diff --git a/.Rhistory b/.Rhistory
deleted file mode 100644
index 8e3072e..0000000
--- a/.Rhistory
+++ /dev/null
@@ -1,474 +0,0 @@
-library(devtools)
-devtools::use_testthat()
-tempfile()
-download.nhanes.file <- function(file.name, year, destination = tempfile(), overwrite = TRUE) {
-url <- paste0("http://wwwn.cdc.gov/nchs/nhanes/", year, '/', file.name)
-# Make sure the destination folder ends in a trailing slash
-lastChar <- substr(destination, nchar(destination) - 1, nchar(destination))
-if(lastChar != '/') {
-lastChar <- paste0(lastChar, '/')
-}
-destination <- paste0(destination, file.name)
-if(overwrite == FALSE) {
-if(file.exists(destination) == TRUE) {
-return(destination)
-}
-}
-download.file(url, destination, method='curl', mode='w')
-return(destination)
-}
-download.nhanes.file("HEPG_G", "2011-2012")
-?file.path
-file.path("C:\\Users\\susmann\\AppData\\Local\\Temp", "test")
-download.nhanes.file <- function(file.name, year, destination = tempfile(), overwrite = TRUE) {
-url <- paste0("http://wwwn.cdc.gov/nchs/nhanes/", year, '/', file.name)
-destination <- file.path(destination, file.name)
-if(overwrite == FALSE) {
-if(file.exists(destination) == TRUE) {
-return(destination)
-}
-}
-download.file(url, destination, method='curl', mode='w')
-return(destination)
-}
-download.nhanes.file("HEPG_G", "2011-2012")
-download.nhanes.file("HEPG_G", "2011-2012")
-download.nhanes.file("HEPG_G", "2011-2012")
-?tempfile
-tempdir()
-download.nhanes.file <- function(file.name, year, destination = tempdir(), overwrite = TRUE) {
-url <- paste0("http://wwwn.cdc.gov/nchs/nhanes/", year, '/', file.name)
-destination <- file.path(destination, file.name)
-if(overwrite == FALSE) {
-if(file.exists(destination) == TRUE) {
-return(destination)
-}
-}
-download.file(url, destination, method='curl', mode='w')
-return(destination)
-}
-download.nhanes.file("HEPG_G", "2011-2012")
-file.path(tempdir(), "HEPG_G")
-file.path(tempdir(), "HEPG_G", ".XPT")
-download.nhanes.file <- function(file.name, year, destination = tempdir(), overwrite = TRUE) {
-url <- paste0("http://wwwn.cdc.gov/nchs/nhanes/", year, '/', file.name)
-if(grepl(".XPT", file.name) == FALSE) {
-file.name <- paste0(file.name, ".XPT")
-}
-destination <- file.path(destination, file.name)
-if(overwrite == FALSE) {
-if(file.exists(destination) == TRUE) {
-return(destination)
-}
-}
-download.file(url, destination, method='curl', mode='w')
-return(destination)
-}
-download.nhanes.file("HEPG_G", "2011-2012")
-valid <- switch(year,
-'2001-2002' = TRUE,
-'2003-2004' = TRUE,
-'2005-2006' = TRUE,
-'2007-2008' = TRUE,
-'2009-2010' = TRUE,
-'2011-2012' = TRUE,
-'2013-2014' = TRUE)
-year = '2001-2002'
-valid <- switch(year,
-'2001-2002' = TRUE,
-'2003-2004' = TRUE,
-'2005-2006' = TRUE,
-'2007-2008' = TRUE,
-'2009-2010' = TRUE,
-'2011-2012' = TRUE,
-'2013-2014' = TRUE)
-valid
-year = 'test'
-valid <- switch(year,
-'2001-2002' = TRUE,
-'2003-2004' = TRUE,
-'2005-2006' = TRUE,
-'2007-2008' = TRUE,
-'2009-2010' = TRUE,
-'2011-2012' = TRUE,
-'2013-2014' = TRUE)
-valid
-?switch
-valid <- switch(year,
-'2001-2002' = TRUE,
-'2003-2004' = TRUE,
-'2005-2006' = TRUE,
-'2007-2008' = TRUE,
-'2009-2010' = TRUE,
-'2011-2012' = TRUE,
-'2013-2014' = TRUE,
-FALSE)
-valid
-validate.year <- function(year) {
