TRACE-LAC -- ColOpenData

Description

ColOpenData allows users to download and clean epidemiological data from the Sivigila datasets.

This package allows users to download and clean epidemiological data from the Sivigila datasets. The package is divided into two main functions: download and clean. The download function allows users to download the data from the Sivigila website. The clean function allows users to clean the data downloaded from the Sivigila website.

Dependencies

python 3.6+
R 3.6.1+
pandas
numpy
os
selenium
reticulate

Usage

The main functions in this package are the following:

    downloadSivigilaData(years_to_download, events_to_download)

Tha paramaters for downloadSivigilaData are:

1. years_to_download: a list of years to download. The years must be between 2007 and 2020.

2. events_to_download: a list of events to download. Note that the events must be in the Sivigila website.

    preprocessData(years_to_preprocess, events_to_preprocess, save)
   

The paramaters for preprocessData are:

1. years_to_preprocess: a list of years to preprocess. The years must be between 2007 and 2020.

2. events_to_preprocess: a list of events to preprocess. Note that the events must be in the Sivigila website.

3. save: a boolean variable that indicates if the user wants to save the data or not.

    preprocessDataDemographics(save)
   

The paramaters for preprocessDataDemographics are:

1. save: a boolean variable that indicates if the user wants to save the data or not.

    preprocessDataHouseholds(save)
   

The paramaters for preprocessDataHouseholds are:

1. save: a boolean variable that indicates if the user wants to save the data or not.

Event and code dictionary

The following table shows the events and codes that can be downloaded from the Sivigila website.

