Package 'nhanesA' reference manual

Title:	NHANES Data Retrieval
Description:	Utility to retrieve data from the National Health and Nutrition Examination Survey (NHANES) website <https://www.cdc.gov/nchs/nhanes/index.htm>.
Authors:	Christopher Endres [aut, cre], Laha Ale [aut] , Robert Gentleman [aut], Deepayan Sarkar [aut]
Maintainer:	Christopher Endres <[email protected]>
License:	GPL (>= 2)
Version:	1.1.7
Built:	2024-11-27 01:23:12 UTC
Source:	https://github.com/cjendres1/nhanes

Open a browser to NHANES.

Description

The browser may be directed to a specific year, survey, or table.

Usage

browseNHANES(
  year = NULL,
  data_group = NULL,
  nh_table = NULL,
  local = TRUE,
  browse = TRUE
)
browseNHANES(
  year = NULL,
  data_group = NULL,
  nh_table = NULL,
  local = TRUE,
  browse = TRUE
)

Arguments

`year`	The year in yyyy format where 1999 <= yyyy.
`data_group`	The type of survey (DEMOGRAPHICS, DIETARY, EXAMINATION, LABORATORY, QUESTIONNAIRE). Abbreviated terms may also be used: (DEMO, DIET, EXAM, LAB, Q).
`nh_table`	The name of an NHANES table.
`local`	logical flag. If `TRUE`, and a local or alternative source was specificed using the environment variable `NHANES_TABLE_BASE`, this will be used in preference to the CDC website at https://wwwn.cdc.gov for named tables.
`browse`	logical flag, indicating whether the specific NHANES site should be opened using a browser (which is the default behaviour).

Details

By default, browseNHANES will open a web browser to the specified NHANES site.

Value

A character string giving the URL, invisibly if the URL is also opened using browseURL.

Examples

browseNHANES(browse = FALSE)       # Defaults to the main data sets page
browseNHANES(2005)                 # The main page for the specified survey year
browseNHANES(2009, 'EXAM')         # Page for the specified year and survey group
browseNHANES(nh_table = 'VIX_D')   # Page for a specific table
browseNHANES(nh_table = 'DXA')     # DXA main page
browseNHANES(browse = FALSE)       # Defaults to the main data sets page
browseNHANES(2005)                 # The main page for the specified survey year
browseNHANES(2009, 'EXAM')         # Page for the specified year and survey group
browseNHANES(nh_table = 'VIX_D')   # Page for a specific table
browseNHANES(nh_table = 'DXA')     # DXA main page

Download an NHANES table and return as a data frame.

Description

Use to download NHANES data tables that are in SAS format.

Usage

nhanes(
  nh_table,
  includelabels = FALSE,
  translated = TRUE,
  cleanse_numeric = FALSE,
  nchar = 128,
  adjust_timeout = TRUE
)
nhanes(
  nh_table,
  includelabels = FALSE,
  translated = TRUE,
  cleanse_numeric = FALSE,
  nchar = 128,
  adjust_timeout = TRUE
)

Arguments

`nh_table`	The name of the specific table to retrieve.
`includelabels`	If TRUE, then include SAS labels as variable attribute (default = FALSE).
`translated`	translated whether the variables are translated.
`cleanse_numeric`	Logical flag. If `TRUE`, some special codes in numeric variables, such as ‘Refused’ and ‘Don't know’ will be converted to `NA`.
`nchar`	Maximum length of translated string (default = 128). Ignored if translated=FALSE.
`adjust_timeout`	Typically a logical flag indicating whether the default `download.file` timeout option should be adjusted by taking into account the size of the file to be downloaded, as reported by the server. The value can also be a positive numeric value, in which case it is used as a further multiplicative factor for the default calculation.

Details

Downloads a table from the NHANES website as is, i.e. in its entirety with no modification or cleansing. If the environment variable NHANES_TABLE_BASE was set during startup, the value of this variable is used as the base URL instead of https://wwwn.cdc.gov (this allows the use of a local or alternative mirror of the CDC data). NHANES tables are stored in SAS '.XPT' format but are imported as a data frame. The nhanes function cannot be used to import limited access data.

Value

The table is returned as a data frame.

