Namespace and documentation fixes

R/demodata.R

@@ -160,8 +160,8 @@ populate_concept <- function(ont, modi, scheme, project, host = "", admin = "",
 
   # Get the name of the ontology from the scheme
   list_ont(host, admin, pass) %>%
-    filter(c_table_cd == scheme) %>%
-    pull(c_name) ->
+    dplyr::filter(c_table_cd == scheme) %>%
+    dplyr::pull(c_name) ->
   name
 
   # Create the data frame holding the contents of the new table
@@ -220,8 +220,8 @@ populate_provider <- function(ont, scheme, project, host = "", admin = "", pass
 
   # Get the name of the ontology from the scheme
   list_ont(host, admin, pass) %>%
-    filter(c_table_cd == scheme) %>%
-    pull(c_name) ->
+    dplyr::filter(c_table_cd == scheme) %>%
+    dplyr::pull(c_name) ->
   name
 
   # Create the data frame holding the contents of the new table

R/i2b2_msg.R

@@ -26,6 +26,7 @@ base_msg <- function()
 #' @param msg The XML message to add the header to
 #' @param username The username to connect with
 #' @param password The password for the user
+#' @param domain The domain to act on
 #' @return The XML message list object
 #' @export
 add_header <- function(msg, username, password, domain = "")

R/metadata.R

@@ -192,8 +192,8 @@ populate_ont <- function(ont, modi = NULL, scheme, include_code = T, def_facttab
 
   # Get the name of the ontology from the scheme
   list_ont(host, admin, pass) %>%
-    filter(c_table_cd == scheme) %>%
-    pull(c_name) ->
+    dplyr::filter(c_table_cd == scheme) %>%
+    dplyr::pull(c_name) ->
   name
 
   ont %>%

man/add_header.Rd

@@ -12,6 +12,8 @@ add_header(msg, username, password, domain = "")
 \item{username}{The username to connect with}
 
 \item{password}{The password for the user}
+
+\item{domain}{The domain to act on}
 }
 \value{
 The XML message list object