cleanup docs

IQSS · Apr 2, 2016 · 2f31967 · 2f31967
1 parent eafbe38
commit 2f31967
Show file tree

Hide file tree

Showing 31 changed files with 217 additions and 748 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: dataverse
-Version: 0.1.14
-Date: 2016-04-01
+Version: 0.1.15
+Date: 2016-04-02
 Title: Client for Dataverse 4 Repositories
 Authors@R: c(person("Thomas J.", "Leeper", role = c("aut", "cre"),
                     email = "thosjleeper@gmail.com"),

diff --git a/R/dataAccess.R b/R/dataAccess.R
@@ -37,7 +37,7 @@
 #' @export
 dataverse_file <- 
 function(file, 
-         ds = NULL,
+         dataset = NULL,
          format = c("original", "RData", "prep", "bundle"),
          # thumb = TRUE,
          vars = NULL,
@@ -48,7 +48,7 @@ function(file,
     format <- match.arg(format)
 
     # from doi get file ID
-    if (!is.null(ds) && !is.numeric(file)) {
+    if (!is.null(dataset) && !is.numeric(file)) {
         file <- (function(doi, filename, ...) {
             files <- dataset_files(prepend_doi(doi))
             ids <- unlist(lapply(files, function(x) x[["datafile"]][["id"]]))
@@ -67,7 +67,7 @@ function(file,
                 id <- ids[w]
             }
             id
-        })(ds, file)
+        })(dataset, file)
 
     }
 
@@ -116,7 +116,7 @@ function(file,
     u <- paste0(api_url(server), "access/datafile/", file, "/metadata/", format)
     r <- httr::GET(u, httr::add_headers("X-Dataverse-key" = key), ...)
     httr::stop_for_status(r)
-    content(r, as = "text", encoding = "UTF-8")
+    httr::content(r, as = "text", encoding = "UTF-8")
 }
 
 

diff --git a/R/native_dataset_publish.R b/R/native_dataset_publish.R
@@ -10,8 +10,10 @@
 #' @examples
 #' \dontrun{
 #' meta <- list()
-#' 
-#' d <- create_dataset("mydataverse", body = list())
+#' ds <- create_dataset("mydataverse", body = meta)
+#'
+#' # cleanup
+#' delete_dataset(ds)
 #' }
 #' @export
 create_dataset <- function(dataverse, body, key = Sys.getenv("DATAVERSE_KEY"), server = Sys.getenv("DATAVERSE_SERVER"), ...) {
@@ -33,7 +35,14 @@ create_dataset <- function(dataverse, body, key = Sys.getenv("DATAVERSE_KEY"), s
 #' @seealso \code{\link{get_dataset}}, \code{\link{create_dataset}}, \code{\link{delete_dataset}}, \code{\link{publish_dataset}}
 #' @examples
 #' \dontrun{
+#' meta1 <- list()
+#' ds <- create_dataset("mydataverse", body = meta1)
 #' 
+#' meta2 <- list()
+#' update_dataset(ds, body = meta2)
+#'
+#' # cleanup
+#' delete_dataset(ds)
 #' }
 #' @export
 update_dataset <- function(dataset, body, key = Sys.getenv("DATAVERSE_KEY"), server = Sys.getenv("DATAVERSE_SERVER"), ...) {
@@ -49,15 +58,16 @@ update_dataset <- function(dataset, body, key = Sys.getenv("DATAVERSE_KEY"), ser
 #' @template ds
 #' @param minor A logical specifying whether the new release of the dataset is a \dQuote{minor} release (\code{TRUE}, by default), resulting in a minor version increase (e.g., from 1.1 to 1.2). If \code{FALSE}, the dataset is given a \dQuote{major} release (e.g., from 1.1 to 2.0).
 #' @template envvars
+#' @template dots
 #' @details Use this function to \dQuote{publish} (i.e., publicly release) a draft Dataverse dataset. This creates a publicly visible listing of the dataset, accessible by its DOI, with a numbered version. This action cannot be undone.
 #' There are no requirements for what constitutes a major or minor release, but a minor release might be used to update metadata (e.g., a new linked publication) or the addition of supplemental files. A major release is best used to reflect a substantial change to the dataset, such as would require a published erratum or a substantial change to data or code.
-#' @template envvars
-#' @template dots
 #' @return A list.
 #' @seealso \code{\link{get_dataset}}, \code{\link{publish_dataverse}}
 #' @examples
 #' \dontrun{
-#' 
+#' meta <- list()
+#' ds <- create_dataset("mydataverse", body = meta)
+#' publish_dataset(ds)
 #' }
 #' @export
 publish_dataset <- function(dataset, minor = TRUE, key = Sys.getenv("DATAVERSE_KEY"), server = Sys.getenv("DATAVERSE_SERVER"), ...) {
@@ -78,7 +88,9 @@ publish_dataset <- function(dataset, minor = TRUE, key = Sys.getenv("DATAVERSE_K
 #' @seealso \code{\link{get_dataset}}, \code{\link{create_dataset}}, \code{\link{update_dataset}}, \code{\link{delete_dataset}}, \code{\link{publish_dataset}}
 #' @examples
 #' \dontrun{
-#' 
+#' meta <- list()
+#' ds <- create_dataset("mydataverse", body = meta)
+#' delete_dataset(ds)
 #' }
 #' @export
 delete_dataset <- function(dataset, key = Sys.getenv("DATAVERSE_KEY"), server = Sys.getenv("DATAVERSE_SERVER"), ...) {

