Package 'NHSDataDictionaRy'

Title: NHS Data Dictionary Toolset for NHS Lookups
Description: Providing a common set of simplified web scraping tools for working with the NHS Data Dictionary <https://datadictionary.nhs.uk/data_elements_overview.html>. The intended usage is to access the data elements section of the NHS Data Dictionary to access key lookups. The benefits of having it in this package are that the lookups are the live lookups on the website and will not need to be maintained. This package was commissioned by the NHS-R community <https://nhsrcommunity.com/> to provide this consistency of lookups. The OpenSafely lookups have now been added <https://www.opencodelists.org/docs/>.
Authors: Gary Hutson [aut, cre] , Calum Polwart [aut], Tom Jemmett [aut]
Maintainer: Gary Hutson <[email protected]>
License: MIT + file LICENSE
Version: 1.2.5
Built: 2024-12-02 06:49:23 UTC
Source: CRAN

Help Index

left_xl function This function replicates the LEFT function in Excel and is utilised for left trimming of character strings

Description

left_xl function This function replicates the LEFT function in Excel and is utilised for left trimming of character strings

Usage

left_xl(text, num_char = 0)

Arguments

text

The text you want to LEFT trim
num_char

The number of characters your want to trim by

Value

Trims the text entered by the number of character parameter and returns the trimmed string

Examples

left_xl(text= "This is some example text", num_char = 4)

len_xl function

Description

This function replicates the LEN function in Excel and is utilised for finding the length of character strings.

Usage

len_xl(text, ...)

Arguments

text

The text you want to calculate the length
...

Function forwarding to work with the base nchar method

Value

An integer value calculating the length of the text passed

Examples

len_xl("Guess the length of me!")

linkScrapeR

Description

This is used to scrape all hyperlinks from a specific web page.

Usage

linkScrapeR(url, SSL_needed = FALSE)

Arguments

url

The website URL to detect active anchor hyperlink tags and extract them into a tibble
SSL_needed

Default - FALSE - Boolean to indicate whether to need a SSL certificate

Details

Once the links have been scraped they will be outputted into a tibble for exploration.

This can be used on any website to pull back the hyperlink content of a web page.

Value

A tibble (class data.frame) with all active hyperlinks on the website for the URL (uniform resource locator) passed to the function.

  • result - the extracted html table from url and xpath passed

  • link_name - the name of the link

  • url - the full url of the active href tag from HTML

Examples

linkScrapeR("https://www.datadictionary.nhs.uk/", FALSE)

mid_xl function

Description

This function replicates the MID function in Excel and is utilised for left trimming of character strings.

Usage

mid_xl(text, start_num = 1, num_char = 0)

Arguments

text

The text you want to MID trim
start_num

The start number to start the trim. This needs to be numeric.
num_char

The number of characters your want to trim by. This field needs to be numeric.

Details

This has been included as a convenience function for working with text and string data.

Value

The extracted text between the start_num and the num_char to produce a sub string result.

Examples

mid_xl(text= "This is some example text", start_num = 6, num_char = 10)


mid_xl(text= "This is some example text", start_num = 6, num_char = 10)

NHS data elements method

Description

Searches all the data elements in the data element index of the NHS data dictionary and returns the links.

Usage

nhs_data_elements()

Details

This function has no input parameters and returns the

Value

A tibble (class data frame) with the results of scraping the NHS Data Dictionary website for the data elements look ups, if no return this will produce an appropriate informational message.

  • link_name - the name of the scraped link. This relates to the actual name of the data element from the NHS Data Dictionary.

  • url - the url passed to the parameter

  • full_url - the full url of where the data element is on the NHS Data Dictionary website

  • xpath_nat_code - utilises the element in the website and appends the link_short - to pull back only national codes from the dictionary site. NOTE: not all of the returns will have national code tables.

  • xpath_default_codes - pulls back the data dictionary default codes - these can be then used with the national codes

  • xpath_also_known - pulls back the data dictionary elements alias table - this will be available for all data elements

Examples

nhs_data_lookup <- nhs_data_elements()
head(nhs_data_lookup, 10)

nhs_table_findeR function

Description

This function uses the tableR parent function to return a table of elements, specifically from the NHS Data Dictionary

Usage

nhs_table_findeR(data_element_name, ...)

Arguments

data_element_name

The data element name from NHS Data Dictionation i.e. ACCOMMODATION STATUS CODE
...