Examples

bpx_e = nhanes('BPX_E')
dim(bpx_e)
folate_f = nhanes('FOLATE_F', includelabels = TRUE)
dim(folate_f)
bpx_e = nhanes('BPX_E')
dim(bpx_e)
folate_f = nhanes('FOLATE_F', includelabels = TRUE)
dim(folate_f)

Returns the attributes of an NHANES data table.

Description

Returns attributes such as number of rows, columns, and memory size, but does not return the table itself.

Usage

nhanesAttr(nh_table)
nhanesAttr(nh_table)

Arguments

nh_table

The name of the specific table to retrieve

Details

nhanesAttr allows one to check the size and other charactersistics of a data table before importing into R. To retrieve these characteristics, the specified table is downloaded, characteristics are determined, then the table is deleted. Downloads a table from the NHANES website as is, i.e. in its entirety with no modification or cleansing. If the environment variable NHANES_TABLE_BASE was set during startup, the value of this variable is used as the base URL instead of https://wwwn.cdc.gov (this allows the use of a local or alternative mirror of the CDC data).

Value

The following attributes are returned as a list
nrow = number of rows
ncol = number of columns
names = name of each column
unique = true if all SEQN values are unique
na = number of 'NA' cells in the table
size = total size of table in bytes
types = data types of each column

Examples

bpx_e = nhanesAttr('BPX_E')
length(bpx_e)
folate_f = nhanesAttr('FOLATE_F')
length(folate_f)
bpx_e = nhanesAttr('BPX_E')
length(bpx_e)
folate_f = nhanesAttr('FOLATE_F')
length(folate_f)

Display codebook for selected variable.

Description

Returns full NHANES codebook including Variable Name, SAS Label, English Text, Target, and Value distribution.

Usage

nhanesCodebook(nh_table, colname = NULL, dxa = FALSE)
nhanesCodebook(nh_table, colname = NULL, dxa = FALSE)

Arguments

`nh_table`	The name of the NHANES table that contains the desired variable.
`colname`	The name of the table column (variable).
`dxa`	If TRUE then the 2005-2006 DXA codebook will be used (default=FALSE).

Details

Each NHANES variable has a codebook that provides a basic description as well as the distribution or range of values. This function returns the full codebook information for the selected variable. If the environment variable NHANES_TABLE_BASE was set during startup, the value of this variable is used as the base URL instead of https://wwwn.cdc.gov (this allows the use of a local or alternative mirror of the CDC documentation).

Value

The codebook is returned as a list object. Returns NULL upon error.

Examples

nhanesCodebook('AUX_D', 'AUQ020D')
nhanesCodebook('BPX_J', 'BPACSZ')
bpx_code = nhanesCodebook('BPX_J')
length(bpx_code)
nhanesCodebook('AUX_D', 'AUQ020D')
nhanesCodebook('BPX_J', 'BPACSZ')
bpx_code = nhanesCodebook('BPX_J')
length(bpx_code)

Parse NHANES doc URL

Description

Download and parse an NHANES doc file from a URL

Usage

nhanesCodebookFromURL(url)
nhanesCodebookFromURL(url)

Arguments

url

URL to be downloaded

Details

Downloads and parses an NHANES doc file from a URL and returns it as a list

Value

list with one element for each variable

Import Dual Energy X-ray Absorptiometry (DXA) data.

Description

DXA data were acquired from 1999-2006.

Usage

nhanesDXA(year, suppl = FALSE, destfile = NULL, adjust_timeout = TRUE)
nhanesDXA(year, suppl = FALSE, destfile = NULL, adjust_timeout = TRUE)

Arguments

`year`	The year of the data to import, where 1999<=year<=2006.
`suppl`	If TRUE then retrieve the supplemental data (default=FALSE).
`destfile`	The name of a destination file. If NULL then the data are imported into the R environment but no file is created.
`adjust_timeout`	Typically a logical flag indicating whether the default `download.file` timeout option should be adjusted by taking into account the size of the file to be downloaded, as reported by the server. The value can also be a positive numeric value, in which case it is used as a further multiplicative factor for the default calculation.

Details

Provide destfile in order to write the data to file. If destfile is not provided then the data will be imported into the R environment.