diff --git a/R/native_dv.R b/R/native_dv.R
@@ -108,10 +108,6 @@ get_facets <- function(dataverse, key = Sys.getenv("DATAVERSE_KEY"), server = Sy
 #' monogan <- get_dataverse("monogan")
 #' monogan_data <- dataverse_contents(monogan)
 #' dataverse_metadata(monogan)
-#' 
-#' # get metadata
-#' dataverse_metadata(monogan)
-#' 
 #' }
 #' @export
 dataverse_metadata <- function(dataverse, key = Sys.getenv("DATAVERSE_KEY"), server = Sys.getenv("DATAVERSE_SERVER"), ...) {

diff --git a/R/native_dv_publish.R b/R/native_dv_publish.R
@@ -11,7 +11,10 @@
 #' @seealso To manage Dataverses: \code{\link{delete_dataverse}}, \code{\link{publish_dataverse}}, \code{\link{dataverse_contents}}; to get datasets: \code{\link{get_dataset}}; to search for Dataverses, datasets, or files: \code{\link{dataverse_search}}
 #' @examples
 #' \dontrun{
+#' (dv <- create_dataverse("mydataverse"))
 #' 
+#' # cleanup
+#' delete_dataverse("mydataverse")
 #' }
 #' @export
 create_dataverse <- function(dataverse, key = Sys.getenv("DATAVERSE_KEY"), server = Sys.getenv("DATAVERSE_SERVER"), ...) {
@@ -35,7 +38,8 @@ create_dataverse <- function(dataverse, key = Sys.getenv("DATAVERSE_KEY"), serve
 #' @seealso To manage Dataverses: \code{\link{create_dataverse}}, \code{\link{publish_dataverse}}, \code{\link{dataverse_contents}}; to get datasets: \code{\link{get_dataset}}; to search for Dataverses, datasets, or files: \code{\link{dataverse_search}}
 #' @examples
 #' \dontrun{
-#' 
+#' dv <- create_dataverse("mydataverse")
+#' delete_dataverse(dv)
 #' }
 #' @export
 delete_dataverse <- function(dataverse, key = Sys.getenv("DATAVERSE_KEY"), server = Sys.getenv("DATAVERSE_SERVER"), ...) {
@@ -56,10 +60,6 @@ delete_dataverse <- function(dataverse, key = Sys.getenv("DATAVERSE_KEY"), serve
 #' @template dots
 #' @return A list
 #' @seealso \code{\link{dataverse_metadata}}
-#' @examples
-#' \dontrun{
-#' 
-#' }
 #' @export
 set_dataverse_metadata <- function(dataverse, body, root = TRUE, key = Sys.getenv("DATAVERSE_KEY"), server = Sys.getenv("DATAVERSE_SERVER"), ...) {
     dataverse <- dataverse_id(dataverse)

