Merge pull request #176 from ropensci/T171_fix_description

T171 fix value fields in .RD files

DESCRIPTION

@@ -1,12 +1,12 @@
 Package: rsnps
-Title: Get 'SNP' ('Single-Nucleotide' 'Polymorphism') Data on the Web
-Description: A programmatic interface to various 'SNP' 'datasets'
-    on the web: 'OpenSNP' (<https://opensnp.org>), and 'NBCIs' 'dbSNP' database
+Title: Get SNP (Single-Nucleotide Polymorphism) Data on the Web
+Description: A programmatic interface to various SNP datasets
+    on the web: OpenSNP (<https://opensnp.org>), and NBCIs dbSNP database
     (<https://www.ncbi.nlm.nih.gov/projects/SNP/>). Functions
-    are included for searching for 'NCBI'. For 'OpenSNP', functions are included 
-    for getting 'SNPs', and data for 'genotypes', 'phenotypes', annotations, 
+    are included for searching for NCBI. For OpenSNP, functions are included 
+    for getting SNPs, and data for genotypes, phenotypes, annotations, 
     and bulk downloads of data by user.
-Version: 0.6.1
+Version: 0.6.2
 License: MIT + file LICENSE
 Authors@R: c(
     person("Julia", "Gustavsen", role = c("aut", "cre"),

NAMESPACE

@@ -17,7 +17,6 @@ export(phenotypes)
 export(phenotypes_byid)
 export(read_users)
 export(rsnpsCache)
-export(tryget)
 export(users)
 importFrom(crul,HttpClient)
 importFrom(plyr,compact)

NEWS.md

@@ -1,3 +1,11 @@
+rsnps 0.6.2
+===========
+
+### MINOR IMPROVEMENTS
+
+* removed quotes from abbreviation in package description upon request from CRAN
+
+
 rsnps 0.6.0
 ===========
 

R/LDSearch.R

@@ -1,6 +1,7 @@
 #' This function is defunct.
 #' @export
 #' @rdname ld_search-defunct
+#' @return a error message telling the user that this function has been removed
 #' @keywords internal
 ld_search <- function(...) {
   .Defunct(msg = "This function is defunct; SNAP has been taken down.

R/allphenotypes.R

@@ -11,12 +11,12 @@
 #' can take multiple values, so the other columns id, characteristic, and
 #' number_of_users are replicated in the data.frame. Default: `FALSE`
 #' @param ... Curl options passed on to [crul::HttpClient]
-#' @return data.frame of results, or list if `df=FALSE`
+#' @return data.frame of openSNP phenotypes, variants and users per phenotype, or list if `df=FALSE`
 #' @examples \dontrun{
 #' # Get all data
 #' allphenotypes(df = TRUE)
 #'
-#' # Output a list, then call the characterisitc of interest by 'id' or
+#' # Output a list, then call the characteristic of interest by 'id' or
 #' # 'characteristic'
 #' datalist <- allphenotypes()
 #' names(datalist) # get list of all characteristics you can call

R/annotations.R

@@ -12,7 +12,7 @@
 #' 		are: 'plos', 'mendeley', 'snpedia', 'metadata'). 'metadata' gives the
 #' 		metadata for the response.
 #' @param ... Curl options passed on to [crul::HttpClient]
-#' @return data.frame of results
+#' @return data.frame of openSNP phenotypes from specified source
 #' @examples \dontrun{
 #' # Get all data
 #' ## get just the metadata

