Merge pull request #44 from lawinslow/master

Fixed up documentation a bit

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: sbtools
 Title: USGS SB tools
 Maintainer: Luke Winslow <lwinslow@usgs.gov>
-Version: 0.8.1
+Version: 0.8.2
 Author: Luke Winslow
 Description: Tools for interacting with SB interfaces. 
 Imports: 

R/authenticate_sb.R

@@ -2,13 +2,16 @@
 #'
 #'@title Authenticate to SB for subsequent calls
 #'
+#'@param username Sciencebase username
+#'@param password (optional) Sciencebase password, prompts user if not supplied
 #'
+#'@description 
+#'This connects to SB, authenticates and gets a session token for 
+#'communicating with SB.
 #'
+#'@import httr
 #'
 #'
-#'
-#'
-#'@import httr
 #'@export
 authenticate_sb = function(username, password){
 

R/item_append_files.R

@@ -3,13 +3,14 @@
 #'
 #'@param id A ScienceBase item ID to upload to.
 #'@param files A file path to upload.
-#'@param sb_session A ScienceBase session object from authenticate_sb.
+#'@param session A ScienceBase session object from authenticate_sb.
 #'
 #'@return ScienceBase Item.
 #'
 #'@import httr
 #'
-#'@examples \dontrun{
+#'@examples 
+#'\dontrun{
 #'  sb_session<-authenticate_sb(sbusername)
 #'  item_append_files("54e265a4e4b08de9379b4dfb", '/foo/bar/baz.zip', sb)
 #' }

R/item_create.R

@@ -2,11 +2,12 @@
 #'@title Create a new SB item
 #'
 #'@param parent_id ID of the parent item
+#'@param title The title of the new SB item
 #'@param session Authenticated session object (from \link{authenticate_sb})
 #'@param info (optional) list of metadata info for the new item
 #'@return SB ID for the newly created item
 #'
-#'
+#'x
 #'@import httr 
 #'
 #'@export

R/item_file_download.R

@@ -6,6 +6,7 @@
 #'@param destinations String vector list of destinations for requested files. Must be same length as \code{names}
 #'@param dest_dir A directory path for saving files when \code{names} parameter is omitted
 #'@param session Session object from \code{\link{authenticate_sb}}
+#'@param overwrite_file Boolean indicating if file should be overwritten if it already exists locally
 #'
 #'@description 
 #'Function to downlod files attached to an item on SB. Either files can be specified directly

R/item_list_files.R

@@ -1,7 +1,7 @@
 #'@title Get list of files attached to SB item
 #'
 #'@param id item ID
-#'@param Session Session object from \link{authenticate_sb}
+#'@param session Session object from \link{authenticate_sb}
 #'
 #'@return 
 #'A data.frame with columns fname, size, and url. 

R/item_rm.R

@@ -1,6 +1,6 @@
 #'@title Remove item from SB
 #'
-#'@param SB item ID
+#'@param id item ID
 #'@param session Session object from \code{\link{authenticate_sb}}
 #'
 #'@return TRUE to indicate success

R/items_query.R → R/query_items.R

@@ -3,8 +3,8 @@
 #'
 #'@param query_list 
 #'
-#'
-#'
+#'@param query_list List of item query selectors
+#'@param session Session object from \code{\link{authenticate_sb}}
 #'
 #'
 #'@export

man/authenticate_sb.Rd

@@ -6,7 +6,16 @@
 \usage{
 authenticate_sb(username, password)
 }
+\arguments{
+\item{username}{Sciencebase username}
+
+\item{password}{(optional) Sciencebase password, prompts user if not supplied}
+}
 \description{
+This connects to SB, authenticates and gets a session token for
+communicating with SB.
+}
+\details{
 
 }
 

man/item_append_files.Rd

@@ -11,7 +11,7 @@ item_append_files(id, files, session)
 
 \item{files}{A file path to upload.}
 
-\item{sb_session}{A ScienceBase session object from authenticate_sb.}
+\item{session}{A ScienceBase session object from authenticate_sb.}
 }
 \value{
 ScienceBase Item.

man/item_create.Rd

@@ -9,12 +9,16 @@ item_create(parent_id, title, session, info)
 \arguments{
 \item{parent_id}{ID of the parent item}
 
+\item{title}{The title of the new SB item}
+
 \item{session}{Authenticated session object (from \link{authenticate_sb})}
 
 \item{info}{(optional) list of metadata info for the new item}
 }
 \value{
 SB ID for the newly created item
+
+x
 }
 \description{
 Create a new SB item

man/item_file_download.Rd

@@ -17,6 +17,8 @@ item_file_download(id, names, destinations, dest_dir, session = NULL,
 \item{dest_dir}{A directory path for saving files when \code{names} parameter is omitted}
 
 \item{session}{Session object from \code{\link{authenticate_sb}}}
+
+\item{overwrite_file}{Boolean indicating if file should be overwritten if it already exists locally}
 }
 \description{
 Function to downlod files attached to an item on SB. Either files can be specified directly

man/item_list_files.Rd

@@ -9,7 +9,7 @@ item_list_files(id, session = NULL)
 \arguments{
 \item{id}{item ID}
 
-\item{Session}{Session object from \link{authenticate_sb}}
+\item{session}{Session object from \link{authenticate_sb}}
 }
 \value{
 A data.frame with columns fname, size, and url.

man/item_rm.Rd

@@ -7,9 +7,9 @@
 item_rm(id, session)
 }
 \arguments{
-\item{session}{Session object from \code{\link{authenticate_sb}}}
+\item{id}{item ID}
 
-\item{SB}{item ID}
+\item{session}{Session object from \code{\link{authenticate_sb}}}
 }
 \value{
 TRUE to indicate success

man/query_items.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.0): do not edit by hand
-% Please edit documentation in R/items_query.R
+% Please edit documentation in R/query_items.R
 \name{query_items}
 \alias{query_items}
 \title{Query SB for items using generic query parameters}
@@ -8,6 +8,10 @@ query_items(query_list, session)
 }
 \arguments{
 \item{query_list}{}
+
+\item{session}{Session object from \code{\link{authenticate_sb}}}
+
+\item{query_list}{List of item query selectors}
 }
 \description{