocInfo}} \item \code{\link{createGroup}}
+\item \code{\link{deleteGroup}} \item
+\code{\link{leaveGroup}} \item \code{\link{unfollowGroup}}
+} \strong{Folder methods} \itemize{ \item
+\code{\link{Folders}} \item \code{\link{folderDocs}} \item
+\code{\link{addFolderDoc}} \item \code{\link{createFolder}}
+\item \code{\link{deleteFolder}} }
 
-  \strong{Public methods} \itemize{ \item
-  \code{\link{authored}} \item \code{\link{authors}} \item
-  \code{\link{categories}} \item \code{\link{details}}
-  \item \code{\link{groups}} \item \code{\link{papers}}
-  \item \code{\link{public_groups_details}} \item
-  \code{\link{public_groups_documents}} \item
-  \code{\link{msearch}} \item \code{\link{subcategories}}
-  \item \code{\link{tagged}} \item \code{\link{tags}} }
+\strong{Public methods} \itemize{ \item
+\code{\link{authored}} \item \code{\link{authors}} \item
+\code{\link{categories}} \item \code{\link{details}} \item
+\code{\link{groups}} \item \code{\link{papers}} \item
+\code{\link{public_groups_details}} \item
+\code{\link{public_groups_documents}} \item
+\code{\link{msearch}} \item \code{\link{subcategories}}
+\item \code{\link{tagged}} \item \code{\link{tags}} }
 
-  \strong{Useful links} \itemize{ \item
-  \href{http://mendeley.com/}{Mendeley} \item
-  \href{http://apidocs.mendeley.com/}{Full API
-  documentation} }
+\strong{Useful links} \itemize{ \item
+\href{http://mendeley.com/}{Mendeley} \item
+\href{http://apidocs.mendeley.com/}{Full API documentation}
+}
 }