Value

By default the table is returned as a data frame. When downloading to file, the return argument is the integer code from download.file where 0 means success and non-zero indicates failure to download.

Examples

dxa_b <- nhanesDXA(2001)
dxa_c_s <- nhanesDXA(2003, suppl=TRUE)
## Not run: dxa = nhanesDXA(1999, destfile="dxx.xpt")
dxa_b <- nhanesDXA(2001)
dxa_c_s <- nhanesDXA(2003, suppl=TRUE)
## Not run: dxa = nhanesDXA(1999, destfile="dxx.xpt")

Parse NHANES doc URL

Description

Download an NHANES table from URL

Usage

nhanesFromURL(
  url,
  translated = TRUE,
  cleanse_numeric = TRUE,
  nchar = 128,
  adjust_timeout = TRUE
)
nhanesFromURL(
  url,
  translated = TRUE,
  cleanse_numeric = TRUE,
  nchar = 128,
  adjust_timeout = TRUE
)

Arguments

`url`	URL of XPT file to be downloaded
`translated`	logical, whether variable codes should be translated
`cleanse_numeric`	Logical flag. If `TRUE`, some special codes in numeric variables, such as ‘Refused’ and ‘Don't know’ will be converted to `NA`.
`nchar`	integer, labels are truncated after this
`adjust_timeout`	Typically a logical flag indicating whether the default `download.file` timeout option should be adjusted by taking into account the size of the file to be downloaded, as reported by the server. The value can also be a positive numeric value, in which case it is used as a further multiplicative factor for the default calculation.

Details

Downloads an NHANES table from a URL and returns it as a data frame

Value

data frame

Download and parse NHANES manifests

Description

Downloads and parses NHANES manifests for public data (available at https://wwwn.cdc.gov/Nchs/Nhanes/search/DataPage.aspx), limited access data (https://wwwn.cdc.gov/Nchs/Nhanes/search/DataPage.aspx?Component=LimitedAccess), and variables (https://wwwn.cdc.gov/nchs/nhanes/search/variablelist.aspx?Component=Demographics, etc.), and returns them as data frames.

Usage

nhanesManifest(
  which = c("public", "limitedaccess", "variables"),
  sizes = FALSE,
  dxa = FALSE,
  component = NULL,
  verbose = getOption("verbose"),
  use_cache = TRUE,
  max_age = 24 * 60 * 60
)
nhanesManifest(
  which = c("public", "limitedaccess", "variables"),
  sizes = FALSE,
  dxa = FALSE,
  component = NULL,
  verbose = getOption("verbose"),
  use_cache = TRUE,
  max_age = 24 * 60 * 60
)

Arguments

`which`	Either "public" or "limitedaccess" to get a manifest of available tables, or "variables" to get a manifest of available variables.
`sizes`	Logical, whether to compute data file sizes (as reported by the server) and include them in the result.
`dxa`	Logical, whether to include information on DXA tables. These tables contain imputed imputed Dual Energy X-ray Absorptiometry measurements, and are listed separately, not in the main listing.
`component`	An optional character string specifying the component for which the public data manifest is to be downloaded. Valid values are `"demographics"`, `"dietary"`, `"examination"`, `"laboratory"`, and `"questionnaire"`. Partial matching is allowed, and case is ignored. Specifying a component will return a subset of the tables, but has the advantage that the result will include a description of each table.
`verbose`	Logical flag indicating whether information on progress should be reported.
`use_cache`	Logical flag indicating whether a cached version (from a previous download in the same session) should be used.
`max_age`	Maximum allowed age of the cache in seconds (defaults to 24 hours). Cached versions that are older are ignored, even if available.

Value

A data frame, with columns that depend on which. For a manifest of tables, columns are "Table", "DocURL", "DataURL", "Years", "Date.Published". If component is specified, an additional column "Description" giving a description of the table will be included. If sizes = TRUE, an additional column "DataSize" giving the data file sizes in bytes (as reported by the server) is included. For limited access tables, the "DataURL" and "DataSize" columns are omitted. For a manifest of variables, columns are "VarName", "VarDesc", "Table", "TableDesc", "BeginYear", "EndYear", "Component", and "UseConstraints".