diff --git a/R/native_role_groups.R b/R/native_role_groups.R
@@ -1,14 +1,16 @@
-#' @title Create role group
-#' @description Create a role group
+#' @rdname role_groups
+#' @title Role groups
+#' @description Create, update, and delete role groups
 #' @details Role groups can be used to organize roles for a Dataverse.
 #' @template dv
+#' @template group
 #' @param alias A character string specifying an alias for the role group.
 #' @param name A character string specifying the name of the role group.
 #' @param description A character string specifying a description of the role group.
 #' @template envvars
 #' @template dots
 #' @return A list of class \dQuote{dataverse_group}.
-#' @seealso \code{\link{list_groups}}, \code{\link{update_group}}, \code{\link{get_group}}, \code{\link{add_roles_to_group}}, \code{\link{delete_group}}
+#' @seealso \code{\link{add_roles_to_group}}
 #' @examples
 #' \dontrun{
 #' # create a group
@@ -40,34 +42,7 @@ create_group <- function(dataverse, alias, name, description, key = Sys.getenv("
     structure(j, class = "dataverse_group")
 }
 
-#' @title Update role group
-#' @description \dots
-#' @details \dots
-#' @template group
-#' @param name A character string specifying the name of the role group.
-#' @param description A character string specifying a description of the role group.
-#' @param dataverse A character string specifying a Dataverse name or an object of class \dQuote{dataverse}. Can be missing if \code{role} is an object of class \dQuote{dataverse_group}.
-#' @template envvars
-#' @template dots
-#' @return A list of class \dQuote{dataverse_group}.
-#' @seealso \code{\link{create_group}}, \code{\link{list_groups}}, \code{\link{get_group}}, \code{\link{add_roles_to_group}}, \code{\link{delete_group}}
-#' @examples
-#' \dontrun{
-#' # create a group
-#' g <- create_group("my_dataverse", "testgroup", "aGroupName", "this is a test group")
-#' 
-#' # update group details
-#' update_group(g, description = "this needs a new description")
-#'
-#' # get group details
-#' get_group(g)
-#'
-#' # list all groups
-#' list_groups("my_dataverse")
-#'
-#' # delete group
-#' delete_group(g)
-#' }
+#' @rdname role_groups
 #' @export
 update_group <- function(group, name, description, dataverse, key = Sys.getenv("DATAVERSE_KEY"), server = Sys.getenv("DATAVERSE_SERVER"), ...) {
     b <- list()
@@ -99,31 +74,7 @@ update_group <- function(group, name, description, dataverse, key = Sys.getenv("
     structure(j, class = "dataverse_group")
 }
 
-#' @title List role groups
-#' @description Returns a list of role groups for a given dataverse
-#' @details Role groups can be used to organize roles for a dataverse.
-#' @template dv
-#' @template envvars
-#' @template dots
-#' @return A list of objects of class \dQuote{dataverse_group}.
-#' @seealso \code{\link{create_group}}, \code{\link{update_group}}, \code{\link{get_group}}, \code{\link{add_roles_to_group}}, \code{\link{delete_group}}
-#' @examples
-#' \dontrun{
-#' # create a group
-#' g <- create_group("my_dataverse", "testgroup", "aGroupName", "this is a test group")
-#' 
-#' # update group details
-#' update_group(g, description = "this needs a new description")
-#'
-#' # get group details
-#' get_group(g)
-#'
-#' # list all groups
-#' list_groups("my_dataverse")
-#'
-#' # delete group
-#' delete_group(g)
-#' }
+#' @rdname role_groups
 #' @export
 list_groups <- function(dataverse, key = Sys.getenv("DATAVERSE_KEY"), server = Sys.getenv("DATAVERSE_SERVER"), ...) {
     dataverse <- dataverse_id(dataverse)
@@ -138,32 +89,7 @@ list_groups <- function(dataverse, key = Sys.getenv("DATAVERSE_KEY"), server = S
     })
 }
 