Function forwarding to parent function to pass additional arguments to function (e.g. title, add_zero_prefix)

Value

A tibble (class data.frame) output from the results of the web scrape

  • result - the extracted national HTML code table from the element page of the NHS Data Dictionary

  • DictType - defaults to Not Specified if nothing passed, however allows for custom dictionary / data frame tags to be created

  • DttmExtracted - a date and time stamp

Examples

#Returns a tibble from tableR parent function
nhs_table_findeR("ACCOMMODATION STATUS CODE", title="ACCOM_STATUS")
nhs_table_findeR("accommodation status code") #Changes case to match

openSafely_listR function

Description

This function uses the tableR parent function to return a table of elements, specifically from the OpenSafely Code List https://www.opencodelists.org/

Usage

openSafely_listR(list_name, version = "", ...)

Arguments

list_name

The code list ID from https://www.opencodelists.org/ for which to return the National table of elements, for example "opensafely/ace-inhibitor-medications"
version

The version of the code list if not the most recent
...

Function forwarding to parent function to pass additional arguments to function (e.g. title, add_zero_prefix)

Value

A tibble (class data.frame) output from the results of the web scrape

  • type - the OpenSafely type

  • id - the id for the OpenSafely element

  • bnf_code - British National Formulary - NICE guidelines code

  • nm - medicine type, dosage and manufacturer

  • Dict_type - title specified for dictionary

  • DttmExtracted - the date and time the code set was extracted

Examples

openSafely_listR("opensafely/ace-inhibitor-medications")
#Pull back current list
openSafely_listR("opensafely/ace-inhibitor-medications", "2020-05-19")
#Pull back list with date

right_xl function

Description

This function replicates the RIGHT function in Excel and is utilised for right trimming of character strings.

Usage

right_xl(text, num_char = 0)

Arguments

text

The text you want to RIGHT trim
num_char

The number of characters your want to trim by. This field needs to be numeric.

Details

This has been included as a convenience function for working with text and string data.

Value

The trimmed string from the text parameter and trimming by the number of characters num_char passed to the parameter.

Examples

right_xl(text= "This is some example text", num_char = 10)


right_xl(text= "This is some example text", num_char = 10)

ScrapeR - scrape web information with scrapeR

Description

Takes the url and xpath and scrapes HTML table elements from a website.

Usage

scrapeR(url, xpath, ...)

Arguments

url

Website address to connect to
xpath

Xpath obtained through inspecting the individual HTML elements
...

Function to pass additional function forwarding options

Details

This function is specifically designed to work with HTML tables and x path links through to direct HTML elements. The function is versatile and can be used on any URL where an xpath can be obtained through the URL and HTML inspection process.

Value

Returns the results of the scraping operation and the relevant fields from the html table - the xpath should make reference to an html table, otherwise an error is returned advising the user to check the xpath and url are correct.

tableR function

Description

This function uses the scapeR parent function to return a table of elements

Usage

tableR(url, xpath, title = "Not Specified", add_zero_prefix = FALSE, ...)

Arguments

url

The URL of the website to scrape the table element from
xpath

The unique xpath of the HTML element to be scraped
title

Unique name for the relevant HTML table that has been scraped
add_zero_prefix

Adds zero prefixes to certain codes that get converted by native functions
...

Function forwarding to parent function to pass additional arguments to function

Value

A tibble (class data.frame) output from the results of the web scrape

  • result - the extracted html table from url and xpath passed

  • DictType - defaults to Not Specified if nothing passed, however allows for custom dictionary / data frame tags to be created

  • DttmExtracted - a date and time stamp

xpathTextR function

Description

Returns xpath text from websites and can be used to access specific HTML nodes

Usage

xpathTextR(url, xpath, ssl_needed = FALSE)

Arguments

url

The link for the website
xpath

The xpath string derived by using the Inspect functionality in a web browser.
ssl_needed

Default - FALSE - Boolean to indicate whether to need a SSL certificate

Value

A list with the results of scraping the specific xpath element

  • result - the extracted text from the website element that has been scraped

  • website_passed - a copy of the input url for the website

  • html_node_result - returns the extracted html node result

  • datetime_access - returns a timestamp of when the results of the scraping operation have been completed

  • person_accessed - retrieves the system environment stored username and domain - this is concatenated together to form a mixed charatcer string