Note

Duplicate rows are removed from the result. Most of these duplicates arise from duplications in the source tables for multi-cycle tables (which are repeated once for each cycle). One special case is the WHQ table which has two variables, WHD120 and WHQ030, duplicated with differing variable descriptions. These are removed explicitly, keeping only the first occurrence.

Examples

manifest <- nhanesManifest(sizes = FALSE)
dim(manifest)

manifest <- nhanesManifest(sizes = FALSE)
dim(manifest)

Options for the nhanesA package

Description

Set and retrieve global options controlling the behaviour of certain functions in the package.

Usage

nhanesOptions(...)
nhanesOptions(...)

Arguments

...

either one or more named arguments giving options to be set (in the form key = value), or a single unnamed character string to retrieve a setting.

Details

The 'nhanesOptions()' function can be used in two forms, to set or get options. Options can be set using 'nhanesOptions(key1 = value1, key2 = value2)'. Options can be retrieved (one at a time) using 'nhanesOptions("key")'. When called with no arguments, all currently set options are returned as a list.

Options currently used in the package are 'use.db' (logical flag controlling whether a database should be used if available), and 'log.access', a logical flag that logs any attempted URL access by printing the URL).

Value

When retrieving an option, the value of the option, or NULL if the option has not been set. When setting one or more options, a list (invisibly) containing the previous values (possibly NULL) of the options being set.

Author(s)

Deepayan Sarkar <[email protected]>

Examples

 nhanesOptions(foo = "bar")
 nhanesOptions()
 print(nhanesOptions(foo = NULL))
nhanesOptions(foo = "bar")
 nhanesOptions()
 print(nhanesOptions(foo = NULL))

Perform a search over the comprehensive NHANES variable list.

Description

The descriptions in the master variable list will be filtered by the provided search terms to retrieve a list of relevant variables. The search can be restricted to specific survey years by specifying ystart and/or ystop.

Usage

nhanesSearch(
  search_terms = NULL,
  exclude_terms = NULL,
  data_group = NULL,
  ignore.case = FALSE,
  ystart = NULL,
  ystop = NULL,
  includerdc = FALSE,
  nchar = 128,
  namesonly = FALSE
)
nhanesSearch(
  search_terms = NULL,
  exclude_terms = NULL,
  data_group = NULL,
  ignore.case = FALSE,
  ystart = NULL,
  ystop = NULL,
  includerdc = FALSE,
  nchar = 128,
  namesonly = FALSE
)

Arguments

`search_terms`	List of terms or keywords.
`exclude_terms`	List of exclusive terms or keywords.
`data_group`	Which data groups (e.g. DIET, EXAM, LAB) to search. Default is to search all groups.
`ignore.case`	Ignore case if TRUE. (Default=FALSE).
`ystart`	Four digit year of first survey included in search, where ystart >= 1999.
`ystop`	Four digit year of final survey included in search, where ystop >= ystart.
`includerdc`	If TRUE then RDC only tables are included in list (default=FALSE).
`nchar`	Truncates the variable description to a max length of nchar.
`namesonly`	If TRUE then only the table names are returned (default=FALSE).

Details

nhanesSearch is useful to obtain a comprehensive list of relevant tables. Search terms will be matched against the variable descriptions in the NHANES Comprehensive Variable Lists. Matching variables must have at least one of the search_terms and not have any exclude_terms. The search may be restricted to specific surveys using ystart and ystop. If no arguments are given, then nhanesSearch returns the complete variable list.

Value

Returns a data frame that describes variables that matched the search terms. If namesonly=TRUE, then a character vector of table names that contain matched variables is returned.

Examples

 bladder = nhanesSearch("bladder", ystart=2001, ystop=2008, nchar=50)
 dim(bladder)
 urin = nhanesSearch("urin", exclude_terms="During", ystart=2009)
 dim(urin)
 urine = nhanesSearch(c("urine", "urinary"), ignore.case=TRUE, ystop=2006, namesonly=TRUE)
 length(urine)
bladder = nhanesSearch("bladder", ystart=2001, ystop=2008, nchar=50)
 dim(bladder)
 urin = nhanesSearch("urin", exclude_terms="During", ystart=2009)
 dim(urin)
 urine = nhanesSearch(c("urine", "urinary"), ignore.case=TRUE, ystop=2006, namesonly=TRUE)
 length(urine)

Search for matching table names

Description

Returns a list of table names that match a specified pattern.