-valid <- switch(year,
-'2001-2002' = TRUE,
-'2003-2004' = TRUE,
-'2005-2006' = TRUE,
-'2007-2008' = TRUE,
-'2009-2010' = TRUE,
-'2011-2012' = TRUE,
-'2013-2014' = TRUE,
-FALSE)
-}
-validate.year(year)
-validate.year <- function(year) {
-valid <- switch(year,
-'2001-2002' = TRUE,
-'2003-2004' = TRUE,
-'2005-2006' = TRUE,
-'2007-2008' = TRUE,
-'2009-2010' = TRUE,
-'2011-2012' = TRUE,
-'2013-2014' = TRUE,
-FALSE)
-return(valid)
-}
-validate.year("2001-2002")
-validate.year <- function(year, throw.error = TRUE) {
-valid <- switch(year,
-'1999-2000' = TRUE,
-'2001-2002' = TRUE,
-'2003-2004' = TRUE,
-'2005-2006' = TRUE,
-'2007-2008' = TRUE,
-'2009-2010' = TRUE,
-'2011-2012' = TRUE,
-'2013-2014' = TRUE,
-FALSE)
-if(throw.error == TRUE && valid == FALSE) {
-stop(pasteo("Invalid year: ", year))
-}
-return(valid)
-}
-validate.year("t")
-validate.year <- function(year, throw.error = TRUE) {
-valid <- switch(year,
-'1999-2000' = TRUE,
-'2001-2002' = TRUE,
-'2003-2004' = TRUE,
-'2005-2006' = TRUE,
-'2007-2008' = TRUE,
-'2009-2010' = TRUE,
-'2011-2012' = TRUE,
-'2013-2014' = TRUE,
-FALSE)
-if(throw.error == TRUE && valid == FALSE) {
-stop(paste0("Invalid year: ", year))
-}
-return(valid)
-}
-validate.year("t")
-validate.year("2011-2012")
-download.nhanes.file <- function(file.name, year, destination = tempdir(), overwrite = TRUE) {
-validate.year()
-if(!dir.exists(destination)) {
-stop(paste0("Directory doesn't exist: ", destination))
-}
-url <- paste0("http://wwwn.cdc.gov/nchs/nhanes/", year, '/', file.name)
-if(grepl(".XPT", file.name) == FALSE) {
-file.name <- paste0(file.name, ".XPT")
-}
-destination <- file.path(destination, file.name)
-if(overwrite == FALSE) {
-if(file.exists(destination) == TRUE) {
-return(destination)
-}
-}
-download.file(url, destination, method='curl', mode='w')
-return(destination)
-}
-download.nhanes.file("HEPG_G", "2011-2012")
-download.nhanes.file <- function(file.name, year, destination = tempdir(), overwrite = TRUE) {
-validate.year(year)
-if(!dir.exists(destination)) {
-stop(paste0("Directory doesn't exist: ", destination))
-}
-url <- paste0("http://wwwn.cdc.gov/nchs/nhanes/", year, '/', file.name)
-if(grepl(".XPT", file.name) == FALSE) {
-file.name <- paste0(file.name, ".XPT")
-}
-destination <- file.path(destination, file.name)
-if(overwrite == FALSE) {
-if(file.exists(destination) == TRUE) {
-return(destination)
-}
-}
-download.file(url, destination, method='curl', mode='w')
-return(destination)
-}
-download.nhanes.file("HEPG_G", "2011-2012")
-download.nhanes.file("HEPG_G", "2011-2012", destination="test")
-?download.file
-download_nhanes_file <- function(file_name, year, destination = tempdir(), overwrite = TRUE) {
-validate_year(year)
-if(!dir.exists(destination)) {
-stop(paste0("Directory doesn't exist: ", destination))
-}
-url <- paste0("http://wwwn.cdc.gov/nchs/nhanes/", year, '/', file.name)
-if(grepl(".XPT", file_name) == FALSE) {
-file_name <- paste0(file_name, ".XPT")
-}
-destination <- file.path(destination, file_name)
-if(overwrite == FALSE) {
-if(file.exists(destination) == TRUE) {
-return(destination)
-}
-}
-download.file(url, destination, method='auto', mode='w')
-return(destination)
-}
-download_nhanes_file("HEPG_G", "2011-2012")
