Nothing
## ----setup, include = FALSE-------------------------------------------------------------
options(width = 90)
knitr::opts_chunk$set(collapse = TRUE, comment = NA)
## ---- eval = FALSE----------------------------------------------------------------------
# library(tidyverse)
# library(duawranglr)
#
# ## get crosswalk and admin data files
# dua_cw_file <- system.file('extdata', 'dua_cw.csv', package = 'duawranglr')
# admin_file <- system.file('extdata', 'admin_data.csv', package = 'duawranglr')
#
# ## set the DUA crosswalk
# set_dua_cw(dua_cw_file)
## ---- echo = FALSE----------------------------------------------------------------------
suppressPackageStartupMessages(library(dplyr))
suppressPackageStartupMessages(library(readr))
library(duawranglr)
dua_cw_file <- system.file('extdata', 'dua_cw.csv', package = 'duawranglr')
admin_file <- system.file('extdata', 'admin_data.csv', package = 'duawranglr')
set_dua_cw(dua_cw_file)
## ---------------------------------------------------------------------------------------
## compare level II and III restrictions
see_dua_options(level = c('level_ii', 'level_iii'))
## ---------------------------------------------------------------------------------------
## check all level restrictions
see_dua_options()
## ---------------------------------------------------------------------------------------
## set DUA level
set_dua_level('level_ii', deidentify_required = TRUE, id_column = 'sid')
## ---------------------------------------------------------------------------------------
## see set DUA level
see_dua_level(show_restrictions = TRUE)
## ---- eval = FALSE----------------------------------------------------------------------
# ## read in raw administrative data
# df <- read_dua_file(admin_file)
# df
## ---- echo = FALSE----------------------------------------------------------------------
## read in raw administrative data
df <- readr::read_csv(admin_file,
col_types = cols(sid = col_character(),
sname = col_character(),
dob = col_character(),
gender = col_integer(),
raceeth = col_integer(),
tid = col_integer(),
tname = col_character(),
zip = col_integer(),
mathscr = col_integer(),
readscr = col_integer()
)
)
df
## ---- echo = FALSE----------------------------------------------------------------------
dff <- df
## ---- echo = FALSE----------------------------------------------------------------------
## deidentify data
tmpdir <- tempdir()
df <- deid_dua(df, write_crosswalk = TRUE, id_length = 20,
crosswalk_filename = file.path(tmpdir, 'tmp.csv'))
## ---- eval = FALSE----------------------------------------------------------------------
# ## deidentify data
# df <- deid_dua(df, write_crosswalk = TRUE, id_length = 20)
## ---- echo = FALSE----------------------------------------------------------------------
## show crosswalk
cw <- readr::read_csv(file.path(tmpdir, 'tmp.csv'),
col_types = cols(.default = 'c'))
cw
rm(tmpdir)
## ---------------------------------------------------------------------------------------
## show data frame
df
## ---- echo = FALSE----------------------------------------------------------------------
df <- dff
## ---- echo = FALSE----------------------------------------------------------------------
tmpdir <- tempdir()
cw2 <- readr::read_csv('../tests/testthat/testdata/crosswalk_full.csv',
col_types = cols(.default = 'c'))
readr::write_csv(cw2, file.path(tmpdir, 'crosswalk_full.csv'))
cw2
## ---- echo = FALSE----------------------------------------------------------------------
df <- deid_dua(df, existing_crosswalk = file.path(tmpdir, 'crosswalk_full.csv'))
rm(tmpdir)
## ---------------------------------------------------------------------------------------
df
## ---- echo = FALSE----------------------------------------------------------------------
df <- dff
## ---- echo = FALSE----------------------------------------------------------------------
tmpdir <- tempdir()
cw3 <- readr::read_csv('../tests/testthat/testdata/crosswalk_partial.csv',
col_types = cols(.default = 'c'))
readr::write_csv(cw3, file.path(tmpdir, 'crosswalk_partial.csv'))
cw3
## ---- echo = FALSE----------------------------------------------------------------------
df <- deid_dua(df, existing_crosswalk = file.path(tmpdir, 'crosswalk_partial.csv'))
## ---------------------------------------------------------------------------------------
df
## ---- echo = FALSE----------------------------------------------------------------------
cw4 <- readr::read_csv(file.path(tmpdir, 'crosswalk_partial.csv'),
col_types = cols(.default = 'c'))
rm(tmpdir)
cw4
## ---------------------------------------------------------------------------------------
## write data to disk with one last check
write_dua_df(df, 'cleaned_data.csv', output_type = 'csv')
## ---------------------------------------------------------------------------------------
## check
check_dua_restrictions(df)
## ---------------------------------------------------------------------------------------
## remove restricted columns
df <- df %>% select(-c(sname, dob, tname, zip))
## check again
check_dua_restrictions(df)
## ---------------------------------------------------------------------------------------
df
## ---- eval = FALSE----------------------------------------------------------------------
# ## write data to disk
# write_dua_df(df, 'cleaned_data_lev_ii.csv', output_type = 'csv')
## ---- eval = FALSE----------------------------------------------------------------------
# ## save template to disk
# make_dua_template('clean_data.R')
## ---- echo = FALSE----------------------------------------------------------------------
file <- file.path(tempdir(), 'clean_data.R')
make_dua_template(file, answer_list = list('N','','N','',''))
writeLines(readLines(file))
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