Usage

nhanesSearchTableNames(
  pattern = NULL,
  ystart = NULL,
  ystop = NULL,
  includerdc = FALSE,
  includewithdrawn = FALSE,
  nchar = 128,
  details = FALSE
)
nhanesSearchTableNames(
  pattern = NULL,
  ystart = NULL,
  ystop = NULL,
  includerdc = FALSE,
  includewithdrawn = FALSE,
  nchar = 128,
  details = FALSE
)

Arguments

`pattern`	Pattern of table names to match
`ystart`	Four digit year of first survey included in search, where ystart >= 1999.
`ystop`	Four digit year of final survey included in search, where ystop >= ystart.
`includerdc`	If TRUE then RDC only tables are included (default=FALSE).
`includewithdrawn`	IF TRUE then withdrawn tables are included (default=FALSE).
`nchar`	Truncates the variable description to a max length of nchar.
`details`	If TRUE then complete table information from the comprehensive data list is returned (default=FALSE).

Details

Searches the Doc File field in the NHANES Comprehensive Data List (see https://wwwn.cdc.gov/nchs/nhanes/search/DataPage.aspx) for tables that match a given name pattern. Only a single pattern may be entered.

Value

Returns a character vector of table names that match the given pattern. If details=TRUE, then a data frame of table attributes is returned. NULL is returned when an HTML read error is encountered.

Examples

bmx = nhanesSearchTableNames('BMX')
length(bmx)
hepbd = nhanesSearchTableNames('HEPBD')
dim(hepbd)
hpvs = nhanesSearchTableNames('HPVS', includerdc=TRUE, details=TRUE)
dim(hpvs)
bmx = nhanesSearchTableNames('BMX')
length(bmx)
hepbd = nhanesSearchTableNames('HEPBD')
dim(hepbd)
hpvs = nhanesSearchTableNames('HPVS', includerdc=TRUE, details=TRUE)
dim(hpvs)

Search for tables that contain a specified variable.

Description

Returns a list of table names that contain the variable

Usage

nhanesSearchVarName(
  varname = NULL,
  ystart = NULL,
  ystop = NULL,
  includerdc = FALSE,
  nchar = 128,
  namesonly = TRUE
)
nhanesSearchVarName(
  varname = NULL,
  ystart = NULL,
  ystop = NULL,
  includerdc = FALSE,
  nchar = 128,
  namesonly = TRUE
)

Arguments

`varname`	Name of variable to match.
`ystart`	Four digit year of first survey included in search, where ystart >= 1999.
`ystop`	Four digit year of final survey included in search, where ystop >= ystart.
`includerdc`	If TRUE then RDC only tables are included in list (default=FALSE).
`nchar`	Truncates the variable description to a max length of nchar.
`namesonly`	If TRUE then only the table names are returned (default=TRUE).

Details

The NHANES Comprehensive Variable List is scanned to find all data tables that contain the given variable name. Only a single variable name may be entered, and only exact matches will be found.

Value

By default, a character vector of table names that include the specified variable is returned. If namesonly=FALSE, then a data frame of table attributes is returned.

Examples

nhanesSearchVarName('BMXLEG')
nhanesSearchVarName('BMXHEAD', ystart=2003)
nhanesSearchVarName('BMXLEG')
nhanesSearchVarName('BMXHEAD', ystart=2003)

Returns a list of table names for the specified survey group.

Description

Enables quick display of all available tables in the survey group.

Usage

nhanesTables(
  data_group,
  year,
  nchar = 128,
  details = FALSE,
  namesonly = FALSE,
  includerdc = FALSE
)
nhanesTables(
  data_group,
  year,
  nchar = 128,
  details = FALSE,
  namesonly = FALSE,
  includerdc = FALSE
)

Arguments

`data_group`	The type of survey (DEMOGRAPHICS, DIETARY, EXAMINATION, LABORATORY, QUESTIONNAIRE). Abbreviated terms may also be used: (DEMO, DIET, EXAM, LAB, Q).
`year`	The year in yyyy format where 1999 <= yyyy.
`nchar`	Truncates the table description to a max length of nchar.
`details`	If TRUE then a more detailed description of the tables is returned (default=FALSE).
`namesonly`	If TRUE then only the table names are returned (default=FALSE).
`includerdc`	If TRUE then RDC only tables are included in list (default=FALSE).

