Welcome to fingertips_py’s documentation

Introduction

This is a python package to interact with Public Health England’s [Fingertips](https://fingertips.phe.org.uk/) data tool. Fingertips is a major repository of population and public health indicators for England. The site presents the information in many ways to improve accessibility for a wide range of audiences ranging from public health professionals and researchers to the general public. The information presented is a mixture of data available from other public sources, and those that are available through user access agreements with other organisations. The source of each indicator presented is available using the get_metadata_for_indicator() function.

This package can be used to load data from the Fingertips API into python for further use.

Installation

This packaged should be installed using pip:

` pip install fingertips_py `

Or it can be compiled from source (still requires pip):

` pip install git+https://github.com/PublicHealthEngland/PHDS_fingertips_py.git `

Usage

fingertips_py should be imported and used in line with standard python conventions. It is suggested that if the whole package is to be imported

then the following convention is used:

` import fingertips_py as ftp `

The package returns data in a variety of types dependent on the function.

For more information on any function, you can use:

` help(*fingertips_py function name*) `

Or you can view the documents [here](https://fingertips-py.readthedocs.io/en/latest/).

Example

This is an example of a workflow for retrieving data for the indicator on Healthy Life Expectancy at Birth from the Public Health Outcomes Framework profile.

``` import fingertips_py as ftp

phof = ftp.get_profile_by_name(‘public health outcomes framework’) phof_meta = ftp.get_metadata_for_profile_as_dataframe(phof[‘Id’]) indicator_meta = phof_indicators[phof_meta[‘Indicator’].str.contains(‘Healthy’)] print(indicator_meta)

Indicator ID Indicator …

0 90362 0.1i - Healthy life expectancy at birth … 55 92543 2.05ii - Proportion of children aged 2-2½yrs r… … ```

We can see that the Healthy life expectancy at birth indicator has an id of 90362. The data for this indicator at all geographical breakdowns can be retrieved using get_data_for_indicator_at_all_available_geographies()

` healthy_life_data = ftp.get_data_for_indicator_at_all_available_geographies(90362) `

Licence

This project is released under the [GPL-3](https://opensource.org/licenses/GPL-3.0) licence.

metadata.py

Calls used to retrieve metadata about areas, ages, sexes, value notes, calculation methods, rates, and indicator metadata.

fingertips_py.metadata.get_age_from_id(age_id)

Returns an age name from given id.

Parameters:age_id – Age id used in Fingertips as an integer
Returns:Age or age range as a string
fingertips_py.metadata.get_age_id(age)

Returns an ID for a given age.

Parameters:age – Search term of an age or age range as a string
Returns:Code used in Fingertips to represent the age or age range as a string
fingertips_py.metadata.get_all_ages()

Returns a dictionary of all the age categories and their IDs.

Returns:Age codes used in Fingertips in a tuple
fingertips_py.metadata.get_all_areas()

Retreives all area types.

Returns:A dictionary of all area types used in Fingertips
fingertips_py.metadata.get_all_profiles()

Returns all profiles.

Returns:A dictionary of all profiles in Fingertips including information on domains and sequencing
fingertips_py.metadata.get_all_sexes()

Returns a tuple of all sex categories and their IDs.

Returns:Sex categories used in Fingertips with associated codes as a tuple
fingertips_py.metadata.get_all_value_notes()

Returns a dictionary of all value notes and their IDs.

Returns:Data value notes and their associated codes that are used in Fingertips as a list of tuples
fingertips_py.metadata.get_area_type_ids_for_profile(profile_id)

Returns a list of area types used within a given profile.

Parameters:profile_id – ID used in Fingertips to identify a profile as integer or string
Returns:A list of area types used within a given profile
fingertips_py.metadata.get_area_types_as_dict()

Returns all area types and related information such as ID and name.

Returns:A dictionary of area types
fingertips_py.metadata.get_area_types_for_profile(profile_id)

Retrieves all the area types that have data for a given profile.

Parameters:profile_id – ID used in Fingertips to identify a profile as integer or string
Returns:A list of dictionaries of area types with relevant information
fingertips_py.metadata.get_areas_for_area_type(area_type_id)

Returns a dictionary of areas that match an area type id given the id as integer or string.

