Version 0.6.1 release

cjendres1 · Oct 8, 2015 · 6750eec · 6750eec
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: nhanesA
 Version: 0.6.1
-Date: 2015-09-30
+Date: 2015-10-07
 Title: NHANES Data Retrieval
 Author: Christopher Endres
 Maintainer: Christopher Endres <[email protected]>
@@ -10,7 +10,7 @@ Description: Utility to retrieve data from the National Health and Nutrition Exa
 License: GPL (>= 2)
 LazyData: FALSE
 URL: https://github.com/cjendres1/nhanes
-Packaged: 2015-09-30 18:15:14 UTC; Endres
+Packaged: 2015-10-07 18:15:14 UTC; Endres
 Suggests: knitr,
     rmarkdown
 VignetteBuilder: knitr
diff --git a/INDEX b/INDEX
@@ -1,6 +1,7 @@
 Functions:
 =========
 
+browseNHANES			      Browse the NHANES website
 nhanes                        Download an nhanes table
 nhanesDisplayTableNames       Display names of nhanes tables in a given survey
 nhanesDisplayTableVariables   Display names of Variables in a given nhanes table

diff --git a/NAMESPACE b/NAMESPACE
@@ -21,5 +21,6 @@ importFrom(stringr,str_split)
 importFrom(stringr,str_sub)
 importFrom(stringr,str_to_title)
 importFrom(stringr,str_to_upper)
+importFrom(utils,browseURL)
 importFrom(utils,object.size)
 importFrom(xml2,read_html)
diff --git a/R/nhanes.R b/R/nhanes.R
@@ -55,12 +55,9 @@ data_idx["I"] <- '2015-2016'
 
 anomalytables2005 <- c('CHLMD_DR', 'SSUECD_R', 'HSV_DR')
 
-# An internal function that converts a year into the nhanes interval.
-# E.g. 2003 is converted to '2003-2004'
-# @param year where year is numeric in yyyy format
-# @return The 2-year interval that includes the year, e.g. 2001-2002
-# 
 #------------------------------------------------------------------------------
+# An internal function that determines which survey year the table belongs to.
+# For most tables the year can be determined by the letter suffix.
 get_year_from_nh_table <- function(nh_table) {
 if(nh_table %in% anomalytables2005) {return('2005-2006')}
 nhloc <- data.frame(stringr::str_locate_all(nh_table, '_'))
@@ -75,13 +72,17 @@ if(nn!=0){ #Underscores were found
       } else {stop('Invalid table name')}
     }
     return(data_idx[idx])
-  } else { ## Undersore not 2nd to last. Assume table is from the first set.
+  } else { ## Underscore not 2nd to last. Assume table is from the first set.
     return("1999-2000")}
 } else #If there are no underscores then table must be from first survey
   nh_year <- "1999-2000"
 }
 #------------------------------------------------------------------------------
-
+# An internal function that converts a year into the nhanes interval.
+# E.g. 2003 is converted to '2003-2004'
+# @param year where year is numeric in yyyy format
+# @return The 2-year interval that includes the year, e.g. 2001-2002
+# 
 get_nh_survey_years <- function(year) {
   if(as.character(year) %in% names(nh_years)) {
     return( as.character(nh_years[as.character(year)]) )
@@ -237,8 +238,8 @@ nhanesTableVars <- function(nh_surveygroup, nh_table, details = FALSE, nchar=100
 #' @param nh_table The name of the specific table to retrieve.
 #' @return The table is returned as a data frame.
 #' @details Downloads a table from the NHANES website in its entirety. NHANES tables 
-#' are stored in SAS '.XPT' format. Function nhanes uses sasxport.get from package H
-#' misc to retrieve the data.
+#' are stored in SAS '.XPT' format. Function nhanes uses sasxport.get from package Hmisc 
+#' to retrieve the data.
 #' @examples 
 #' nhanes('BPX_E')
 #' nhanes('FOLATE_F')
@@ -272,7 +273,7 @@ nhanes <- function(nh_table) {
 #' but does not return the table itself.
 #' 
 #' @importFrom Hmisc sasxport.get
-#' @importFrom stringr str_c
+#' @importFrom stringr str_c str_to_upper
 #' @importFrom utils object.size
 #' @param nh_table The name of the specific table to retrieve
 #' @return The following attributes are returned as a list \cr
@@ -296,6 +297,7 @@ nhanesAttr <- function(nh_table) {
     nh_year <- get_year_from_nh_table(nh_table)
     url <- str_c(nhanesURL, nh_year, '/', nh_table, '.XPT', collapse='')
     tmp <- sasxport.get(url)
+    names(tmp) <- str_to_upper(names(tmp))
     nhtatt <- attributes(tmp)
     nhtatt$row.names <- NULL
     nhtatt$nrow <- nrow(tmp)
@@ -346,6 +348,7 @@ nhanesAttr <- function(nh_table) {
 #' @examples
 #' nhanesTranslate('DEMO_B', c('DMDBORN','DMDCITZN'))
 #' nhanesTranslate('BPX_F', 'BPACSZ', details=TRUE)
+#' \donttest{nhanesTranslate('BPX_F', 'BPACSZ', data=nhanes('BPX_F'))}
 #' @export
 #' 
 nhanesTranslate <- function(nh_table, colnames, data = NULL, nchar = 32, details=FALSE) {
@@ -436,6 +439,7 @@ nhanesTranslate <- function(nh_table, colnames, data = NULL, nchar = 32, details
 #' The browser may be directed to a specific year, survey, or table.
 #' 
 #' @importFrom stringr str_c str_to_title str_split str_sub str_extract_all
+#' @importFrom utils browseURL
 #' @param year The year in yyyy format where 1999 <= yyyy <= 2014.
 #' @param nh_surveygroup The type of survey (DEMOGRAPHICS, DIETARY, EXAMINATION, LABORATORY, QUESTIONNAIRE).
 #' Abbreviated terms may also be used: (DEMO, DIET, EXAM, LAB, Q).