-demography_filename <- function(year) {
-validate_year(year)
-if(year == '1999-2000') {
-return("DEMO.XPT")
-}
-suffix = switch(year,
-'2001-2002' = 'B',
-'2003-2004' = 'C',
-'2005-2006' = 'D',
-'2007-2008' = 'E',
-'2009-2010' = 'F',
-'2011-2012' = 'G',
-'2013-2014' = 'H'
-)
-return(paste0("DEMO_", suffix, ".XPT"))
-}
-validate_year <- function(year, throw_error = TRUE) {
-valid <- switch(year,
-'1999-2000' = TRUE,
-'2001-2002' = TRUE,
-'2003-2004' = TRUE,
-'2005-2006' = TRUE,
-'2007-2008' = TRUE,
-'2009-2010' = TRUE,
-'2011-2012' = TRUE,
-'2013-2014' = TRUE,
-FALSE)
-if(throw_error == TRUE && valid == FALSE) {
-stop(paste0("Invalid year: ", year))
-}
-return(valid)
-}
-download_nhanes_file <- function(file_name, year, destination = tempdir(), overwrite = TRUE) {
-validate_year(year)
-if(!dir.exists(destination)) {
-stop(paste0("Directory doesn't exist: ", destination))
-}
-url <- paste0("http://wwwn.cdc.gov/nchs/nhanes/", year, '/', file.name)
-if(grepl(".XPT", file_name) == FALSE) {
-file_name <- paste0(file_name, ".XPT")
-}
-destination <- file.path(destination, file_name)
-if(overwrite == FALSE) {
-if(file.exists(destination) == TRUE) {
-return(destination)
-}
-}
-download.file(url, destination, method='auto', mode='w')
-return(destination)
-}
-load_nhanes_lab_data <- function(file_name, year, destination = tempdir(), merge_demographics = FALSE, overwrite = FALSE) {
-validate_year(year)
-full_path <- download_nhanes_file(file_name, year, destination, overwrite = overwrite)
-dat <- read.xport(full_path)
-return(dat)
-}
-load_nhanes_demography_data <- function(year, destination = tempdir(), overwrite = FALSE) {
-validate_year(year)
-full_path <- download_nhanes_file(demography_filename(year), year, destination, overwrite = overwrite)
-dat <- read.xport(full_path)
-return(dat)
-}
-download_nhanes_file("HEPG_G", "2011-2012")
-download_nhanes_file <- function(file_name, year, destination = tempdir(), overwrite = TRUE) {
-validate_year(year)
-if(!dir.exists(destination)) {
-stop(paste0("Directory doesn't exist: ", destination))
-}
-url <- paste0("http://wwwn.cdc.gov/nchs/nhanes/", year, '/', file_name)
-if(grepl(".XPT", file_name) == FALSE) {
-file_name <- paste0(file_name, ".XPT")
-}
-destination <- file.path(destination, file_name)
-if(overwrite == FALSE) {
-if(file.exists(destination) == TRUE) {
-return(destination)
-}
-}
-download.file(url, destination, method='auto', mode='w')
-return(destination)
-}
-download_nhanes_file("HEPG_G", "2011-2012")
-download_nhanes_file <- function(file_name, year, destination = tempdir(), overwrite = TRUE) {
-validate_year(year)
-if(!dir.exists(destination)) {
-stop(paste0("Directory doesn't exist: ", destination))
-}
-if(grepl(".XPT", file_name) == FALSE) {
-file_name <- paste0(file_name, ".XPT")
-}
-destination <- file.path(destination, file_name)
-if(overwrite == FALSE) {
-if(file.exists(destination) == TRUE) {
-return(destination)
-}
-}
-url <- paste0("http://wwwn.cdc.gov/nchs/nhanes/", year, '/', file_name)
-download.file(url, destination, method='auto', mode='w')
-return(destination)
-}
-download_nhanes_file("HEPG_G", "2011-2012")
-download_nhanes_file <- function(file_name, year, destination = tempdir(), overwrite = TRUE) {
-validate_year(year)
-if(!dir.exists(destination)) {