"ACCIDENTE OFIDICO": "100", 
"COLERA" : "200",
"DENGUE": "210", 
"DENGUE CLASICO": "210", 
"DENGUE GRAVE": "220", 
"DENGUE HEMORRAGICO": "220", 
"EVENTO ADVERSO SEGUIDO A LA VACUNACION.": "298", 
"AGRESIONES POR ANIMALES POTENCIALMENTE TRANSMISORES DE RABIA": "300", 
"EXPOSICION RABICA": "300", 
"INTOXICACION POR PLAGUICIDAS": "360", 
"INTOXICACION POR FARMACOS": "370", 
"HEPATITIS A": "330", 
"FIEBRE AMARILLA": "310", 
"FIEBRE TIFOIDEA Y PARATIFOIDEA": "320", 
"HEPATITIS B": "340", 
"INTOXICACION POR METANOL": "380", 
"INTOXICACION POR METALES PESADOS": "390", 
"INTOXICACION POR SOLVENTES": "400", 
"LEISHMANIASIS CUTANEA": "420", 
"LEISHMANIASIS MUCOSA": "430", 
"LEISHMANIASIS MUCOCUTANEA": "430", 
"LEISHMANIASIS VISCERAL": "440", 
"LEISHMANIASIS SIN ESPECIFICAR": "420", 
"LEPRA": "450", 
"LEPTOSPIROSIS": "455", 
"LESIONES POR POLVORA": "458", 
"MALARIA ASOCIADA (FORMAS MIXTAS)": "465", 
"MALARIA ASOCIADA": "465", 
"HIPOTIROIDISMO CONGENITO": "343", 
"MALARIA FALCIPARUM": "465", 
"MALARIA MALARIE": "480", 
"MALARIA VIVAX": "465", 
"MALARIA COMPLICADA": "495", 
"MENINGITIS  MENINGOCOCCICA": "500", 
"MENINGITIS POR HAEMOPHILUS INFLUENZAE": "510", 
"MENINGITIS POR NEUMOCOCO": "520", 
"MENINGITIS TUBERCULOSA": "530", 
"MORTALIDAD POR MALARIA": "540", 
"MORTALIDAD MALARIA": "540", 
"MORTALIDAD MATERNA": "550", 
"MORTALIDAD PERINATAL Y NEONATAL TARDIA": "560", 
"MORTALIDAD PERINATAL": "560", 
"PAROTIDITIS": "620", 
"SIFILIS CONGENITA": "740", 
"MORTALIDAD POR DENGUE": "580", 
"MORTALIDAD POR EDA 0-4 ANOS": "590", 
"MORTALIDAD POR IRA": "600", 
"MORTALIDAD POR IRA 0-4 ANOS": "600", 
"RABIA HUMANA": "670", 
"RABIA ANIMAL": "670", 
"RUBEOLA": "710", 
"SIFILIS GESTACIONAL": "750", 
"SIFILIS OTRAS FORMAS": "750", 
"TETANOS ACCIDENTAL": "760", 
"TETANOS OTROS": "760", 
"TETANOS NEONATAL": "770", 
"TOS FERINA": "800", 
"TOSFERINA": "800", 
"TUBERCULOSIS EXTRA PULMONAR": "810", 
"TUBERCULOSIS PULMONAR": "820", 
"VARICELA INDIVIDUAL": "831", 
"VIH/SIDA/MORTALIDAD POR SIDA": "850", 
"VIH": "850",
"SIDA": "850",
"ESI - IRAG (VIGILANCIA CENTINELA)": "345", 
"LEUCEMIA AGUDA PEDIATRICA LINFOIDE": "456", 
"LEUCEMIA AGUDA PEDIATRICA MIELOIDE": "457", 
"PARALISIS FLACIDA AGUDA (MENORES DE 15 ANOS)": "610", 
"PARALISIS FLACIDA AGUDA (< DE 15 ANOS)": "610", 
"PARALISIS FLACIDA AGUDA": "610", 
"INFECCION RESPIRATORIA AGUDA GRAVE IRAG INUSITADA": "348", 
"ANOMALIAS CONGENITAS": "735", 
"INTOXICACION POR MONOXIDO DE CARBONO Y OTROS GASES": "412", 
"INTOXICACION POR SUSTANCIAS PSICOACTIVAS": "414", 
"TUBERCULOSIS FARMACORRESISTENTE": "825", 
"SARAMPION": "730", 
"BAJO PESO AL NACER": "110", 
"MORBILIDAD MATERNA EXTREMA": "549", 
"VCM VIF VSX": "875", 
"INTOXICACION POR OTRAS SUSTANCIAS QUIMICAS": "410", 
"INTOXICACION POR OTRAS SUSTANCIAS QUIM.": "410", 
"INTOXICACIONES NO ALIMENTARIAS": "410", 
"EXPOSICION A FLUOR": "228", 
"CHAGAS": "205", 
"MORTALIDAD POR DESNUTRICION": "112", 
"TIFUS ENDEMICO TRASMITIDO POR PULGAS": "790", 
"CHIKUNGUNYA": "217", 
"HEPATITIS C": "341", 