-#' @title Get role group
-#' @description \dots
-#' @details \dots
-#' @template group
-#' @param dataverse A character string specifying a Dataverse name or an object of class \dQuote{dataverse}. Can be missing if \code{role} is an object of class \dQuote{dataverse_group}.
-#' @template envvars
-#' @template dots
-#' @return A list of class \dQuote{dataverse_group}.
-#' @seealso \code{\link{list_groups}}, \code{\link{create_group}}, \code{\link{update_group}}, \code{\link{add_roles_to_group}}, \code{\link{delete_group}}
-#' @examples
-#' \dontrun{
-#' # create a group
-#' g <- create_group("my_dataverse", "testgroup", "aGroupName", "this is a test group")
-#' 
-#' # update group details
-#' update_group(g, description = "this needs a new description")
-#'
-#' # get group details
-#' get_group(g)
-#'
-#' # list all groups
-#' list_groups("my_dataverse")
-#'
-#' # delete group
-#' delete_group(g)
-#' }
+#' @rdname role_groups
 #' @export
 get_group <- function(group, dataverse, key = Sys.getenv("DATAVERSE_KEY"), server = Sys.getenv("DATAVERSE_SERVER"), ...) {
     if (inherits(group, "dataverse_group")) {
@@ -180,31 +106,7 @@ get_group <- function(group, dataverse, key = Sys.getenv("DATAVERSE_KEY"), serve
     structure(j, class = "dataverse_group")
 }
 
-#' @title Delete role group
-#' @description \dots
-#' @details \dots
-#' @template group
-#' @param dataverse A character string specifying a Dataverse name or an object of class \dQuote{dataverse}. Can be missing if \code{role} is an object of class \dQuote{dataverse_group}.
-#' @template envvars
-#' @template dots
-#' @return A list.
-#' @examples
-#' \dontrun{
-#' # create a group
-#' g <- create_group("my_dataverse", "testgroup", "aGroupName", "this is a test group")
-#' 
-#' # update group details
-#' update_group(g, description = "this needs a new description")
-#'
-#' # get group details
-#' get_group(g)
-#'
-#' # list all groups
-#' list_groups("my_dataverse")
-#'
-#' # delete group
-#' delete_group(g)
-#' }
+#' @rdname role_groups
 #' @export
 delete_group <- function(group, dataverse, key = Sys.getenv("DATAVERSE_KEY"), server = Sys.getenv("DATAVERSE_SERVER"), ...) {
     if (inherits(group, "dataverse_group")) {
@@ -224,19 +126,16 @@ delete_group <- function(group, dataverse, key = Sys.getenv("DATAVERSE_KEY"), se
     }
 }
 
-#' @title Add roles to group
-#' @description \dots
-#' @details \dots
+#' @rdname add_roles
+#' @title Add/Remove role to/from group
+#' @description Add/remove role from group
+#' @details Role groups can be used to organize roles for a Dataverse. These functions add or remove roles from a group
 #' @template group
 #' @template role
 #' @param dataverse A character string specifying a Dataverse name or an object of class \dQuote{dataverse}. Can be missing if \code{role} is an object of class \dQuote{dataverse_group}.
 #' @template envvars
 #' @template dots
 #' @return A list.
-#' @examples
-#' \dontrun{
-#' 
-#' }
 #' @export
 add_roles_to_group <- function(group, role, dataverse, key = Sys.getenv("DATAVERSE_KEY"), server = Sys.getenv("DATAVERSE_SERVER"), ...) {
 
@@ -259,19 +158,7 @@ add_roles_to_group <- function(group, role, dataverse, key = Sys.getenv("DATAVER
     j
 }
 
-#' @title Remove role from group
-#' @description \dots
-#' @details \dots
-#' @template group
-#' @template role
-#' @param dataverse A character string specifying a Dataverse name or an object of class \dQuote{dataverse}. Can be missing if \code{role} is an object of class \dQuote{dataverse_group}.
-#' @template envvars
-#' @template dots
-#' @return A list.
-#' @examples
-#' \dontrun{
-#' 
-#' }
+#' @rdname add_roles
 #' @export
 remove_role_from_group <- function(group, role, dataverse, key = Sys.getenv("DATAVERSE_KEY"), server = Sys.getenv("DATAVERSE_SERVER"), ...) {
     if (inherits(group, "dataverse_group")) {