Details

Function nhanesTables retrieves a list of tables and a description of their contents from the NHANES website. This provides a convenient way to browse the available tables. NULL is returned when an HTML read error is encountered.

Value

Returns a data frame that contains table attributes. If namesonly=TRUE, then a character vector of table names is returned.

Examples

exam = nhanesTables('EXAM', 2007)
dim(exam)
lab = nhanesTables('LAB', 2009, details=TRUE, includerdc=TRUE)
dim(lab)
q = nhanesTables('Q', 2005, namesonly=TRUE)
length(q)
diet = nhanesTables('DIET', 'P')
dim(diet)
exam = nhanesTables('EXAM', 'Y')
dim(exam)
exam = nhanesTables('EXAM', 2007)
dim(exam)
lab = nhanesTables('LAB', 2009, details=TRUE, includerdc=TRUE)
dim(lab)
q = nhanesTables('Q', 2005, namesonly=TRUE)
length(q)
diet = nhanesTables('DIET', 'P')
dim(diet)
exam = nhanesTables('EXAM', 'Y')
dim(exam)

Summarize NHANES table

Description

Summarize a NHANES table

Usage

nhanesTableSummary(nh_table, use = c("data", "codebook", "both"), ...)
nhanesTableSummary(nh_table, use = c("data", "codebook", "both"), ...)

Arguments

`nh_table`	the name of a valid NHANES table
`use`	character string, whether to create a summary from the data itself or the codebook, which respectively use either the NHANES SAS data files or the HTML documentation files. If `use = "both"` then both are computed as merged; the `src` and `...` arguments are ignored in this case.
`...`	additional arguments, usually passed on to either `nhanes` or `nhanesCodebook` as appropriate. Alternatively, the `src` argument can be used to pass on an already available data frame or codebook, but this must be consistent with the `use` argument.

Details

Returns a per-variable summary of a NHANES table either using the actual data or its corresponding codebook

Value

A data frame with one row per variable, with columns depending on the value of the use argument.

Examples

nhanesTableSummary('DEMO_D', use = "data")
nhanesTableSummary('DEMO_D', use = "codebook")
nhanesTableSummary('DEMO_D', use = "data")
nhanesTableSummary('DEMO_D', use = "codebook")

Displays a list of variables in the specified NHANES table.

Description

Enables quick display of table variables and their definitions.

Usage

nhanesTableVars(
  data_group,
  nh_table,
  details = FALSE,
  nchar = 128,
  namesonly = FALSE
)
nhanesTableVars(
  data_group,
  nh_table,
  details = FALSE,
  nchar = 128,
  namesonly = FALSE
)

Arguments

`data_group`	The type of survey (DEMOGRAPHICS, DIETARY, EXAMINATION, LABORATORY, QUESTIONNAIRE). Abbreviated terms may also be used: (DEMO, DIET, EXAM, LAB, Q).
`nh_table`	The name of the specific table to retrieve.
`details`	If TRUE then all columns in the variable description are returned (default=FALSE).
`nchar`	The number of characters in the Variable Description to print. Default length is 128, which is set to enhance readability cause variable descriptions can be very long.
`namesonly`	If TRUE then only the variable names are returned (default=FALSE).

Details

NHANES tables may contain more than 100 variables. Function nhanesTableVars provides a concise display of variables for a specified table, which helps to ascertain quickly if the table is of interest. NULL is returned when an HTML read error is encountered.

Value

Returns a data frame that describes variable attributes for the specified table. If namesonly=TRUE, then a character vector of the variable names is returned.