R/deprecated-defunct.R

@@ -1,6 +1,7 @@
 #' This function is defunct.
 #' @export
 #' @rdname LDSearch-defunct
+#' @return a error message telling the user that this function has been removed
 #' @keywords internal
 LDSearch <- function(...) {
   .Defunct(new = "ld_search", package = "rsnps", msg = "the LDSearch() function name has been changed to ld_search()")
@@ -9,6 +10,7 @@ LDSearch <- function(...) {
 #' This function is defunct.
 #' @export
 #' @rdname NCBI_snp_query-defunct
+#' @return a error message telling the user that this function has been deprecated in favour of another function
 #' @keywords internal
 ncbi_snp_summary <- function(...) {
   .Defunct(new = "ncbi_snp_summary", package = "rsnps", msg = "the ncbi_snp_summary() function name has been changed to ncbi_snp_query()")
@@ -18,6 +20,7 @@ ncbi_snp_summary <- function(...) {
 #' This function is defunct.
 #' @export
 #' @rdname NCBI_snp_query-defunct
+#' @return a error message telling the user that this function has been deprecated in favour of another function
 #' @keywords internal
 ncbi_snp_query2 <- function(...) {
   .Defunct(new = "ncbi_snp_query2", package = "rsnps", msg = "the ncbi_snp_query2() function name has been changed to ncbi_snp_query()")
@@ -26,6 +29,7 @@ ncbi_snp_query2 <- function(...) {
 #' This function is defunct.
 #' @export
 #' @rdname NCBI_snp_query-defunct
+#' @return a error message telling the user that this function has been deprecated in favour of another function
 #' @keywords internal
 NCBI_snp_query <- function(...) {
   .Defunct(new = "ncbi_snp_query", package = "rsnps", msg = "the NCBI_snp_query() function name has been changed to ncbi_snp_query()")
@@ -34,6 +38,7 @@ NCBI_snp_query <- function(...) {
 #' This function is defunct.
 #' @export
 #' @rdname NCBI_snp_query2-defunct
+#' @return a error message telling the user that this function has been deprecated in favour of another function
 #' @keywords internal
 NCBI_snp_query2 <- function(...) {
   .Defunct(new = "ncbi_snp_query2", package = "rsnps", msg = "the NCBI_snp_query2() function name has been changed to ncbi_snp_query()")

R/download_users.R

@@ -64,11 +64,11 @@ get_write <- function(x, y, ...) {
 #' written in the function download_users, and then searches against those
 #' variables for the path to the file saved. Alternatively, you can supply
 #' the path.
-#' @return A data.frame.
+#' @return A data.frame with openSNP user files retrieved from local storage
 #' @examples \dontrun{
-#' # dat <- read_users(name = "kevinmcc")
-#' # head(dat)
-#' # dat <- read_users(id = 285)
+#' dat <- read_users(name = "kevinmcc")
+#' head(dat)
+#' dat <- read_users(id = 285)
 #' }
 read_users <- function(name = NULL, id = NULL, path = NULL, ...) {
   if (is.null(name) && is.null(id) && is.null(path)) {

R/phenotypes.R

@@ -5,7 +5,7 @@
 #' @param userid ID of openSNP user.
 #' @param df Return data.frame (`TRUE`) or not (`FALSE`). Default: `FALSE`
 #' @param ... Curl options passed on to [crul::HttpClient]
-#' @return List of phenotypes for specified user(s).
+#' @return List of phenotypes for specified user(s) from openSNP.
 #'
 #' @examples \dontrun{
 #' phenotypes(userid = 1)

R/phenotypes_byid.R

@@ -7,7 +7,7 @@
 #' @param return_ Return data.frame (`TRUE`) or not (`FALSE`). Default: `FALSE`
 #' @param ... Curl options passed on to [crul::HttpClient]
 #' @return List of description of phenotype, list of known variants, or
-#' data.frame of variants for each user with that phenotype.
+#' data.frame of variants for each user with that phenotype retrieved from openSNP.
 #'
 #' @examples \dontrun{
 #' phenotypes_byid(phenotypeid = 12, return_ = "desc")

R/users.R

@@ -4,7 +4,7 @@
 #' @family opensnp-fxns
 #' @param df Return data.frame (`TRUE`) or not (`FALSE`). Default: `FALSE`
 #' @param ... Curl options passed on to [crul::HttpClient]
-#' @return List of openSNP users, their ID numbers, and XX if available.
+#' @return List of openSNP users, their ID numbers, and genome data if available.
 #' @examples \dontrun{
 #' # just the list
 #' data <- users(df = FALSE)

R/utils.R

@@ -82,15 +82,7 @@ split_to_df <- function(x, sep, fixed = FALSE, perl = TRUE, useBytes = FALSE, na
   return(tmp)
 }
 
-#' Tryget
-#'
-#' @export
-#' @keywords internal
-tryget <- function(x) {
-  return(tryCatch(return(x), error = function(e) {
-    return(NA)
-  }))
-}
+
 
 strtrim <- function(str) {
   gsub("^\\s+|\\s+$", "", str)