-stop(paste0("Directory doesn't exist: ", destination))
-}
-if(grepl(".XPT", file_name) == FALSE) {
-file_name <- paste0(file_name, ".XPT")
-}
-destination <- file.path(destination, file_name)
-if(overwrite == FALSE) {
-if(file.exists(destination) == TRUE) {
-return(destination)
-}
-}
-url <- paste0("http://wwwn.cdc.gov/nchs/nhanes/", year, '/', file_name)
-download.file(url, destination, method='curl', mode='w')
-return(destination)
-}
-download_nhanes_file("HEPG_G", "2011-2012")
-download_nhanes_file <- function(file_name, year, destination = tempdir(), overwrite = TRUE) {
-validate_year(year)
-if(!dir.exists(destination)) {
-stop(paste0("Directory doesn't exist: ", destination))
-}
-if(grepl(".XPT", file_name) == FALSE) {
-file_name <- paste0(file_name, ".XPT")
-}
-destination <- file.path(destination, file_name)
-if(overwrite == FALSE) {
-if(file.exists(destination) == TRUE) {
-return(destination)
-}
-}
-url <- paste0("http://wwwn.cdc.gov/nchs/nhanes/", year, '/', file_name)
-download.file(url, destination, method='auto', mode='w')
-return(destination)
-}
-download_nhanes_file("HEPG_G", "2011-2012")
-download_nhanes_file <- function(file_name, year, destination = tempdir(), overwrite = TRUE) {
-validate_year(year)
-if(!dir.exists(destination)) {
-stop(paste0("Directory doesn't exist: ", destination))
-}
-if(grepl(".XPT", file_name) == FALSE) {
-file_name <- paste0(file_name, ".XPT")
-}
-destination <- file.path(destination, file_name)
-if(overwrite == FALSE) {
-if(file.exists(destination) == TRUE) {
-return(destination)
-}
-}
-url <- paste0("http://wwwn.cdc.gov/Nchs/Nhanes/", year, '/', file_name)
-download.file(url, destination, method='auto', mode='w')
-return(destination)
-}
-download_nhanes_file("HEPG_G", "2011-2012")
-download_nhanes_file("HEPA_G", "2011-2012")
-demography_filename("2011-2012")
-demography_filename("1999-2000")
-demography_filename("1999-20002")
-load_nhanes_lab_data <- function(file_name, year, destination = tempdir(), merge_demographics = FALSE, overwrite = FALSE) {
-validate_year(year)
-full_path <- download_nhanes_file(file_name, year, destination, overwrite = overwrite)
-dat <- read.xport(full_path)
-return(dat)
-}
-load_nhanes_lab_data("UHM_G", "2011-2012")
-devtools::use_package("foreign")
-devtools::use_package("survey")
-library(RNHANES)
-library(RNHANES)
-validate_year("2011-2012")
-demography_filename("2011-2012")
-download_nhanes_file("HEPA_G", "2011-2012")
-load_nhanes_lab_data("HEPA_G", "2011-2012")
-devtools::document()
-devtools::document()
-devtools::document()
-load_nhanes_demography_data("2011-2012")
-library(RNHANES)
-load_nhanes_demography_data("2011-2012")
-library(RNHANES)
-library(RNHANES)
-load_nhanes_demography_data("2011-2012")
-library(RNHANES)
-load_nhanes_demography_data("2011-2012")
-library(RNHANES)
-load_nhanes_demography_data("2011-2012")
-read.xport("C:\Users\susmann\AppData\Local\Temp\RtmpW0egpT/DEMO_G.XPT")
-read.xport("C:\\Users\\susmann\\AppData\\Local\\Temp\\RtmpW0egpT/DEMO_G.XPT")
-library(foreign)
-read.xport("C:\\Users\\susmann\\AppData\\Local\\Temp\\RtmpW0egpT/DEMO_G.XPT")
-library(RNHANES)
-read.xport("C:\\Users\\susmann\\AppData\\Local\\Temp\\RtmpW0egpT/DEMO_G.XPT")
-load_nhanes_demography_data("2011-2012")