"LESIONES POR ARTEFACTOS EXPLOSIVOS (POLVORA Y MINAS ANTIPERSONAL)": "452", 
"CANCER INFANTIL": "459", 
"TIFUS EPIDEMICO TRANSMITIDO POR PIOJOS": "780", 
"ZIKA": "895", 
"CANCER DE LA MAMA Y CUELLO UTERINO": "155", 
"DESNUTRICION AGUDA EN MENORES DE 5 ANOS": "113", 
"ENFERMEDADES HUERFANAS - RARAS": "342", 
"INTENTO DE SUICIDIO": "356", 
"INFECCION ASOCIADA A DISPOSITIVOS": "357", 
"DIFTERIA": "230", 
"TRACOMA": "305", 
"DEFECTOS CONGENITOS": "215", 
"MALARIA - TODAS LAS FORMAS": "465", 
"VIGILANCIA EN SALUD PUBLICA DE LA VIOLENCIA DE GENERO E INTRAFAMILIAR": "875", 
"BAJO PESO AL NACER A TERMINO": "110", 
"CANCER EN MENORES DE 18 ANOS": "115", 
"EXPOSICION A FLUOR (VIGILANCIA CENTINELA)": "228", 
"HEPATITIS B, C Y COINFECCION HEPATITIS B Y DELTA": "340", 
"ENDOMETRITIS PUERPERAL": "351", 
"INFECCIONES ASOCIADAS A PROCEDIMIENTO MEDICO QUIRURGICO": "352", 
"INFECCIONES ASOCIADAS A DISPOSITIVOS": "357", 
"INTOXICACIONES": "365", 
"INTOXICACIONES ALIMENTARIAS": "365", 
"MENINGITIS BACTERIANA Y ENFERMEDAD MENINGOCOCICA": "535", 
"MENINGITIS BACTERIANA": "535", 
"MENINGITIS HAEMOPHILUS": "535", 
"TUBERCULOSIS - SENSIBLE": "813", 
"VARICELA": "831", 
"INFECCION RESPIRATORIA AGUDA GRAVE INUSITADA": "348", 
"VIGILANCIA DE MUERTES EN MENORES DE CINCO ANOS POR EDA": "591", 
"VIGILANCIA DE MUERTES EN MENORES DE CINCO ANOS POR IDESNUTRICION": "591", 
"EVENTO ADVERSO SEGUIDO A LA VACUNACION GRAVE": "298", 
"MORTALIDAD MATERNA - TEMPRANA": "551", 
"CHAGAS CRONICO": "205", 
"TUBERCULOSIS - RESISTENTE": "813", 
"VIGILANCIA DE MUERTES EN MENORES DE CINCO ANOS POR IRA": "591", 
"LESIONES DE CAUSA EXTERNA - PROCEDIMIENTOS ESTETICOS": "453", 
"CHAGAS AGUDO": "205", 
"INFECCIONES ASOCIADAS A PROCEDIMIENTOS MEDICO-QUIRURGICOS": "352", 
"INFECCIONES ASOCIADA A DISPOSITIVOS EN AMBITO HOSPITALARIO": "357", 
"INTOXICACION POR MEDICAMENTOS": "370", 
"CANCER INFANTIL": "459", 
"MENINGITIS MENINGOCOCCICA": "500", 
"ANOMALIAS CONGENITAS": "735", 
"SIFILIS CONGENITA": "740", 
"ACCIDENTE OFIDICO": "100", 
"HIPOTIROIDISMO CONGENITO": "343", 
"TUBERCULOSIS FARMACORRESISTENTE": "813", 
"MORTALIDAD MATERNA TEMPRANA": "550", 
"SARAMPION": "730", 
"DESNUTRICION AGUDA EN MENORES DE 5 ANOS": "113", 
"CANCER EN MENORES DE 18 ANOS": "115", 
"EVENTO ADVERSO GRAVE POSTERIOR A LA VACUNACION": "298", 
"HEPATITIS B, C Y COINFECCION HEPATITIS B Y DELTA": "340", 
"INFECCIONES DE SITIO QUIRURGICO ASOCIADAS A PROCEDIMIENTO MEDICO QUIRURGICO": "352", 
"IAD  INFECCIONES ASOCIADAS A DISPOSITIVOS  INDIVIDUAL": "357", 
"INTENTO DE SUICIDIO CON MECANISMO INTOXICACION": "365", 
"LESIONES DE CAUSA EXTERNA": "453", 
"MORTALIDAD PERINATAL Y NEONATAL TARDIA": "560", 
"SINDROME DE RUBEOLA CONGENITA": "720", 
"RUBEOLA CONGENITA": "720", 
"TUBERCULOSIS": "813", 
"VIGILANCIA EN SALUD PUBLICA DE LA VIOLENCIA DE GENERO E INTRAFAMILIAR": "875", 
"MORTALIDAD MATERNA - DATOS BASICOS": "551", 
"VIGILANCIA INTEGRADA DE MUERTES EN MENORES DE CINCO ANOS POR INFECCION RESPIRATORIA AGUDA, ENFERMEDAD DIARREICA AGUDA Y/O DESNUTRICI\u00d3N": "591"