diff --git a/man/nhanes.Rd b/man/nhanes.Rd
@@ -17,8 +17,8 @@ Use to download NHANES data tables that are in SAS format.
 }
 \details{
 Downloads a table from the NHANES website in its entirety. NHANES tables
-are stored in SAS '.XPT' format. Function nhanes uses sasxport.get from package H
-misc to retrieve the data.
+are stored in SAS '.XPT' format. Function nhanes uses sasxport.get from package Hmisc
+to retrieve the data.
 }
 \examples{
 nhanes('BPX_E')

diff --git a/man/nhanesTranslate.Rd b/man/nhanesTranslate.Rd
@@ -38,5 +38,6 @@ values are replaced with the code translations.
 \examples{
 nhanesTranslate('DEMO_B', c('DMDBORN','DMDCITZN'))
 nhanesTranslate('BPX_F', 'BPACSZ', details=TRUE)
+\donttest{nhanesTranslate('BPX_F', 'BPACSZ', data=nhanes('BPX_F'))}
 }
 
diff --git a/vignettes/Introducing_nhanesA.Rmd b/vignettes/Introducing_nhanesA.Rmd
@@ -1,10 +1,10 @@
 ---
-title: "Introducing_nhanesA"
+title: "Introducing nhanesA"
 author: "Christopher Endres"
 date: "`r Sys.Date()`"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{Introducing_nhanesA}
+  %\VignetteIndexEntry{Introducing nhanesA}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---

diff --git a/vignettes/Introducing_nhanesA.html b/vignettes/Introducing_nhanesA.html
@@ -10,9 +10,9 @@
 
 <meta name="author" content="Christopher Endres" />
 
-<meta name="date" content="2015-10-05" />
+<meta name="date" content="2015-10-07" />
 
-<title>Introducing_nhanesA</title>
+<title>Introducing nhanesA</title>
 
 
 
@@ -52,9 +52,9 @@
 
 
 <div id="header">
-<h1 class="title">Introducing_nhanesA</h1>
+<h1 class="title">Introducing nhanesA</h1>
 <h4 class="author"><em>Christopher Endres</em></h4>
-<h4 class="date"><em>2015-10-05</em></h4>
+<h4 class="date"><em>2015-10-07</em></h4>
 </div>