Parameters:area_type_id – ID of area type (ID of General Practice is 7 etc) used in Fingertips as integer or string
Returns:A dictionary of dictionaries with area codes and the names of those areas
fingertips_py.metadata.get_domains_in_profile(profile_id)

Returns the domain IDs for a given profile.

Parameters:profile_id – ID used in Fingertips to identify a profile as integer or string
Returns:A list of domain IDs
fingertips_py.metadata.get_metadata(indicator_ids=None, domain_ids=None, profile_ids=None)

Returns a dataframe object of metadata for a given indicator, domain, and/or profile given the relevant IDs. At least one of these IDs has to be given otherwise an error is raised.

Parameters:
  • indicator_ids – [OPTIONAL] Number used to identify an indicator within Fingertips as integer or string
  • domain_ids – [OPTIONAL] Number used to identify a domain within Fingertips as integer or string
  • profile_ids – [OPTIONAL] ID used in Fingertips to identify a profile as integer or string
Returns:

A dataframe object with metadata for the given IDs or an error if nothing is specified

fingertips_py.metadata.get_metadata_for_all_indicators(include_definition='no', include_system_content='no')

Returns the metadata for all indicators in a dataframe.

Parameters:
  • include_definition – optional to include definitions
  • include_system_content – optional to include system content
Returns:

dataframe of all indicators

fingertips_py.metadata.get_metadata_for_all_indicators_from_csv()

Returns a dataframe from the csv of all metadata for all indicators.

Returns:A dataframe of all metadata for all indicators
fingertips_py.metadata.get_metadata_for_domain_as_dataframe(group_ids)

Returns a dataframe of metadata for a given domain ID or list of domain IDs.

Parameters:group_ids – Number or list of numbers used to identify a domain within Fingertips as integer or string
Returns:Dataframe object with metadata for the indicators for a given domain ID
fingertips_py.metadata.get_metadata_for_indicator(indicator_number)

Returns the metadata for an indicator given the indicator number as integer or string.

Parameters:indicator_number – Number used to identify an indicator within Fingertips as integer or string
Returns:A dictionary of metadata for the given indicator
fingertips_py.metadata.get_metadata_for_indicator_as_dataframe(indicator_ids)

Returns a dataframe of metadata for a given indicator ID or list of indicator IDs.

Parameters:indicator_ids – Number or list of numbers used to identify an indicator within Fingertips as integer or string
Returns:Dataframe object with metadate for the indicator ID
fingertips_py.metadata.get_metadata_for_profile_as_dataframe(profile_ids)

Returns a dataframe of metadata for a given profile ID or list of profile IDs.

Parameters:profile_ids – ID or list of IDs used in Fingertips to identify a profile as integer or string
Returns:Dataframe object with metadata for the indicators for a given group ID
fingertips_py.metadata.get_multiplier_and_calculation_for_indicator(indicator_number)

Returns the multiplier and calculation method for a given indicator.

Parameters:indicator_number – Number used to identify an indicator within Fingertips as integer or string
Returns:A tuple of multiplier and calculation method from Fingetips metadata
fingertips_py.metadata.get_profile_by_id(profile_id)

Returns a profile as an dictionary which contains information about domains and sequencing.

Parameters:profile_id – ID used in Fingertips to identify a profile as integer or string
Returns:A dictionary of information about the profile
fingertips_py.metadata.get_profile_by_name(profile_name)

Returns a profile object given a name to search - try to be specific to get better results.

Parameters:profile_name – A string or part of a string that is used as the profile name
Returns:A dictionary of the profile metadata including domain information or an error message
fingertips_py.metadata.get_sex_from_id(sex_id)

Returns a sex name given an id.

Parameters:sex_id – ID used in Fingertips to represent the sex as integer
Returns:Sex category as string
fingertips_py.metadata.get_sex_id(sex)

Returns an ID for a given sex.

Parameters:sex – Sex category as string (Case sensitive)
Returns:ID used in Fingertips to represent the sex as integer
fingertips_py.metadata.get_value_note_id(value_note)

Returns a value note ID for a given value note.

Parameters:value_note – Value note as string
Returns:ID used in Fingertips to represent the value note as integer

api_calls.py

A group of functions to query the Fingertips api and retrieve data in a variety of formats.

fingertips_py.api_calls.deal_with_url_error(url)