-test <- load_nhanes_demography_data("2011-2012")
-load_nhanes_demography_data("2011-2012")
-test <- load_nhanes_demography_data("2011-2012", overwrite = TRUE)
-read.xport("C:\\Users\\susmann\\AppData\\Local\\Temp\\RtmpYzLB61/DEMO_G.XPT")
-read.xport("C:\\Users\\susmann\\AppData\\Local\\Temp\\RtmpW0egpT/DEMO_G.XPT")
-download.file
-?download.file
-library(RNHANES)
-test <- load_nhanes_demography_data("2011-2012", overwrite = TRUE)
-test
-load_nhanes_demography_data("2011-2012", overwrite = TRUE)
-library(RNHANES)
-devtools::document()
-devtools::document()
-setwd("C:/Users/susmann/Dropbox/RNHANES")
-devtools::document()
-library(RNHANES)
-?load_nhanes_lab_data
-load_nhanes_data <- function(file_name, year, destination = tempdir(), merge_demographics = FALSE, overwrite = FALSE) {
-validate_year(year)
-full_path <- download_nhanes_file(file_name, year, destination, overwrite = overwrite)
-dat <- read.xport(full_path)
-if(merge_demographics == FALSE) {
-demography_data <- load_nhanes_demography_data(year, destination = destination, overwrite = overwrite)
-dat <- merge.data.with.demographics(demography_data, dat)
-}
-return(dat)
-}
-devtools::document()
-library(RNHANES)
-library(RNHANES)
-load_nhanes_data("EPH_E", "2007-2008")
-library(RNHANES)
-load_nhanes_data("EPH_E", "2007-2008")
-with_demo <- load_nhanes_data("EPH_E", "2007-2008", merge_demographics = TRUE)
-head(with_demo)
-"SEQN" %in% names(with_demo)
-"SEQN1" %in% names(with_demo)
-library(RNHANES)
-devtools::document()
-library(RNHANES)
-?load_nhanes_demography_data
-devtools::document()
-library(RNHANES)
-?load_nhanes_data
-library(RNHANES)
-load_nhanes_data("EPH_G", "2011-2012")
-devtools::document()
-library(RNHANES)
-load_nhanes_data("EPH_G", "2011-2012", demographics = TRUE)
-install_github("silentspringinstitute/RNHANES")
-install_github("silentspringinstitute/RNHANES")
diff --git a/.gitignore b/.gitignore
index bc77c15..f7b70de 100644
--- a/.gitignore
+++ b/.gitignore
@@ -4,33 +4,23 @@ ehthumbs.db
 
 # Folder config file
 Desktop.ini
-
 # Recycle Bin used on file shares
 $RECYCLE.BIN/
-
 # Windows Installer files
 *.cab
 *.msi
 *.msm
 *.msp
-
 # Windows shortcuts
 *.lnk
-
 # =========================
 # Operating System Files
-# =========================
-
 # OSX
-# =========================
-
 .DS_Store
 .AppleDouble
 .LSOverride
-
 # Thumbnails
 ._*
-
 # Files that might appear in the root of a volume
 .DocumentRevisions-V100
 .fseventsd
@@ -38,13 +28,16 @@ $RECYCLE.BIN/
 .TemporaryItems
 .Trashes
 .VolumeIcon.icns
-
 # Directories potentially created on remote AFP share
 .AppleDB
 .AppleDesktop
 Network Trash Folder
 Temporary Items
 .apdisk
-
-.Rbuildignore
 .Rproj.user
+inst/doc
+
+vignettes/introduction_cache
+RNHANES.Rproj
+.Rhistory
+.Rdata
diff --git a/RNHANES.Rproj b/RNHANES.Rproj
deleted file mode 100644
index 398aa14..0000000
--- a/RNHANES.Rproj
+++ /dev/null
@@ -1,20 +0,0 @@
-Version: 1.0
-
-RestoreWorkspace: Default
-SaveWorkspace: Default
-AlwaysSaveHistory: Default
-
-EnableCodeIndexing: Yes
-UseSpacesForTab: Yes
-NumSpacesForTab: 2
-Encoding: UTF-8
-
-RnwWeave: knitr
-LaTeX: pdfLaTeX
-
-AutoAppendNewline: Yes
-StripTrailingWhitespace: Yes
-
-BuildType: Package
-PackageUseDevtools: Yes
-PackageInstallArgs: --no-multiarch --with-keep.source