simplified some examples

R/allphenotypes.R

@@ -14,8 +14,6 @@
 #' @return data.frame of openSNP phenotypes, variants and users per phenotype, or list if `df=FALSE`
 #' @examples \donttest{
 #' # Get all data
-#' allphenotypes(df = TRUE)
-#'
 #' # Output a list, then call the characteristic of interest by 'id' or
 #' # 'characteristic'
 #' datalist <- allphenotypes()

R/download_users.R

@@ -8,16 +8,12 @@
 #' @param ... Curl options passed on to [crul::HttpClient]
 #' @return File downloaded to directory you specify (or default), nothing
 #' returned in R.
-#' @examples \dontrun{
+#' @examples \donttest{
 #' # Download a single user file, by id
 #' download_users(id = 14)
 #'
 #' # Download a single user file, by user name
 #' download_users(name = "kevinmcc")
-#'
-#' # Download many user files
-#' lapply(c(14, 22), function(x) download_users(id = x))
-#' read_users(id = 14, nrows = 5)
 #' }
 download_users <- function(name = NULL, id = NULL, dir = "~/", ...) {
   if (is.null(name) && is.null(id)) {

R/fetch_genotypes.R

@@ -30,8 +30,6 @@
 #'
 #' @examples \donttest{
 #' # get a data.frame of the users data
-#' data <- users(df = TRUE)
-#' head(data[[1]]) # users with links to genome data
 #' mydata <- fetch_genotypes(
 #'   url = data[[1]][1, "genotypes.download_url"],
 #'   file = "~/myfile.txt"

R/ncbi_snp_api.R

@@ -218,7 +218,7 @@ get_gene_names <- function(primary_info) {
 #' ncbi_snp_query(SNPs)
 #' # ncbi_snp_query("123456") ##invalid: must prefix with 'rs'
 #' ncbi_snp_query("rs420358")
-#' ncbi_snp_query("rs332") # warning that its merged into another, try that
+#' ncbi_snp_query("rs332") # warning that its merged into another
 #' ncbi_snp_query("rs121909001")
 #' ncbi_snp_query("rs1837253")
 #' ncbi_snp_query("rs1209415715")

R/phenotypes.R

@@ -12,12 +12,6 @@
 #' phenotypes(userid = "1,6,8", df = TRUE)
 #' phenotypes(userid = "1-8", df = TRUE)
 #'
-#' # coerce to data.frame
-#' library(plyr)
-#' df <- ldply(phenotypes(userid = "1-8", df = TRUE))
-#' head(df)
-#' tail(df)
-#'
 #' # pass on curl options
 #' phenotypes(1, verbose = TRUE)
 #' }

R/users.R

@@ -6,10 +6,6 @@
 #' @param ... Curl options passed on to [crul::HttpClient]
 #' @return List of openSNP users, their ID numbers, and genome data if available.
 #' @examples \donttest{
-#' # just the list
-#' data <- users(df = FALSE)
-#' data
-#'
 #' # get a data.frame of the users data
 #' data <- users(df = TRUE)
 #' data[[1]] # users with links to genome data