synthpops.base module¶

The module contains frequently-used functions that do not neatly fit into other areas of the code base.

synthpops.base.norm_dic(dic)¶

Normalize the dictionary dic.

Parameters: dic (dict) – A dictionary with numerical values.
Returns: A normalized dictionary.

synthpops.base.norm_age_group(age_dic, age_min, age_max)¶

Create a normalized dictionary for the range age_min to age_max, inclusive.

Parameters

age_dic (dict) – A dictionary with numerical values.
age_min (int) – The minimum value of the range for the dictionary.
age_max (int) – The maximum value of the range for the dictionary.

Returns

A normalized dictionary for keys in the range age_min to age_max, inclusive.

synthpops.base.get_index_by_brackets_dic(brackets)¶

Create a dictionary mapping each item in the value arrays to the key. For example, if brackets are age brackets, then this function will map each age to the age bracket or bin that it belongs to, so that the resulting dictionary will give by_brackets_dic[age_index] = age bracket of age_index.

Parameters: brackets (dict) – A dictionary mapping bracket or bin keys to the array of values that belong to each bracket.
Returns: A dictionary mapping indices to the brackets or bins each index belongs to.
Return type: dict

synthpops.base.get_age_by_brackets_dic(age_brackets)¶

Create a dictionary mapping age to the age bracket it falls in.

Parameters: age_brackets (dict) – A dictionary mapping age bracket keys to age bracket range.
Returns: A dictionary of age bracket by age.

Example

age_brackets = sp.get_census_age_brackets(sp.datadir,state_location='Washington',country_location='usa')
age_by_brackets_dic = sp.get_age_by_brackets_dic(age_brackets)

synthpops.base.get_ids_by_age_dic(age_by_id_dic)¶

Get lists of IDs that map to each age.

Parameters: age_by_id_dic (dict) – A dictionary with the age of each individual by their ID.
Returns: A dictionary listing IDs for each age from a dictionary that maps ID to age.

synthpops.base.count_ages(popdict)¶

Create an age count from a population dictionary.

Parameters: popdict (dict) – dictionary defining population
Returns: Dictionary of the age count of the population.
Return type: dict

synthpops.base.get_aggregate_ages(ages, age_by_brackets_dic)¶

Create a dictionary of the count of ages by age brackets.

Parameters

ages (dict) – A dictionary of age count by single year.
age_by_brackets_dic (dict) – A dictionary mapping age to the age bracket range it falls within.

Returns

A dictionary of aggregated age count for specified age brackets.

Example

aggregate_age_count = sp.get_aggregate_ages(age_count, age_by_brackets_dic)
aggregate_matrix = symmetric_matrix.copy()
aggregate_matrix = sp.get_aggregate_matrix(aggregate_matrix, age_by_brackets_dic)

synthpops.base.get_aggregate_matrix(matrix, age_by_brackets_dic)¶

Aggregate a symmetric matrix to fewer age brackets. Do not use for homogeneous mixing matrix.

Parameters

matrix (np.ndarray) – A symmetric age contact matrix.
age_by_brackets_dic (dict) – A dictionary mapping age to the age bracket range it falls within.

Returns

A symmetric contact matrix (np.ndarray) aggregated to age brackets.

Example

age_brackets = sp.get_census_age_brackets(sp.datadir,state_location='Washington',country_location='usa')
age_by_brackets_dic = sp.get_age_by_brackets_dic(age_brackets)

aggregate_age_count = sp.get_aggregate_ages(age_count, age_by_brackets_dic)
aggregate_matrix = symmetric_matrix.copy()
aggregate_matrix = sp.get_aggregate_matrix(aggregate_matrix, age_by_brackets_dic)

asymmetric_matrix = sp.get_asymmetric_matrix(aggregate_matrix, aggregate_age_count)

synthpops.base.get_asymmetric_matrix(symmetric_matrix, aggregate_ages)¶

Get the contact matrix for the average individual in each age bracket.

Parameters

symmetric_matrix (np.ndarray) – A symmetric age contact matrix.
aggregate_ages (dict) – A dictionary mapping single year ages to age brackets.

Returns

A contact matrix (np.ndarray) whose elements M_ij describe the contact frequency for the average individual in age bracket i with all possible contacts in age bracket j.

Example

age_brackets = sp.get_census_age_brackets(sp.datadir,state_location='Washington',country_location='usa')
age_by_brackets_dic = sp.get_age_by_brackets_dic(age_brackets)

aggregate_age_count = sp.get_aggregate_ages(age_count, age_by_brackets_dic)
aggregate_matrix = symmetric_matrix.copy()
aggregate_matrix = sp.get_aggregate_matrix(aggregate_matrix, age_by_brackets_dic)

asymmetric_matrix = sp.get_asymmetric_matrix(aggregate_matrix, aggregate_age_count)