Examples

lab_cbc = nhanesTableVars('LAB', 'CBC_E')
dim(lab_cbc)
exam_ohx = nhanesTableVars('EXAM', 'OHX_E', details=TRUE, nchar=50)
dim(exam_ohx)
demo = nhanesTableVars('DEMO', 'DEMO_F', namesonly = TRUE)
length(demo)
lab_cbc = nhanesTableVars('LAB', 'CBC_E')
dim(lab_cbc)
exam_ohx = nhanesTableVars('EXAM', 'OHX_E', details=TRUE, nchar=50)
dim(exam_ohx)
demo = nhanesTableVars('DEMO', 'DEMO_F', namesonly = TRUE)
length(demo)

Display code translation information.

Description

Returns code translations for categorical variables, which appear in most NHANES tables.

Usage

nhanesTranslate(
  nh_table,
  colnames = NULL,
  data = NULL,
  nchar = 128,
  mincategories = 1,
  details = FALSE,
  dxa = FALSE,
  cleanse_numeric = FALSE
)
nhanesTranslate(
  nh_table,
  colnames = NULL,
  data = NULL,
  nchar = 128,
  mincategories = 1,
  details = FALSE,
  dxa = FALSE,
  cleanse_numeric = FALSE
)

Arguments

`nh_table`	The name of the NHANES table to retrieve.
`colnames`	The names of the columns to translate. It will translate all the columns by default.
`data`	If a data frame is passed, then code translation will be applied directly to the data frame. In that case the return argument is the code-translated data frame.
`nchar`	Applies only when data is defined. Code translations can be very long. Truncate the length by setting nchar (default = 128).
`mincategories`	The minimum number of categories needed for code translations to be applied to the data (default=1).
`details`	If TRUE then all available table translation information is displayed (default=FALSE).
`dxa`	If TRUE then the 2005-2006 DXA translation table will be used (default=FALSE).
`cleanse_numeric`	Logical flag. If `TRUE`, some special codes in numeric variables, such as ‘Refused’ and ‘Don't know’ will be converted to `NA`.

Details

Most NHANES data tables have encoded values. E.g. 1 = 'Male', 2 = 'Female'. Thus it is often helpful to view the code translations and perhaps insert the translated values in a data frame. Only a single table may be specified, but multiple variables within that table can be selected. Code translations are retrieved for each variable. If the environment variable NHANES_TABLE_BASE was set during startup, the value of this variable is used as the base URL instead of https://wwwn.cdc.gov (this allows the use of a local or alternative mirror of the CDC documentation).

Value

The code translation table (or translated data frame when data is defined). Returns NULL upon error.

Examples

nhanesTranslate('DEMO_B', c('DMDBORN','DMDCITZN'))
nhanesTranslate('BPX_F', 'BPACSZ', details=TRUE)
nhanesTranslate('BPX_F', 'BPACSZ', data=nhanes('BPX_F'))
trans_demo = nhanesTranslate('DEMO_B')
length(trans_demo)
nhanesTranslate('DEMO_B', c('DMDBORN','DMDCITZN'))
nhanesTranslate('BPX_F', 'BPACSZ', details=TRUE)
nhanesTranslate('BPX_F', 'BPACSZ', data=nhanes('BPX_F'))
trans_demo = nhanesTranslate('DEMO_B')
length(trans_demo)

Package 'nhanesA'

Help Index

Open a browser to NHANES.

Description

Usage

Arguments

Details

Value

Examples

Download an NHANES table and return as a data frame.

Description

Usage

Arguments

Details

Value

Examples

Returns the attributes of an NHANES data table.

Description

Usage

Arguments

Details

Value

Examples

Display codebook for selected variable.

Description

Usage

Arguments

Details

Value

Examples

Parse NHANES doc URL

Description

Usage

Arguments

Details

Value

Import Dual Energy X-ray Absorptiometry (DXA) data.

Description

Usage

Arguments

Details

Value

Examples

Parse NHANES doc URL

Description

Usage

Arguments

Details

Value

Download and parse NHANES manifests

Description

Usage

Arguments

Value

Note

Examples

Options for the nhanesA package

Description

Usage

Arguments

Details

Value

Author(s)

Examples

Perform a search over the comprehensive NHANES variable list.

Description

Usage

Arguments

Details

Value

Examples

Search for matching table names

Description

Usage

Arguments

Details

Value

Examples

Search for tables that contain a specified variable.

Description