pearl.definitions

Global Definitions for Codes used across PEARL.

Module Attributes

POPULATION_TYPE_DICT	Dictionary defining the data types for each column in the population DataFrame.
ART_NAIVE	ART Naive status code 0.
DELAYED	ART Delayed status code 1.
ART_USER	ART User status code 2.
ART_NONUSER	ART Non-user status code 3.
REENGAGED	ART Reengaged status code 4.
LTFU	LTFU status code 5.
DYING_ART_USER	ART Dying User status code 6.
DYING_ART_NONUSER	ART Dying Non-user status code 7.
DEAD_ART_USER	ART Dead User status code 8.
DEAD_ART_NONUSER	ART Dead Non-user status code 9.
SMEARING	Smearing correction factor for log-normal distributions.
STAGE0	List of comorbidities in stage 0.
STAGE1	List of comorbidities in stage 1.
STAGE2	List of comorbidities in stage 2.
STAGE3	List of comorbidities in stage 3.
ALL_COMORBIDITIES	List of all comorbidities.

pearl.definitions.POPULATION_TYPE_DICT = {'age': 'int8', 'age_cat': 'int8', 'anx': 'bool', 'ckd': 'bool', 'dm': 'bool', 'dpr': 'bool', 'esld': 'bool', 'h1yy': 'int16', 'hcv': 'bool', 'ht': 'bool', 'init_age': 'int8', 'intercept': 'int8', 'last_h1yy': 'int16', 'lipid': 'bool', 'ltfu_year': 'int16', 'malig': 'bool', 'mi': 'bool', 'mm': 'int8', 'n_lost': 'int32', 'return_year': 'int16', 'smoking': 'bool', 'sqrtcd4n_exit': 'float64', 'status': 'int8', 't_anx': 'int16', 't_ckd': 'int16', 't_dm': 'int16', 't_dpr': 'int16', 't_esld': 'int16', 't_hcv': 'int16', 't_ht': 'int16', 't_lipid': 'int16', 't_malig': 'int16', 't_mi': 'int16', 't_smoking': 'int16', 'year': 'int16', 'years_out': 'int16'}

Dictionary defining the data types for each column in the population DataFrame.

Type:

Dict[str, str]

pearl.definitions.ART_NAIVE = 0

ART Naive status code 0.

Type:

int

pearl.definitions.DELAYED = 1

ART Delayed status code 1.

Type:

int

pearl.definitions.ART_USER = 2

ART User status code 2.

Type:

int

pearl.definitions.ART_NONUSER = 3

ART Non-user status code 3.

Type:

int

pearl.definitions.REENGAGED = 4

ART Reengaged status code 4.

Type:

int

pearl.definitions.LTFU = 5

LTFU status code 5.

Type:

int

pearl.definitions.DYING_ART_USER = 6

ART Dying User status code 6.

Type:

int

pearl.definitions.DYING_ART_NONUSER = 7

ART Dying Non-user status code 7.

Type:

int

pearl.definitions.DEAD_ART_USER = 8

ART Dead User status code 8.

Type:

int

pearl.definitions.DEAD_ART_NONUSER = 9

ART Dead Non-user status code 9.

Type:

int

pearl.definitions.SMEARING = 1.42

Smearing correction factor for log-normal distributions.

Type:

float

pearl.definitions.STAGE0 = ['hcv', 'smoking']

List of comorbidities in stage 0.

Type:

List[str]

pearl.definitions.STAGE1 = ['anx', 'dpr']

List of comorbidities in stage 1.

Type:

List[str]

pearl.definitions.STAGE2 = ['ckd', 'lipid', 'dm', 'ht']

List of comorbidities in stage 2.

Type:

List[str]

pearl.definitions.STAGE3 = ['malig', 'esld', 'mi']

List of comorbidities in stage 3.

Type:

List[str]

pearl.definitions.ALL_COMORBIDITIES = ['hcv', 'smoking', 'anx', 'dpr', 'ckd', 'lipid', 'dm', 'ht', 'malig', 'esld', 'mi']

List of all comorbidities.

Type:

List[str]