Parameters:url – A url that returns a URL Error based on SSL errors
Returns:A dataframe from the URL with varify set to false.
fingertips_py.api_calls.get_data_in_tuple(url)
Parameters:url – A url to make a request
Returns:A tuple of returned data
fingertips_py.api_calls.get_json(url)
Parameters:url – A url to make a request
Returns:A parsed JSON object
fingertips_py.api_calls.get_json_return_df(url, transpose=True)
Parameters:
  • url – A url to make a request
  • transpose – [OPTIONAL] transposes dataframe. Default True.
Returns:

Dataframe generated from JSON response.

fingertips_py.api_calls.make_request(url, attr=None)
Parameters:
  • url – A url to make a request
  • attr – The attribute that needs to be returned
Returns:

a dict of the attribute and associated data

retrieve_data.py

A group of functions to retrieve data from Fingertips by indicator, profile, domain (group), or geography.

fingertips_py.retrieve_data.get_all_areas_for_all_indicators()

Returns a dataframe of all indicators and their geographical breakdowns.

Returns:Dataframe of all indicators and their geographical breakdowns
fingertips_py.retrieve_data.get_all_data_for_indicators(indicators, area_type_id, parent_area_type_id=15, filter_by_area_codes=None)

Returns a dataframe of data for given indicators at an area.

Parameters:
  • indicators – List or integer or string of indicator Ids
  • area_type_id – ID of area type (eg. ID of General Practice is 7 etc) used in Fingertips as integer or string
  • parent_area_type_id – Area type of parent area - defaults to England value
  • filter_by_area_codes – Option to limit returned data to areas. Areas as either string or list of strings
Returns:

Dataframe of data for given indicators at an area

fingertips_py.retrieve_data.get_all_data_for_profile(profile_id, parent_area_type_id=15, area_type_id=None, filter_by_area_codes=None)

Returns a dataframe of data for all indicators within a profile.

Parameters:
  • profile_id – ID used in Fingertips to identify a profile as integer or string
  • parent_area_type_id – Area type of parent area - defaults to England value
  • area_type_id – Option to only return data for a given area type. Area type ids are string, int or a list.
  • filter_by_area_codes – Option to limit returned data to areas. Areas as either string or list of strings.
Returns:

A dataframe of data for all indicators within a profile with any filters applied

fingertips_py.retrieve_data.get_data_by_indicator_ids(indicator_ids, area_type_id, parent_area_type_id=15, profile_id=None, include_sortable_time_periods=None)

Returns a dataframe of indicator data given a list of indicators and area types.

Parameters:
  • indicator_ids – List of indicator IDs as strings
  • area_type_id – ID of area type (eg. CCG, Upper Tier Local Authority) used in Fingertips as integer or string
  • parent_area_type_id – Area type of parent area - defaults to England value
  • profile_id – ID of profile to select by as either int or string
  • include_sortable_time_periods – Boolean as to whether to include a sort-friendly data field
Returns:

A dataframe of data relating to the given indicators

fingertips_py.retrieve_data.get_data_for_indicator_at_all_available_geographies(indicator_id)

Returns a dataframe of all data for an indicator for all available geographies.

Parameters:indicator_id – Indicator id
Returns:Dataframe of data for indicator for all available areas for all time periods

area_data.py

Functions to retrieve data that are specific to areas and relevant to all indicators. For example: Deprivation decile.

fingertips_py.area_data.defined_qcut(df, value_series, number_of_bins, bins_for_extras, labels=False)

Allows users to define how values are split into bins when clustering.

Parameters:
  • df – Dataframe of values
  • value_series – Name of value column to rank upon
  • number_of_bins – Integer of number of bins to create
  • bins_for_extras – Ordered list of bin numbers to assign uneven splits
  • labels – Optional. Labels for bins if required
Returns:

A dataframe with a new column ‘bins’ which contains the cluster numbers

fingertips_py.area_data.deprivation_decile(area_type_id, year='2015', area_code=None)

Takes in an area type id and returns a pandas series of deprivation deciles for those areas (with the areas as an index. If a specific area is requested, it returns just the deprivation decile value.

Parameters:
  • area_type_id – Area type id as denoted by the Fingertips API
  • year – Year of deprivation score
  • area_code – Optional. Area code for area type to return a single value for that area
Returns:

A pandas series of deprivation scores with area codes as the index. Or single value if area is specified.

Indices and tables