{
"cells": [
{
"cell_type": "markdown",
"id": "f6c02db11f41edaa",
"metadata": {},
"source": [
"
\n"
]
},
{
"cell_type": "markdown",
"id": "9976af9489dc682e",
"metadata": {},
"source": [
"# Hands-on with socio4health: socioeconomic and demographic variables on dengue incidence in Colombia\n"
]
},
{
"cell_type": "markdown",
"id": "35b4ab37a734f323",
"metadata": {},
"source": [
"**Run the tutorial via free cloud platforms:** [](https://mybinder.org/v2/gh/harmonize-tools/socio4health/HEAD?urlpath=%2Fdoc%2Ftree%2Fdocs%2Fsource%2Fnotebooks%2Fexample_colombia.ipynb) \n",
" \n",
""
]
},
{
"cell_type": "markdown",
"id": "372d389479a3fa29",
"metadata": {},
"source": [
"This notebook provides you with a real world example on how to use **socio4health** to **retrieve**, **harmonize** and **analyze** **socioeconomic and demographic** variables related to **dengue** incidence in Colombia and recreate the dataset used in the publication *Exploring Dengue Dynamics: A Multi-Scale Analysis of Spatio-Temporal Trends in Ibagué, Colombia* by Otelo et al., published in *Virus* in 2024 ([DOI](https://doi.org/10.3390/v16060906)). This tutorial assumes you have an **intermediate** or **advanced** understanding of **Python** and data manipulation.\n",
"\n",
"## Setting up the environment\n",
"\n",
"To run this notebook, you need to have the following prerequisites:\n",
"\n",
"- **Python 3.10+**\n",
"\n",
"Additionally, you need to install the `socio4health` and `pandas` package, which can be done using ``pip``:\n",
"\n"
]
},
{
"metadata": {
"ExecuteTime": {
"end_time": "2025-09-23T14:49:06.719174Z",
"start_time": "2025-09-23T14:49:03.443254Z"
}
},
"cell_type": "code",
"source": "!pip install socio4health pandas -q",
"id": "1c66e4be789eb9ca",
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n",
"[notice] A new release of pip is available: 25.1.1 -> 25.2\n",
"[notice] To update, run: python.exe -m pip install --upgrade pip\n"
]
}
],
"execution_count": 1
},
{
"metadata": {},
"cell_type": "markdown",
"source": "In case you want to run this notebook in **Google Colab**, you also need to run the following command to use your files stored in **Google Drive**:",
"id": "8572ca66825b64db"
},
{
"metadata": {},
"cell_type": "code",
"outputs": [],
"execution_count": null,
"source": [
"from google.colab import drive\n",
"drive.mount('/content/drive')"
],
"id": "37fe947f351b28ad"
},
{
"cell_type": "markdown",
"id": "fb366db39d507af0",
"metadata": {},
"source": [
"## Import Libraries\n",
"\n",
"To perform the data extraction, the `socio4health` library provides the `Extractor` class for data extraction, and the `Harmonizer` class for data harmonization of the retrieved date. `pandas` will be used for data manipulation. Additionally, we will use some utility functions from the `socio4health.utils.harmonizer_utils` module to standardize and translate the dictionary.\n"
]
},
{
"metadata": {
"ExecuteTime": {
"end_time": "2025-09-23T14:49:34.438354Z",
"start_time": "2025-09-23T14:49:17.741559Z"
}
},
"cell_type": "code",
"source": [
"import datetime\n",
"import geopandas as gpd\n",
"import numpy as np\n",
"import matplotlib.pyplot as plt\n",
"import pandas as pd\n",
"from socio4health import Extractor\n",
"from socio4health.harmonizer import Harmonizer\n",
"from socio4health.utils import harmonizer_utils"
],
"id": "5378f5ed0fe6a719",
"outputs": [],
"execution_count": 2
},
{
"cell_type": "markdown",
"id": "69f52ae88db42a0f",
"metadata": {},
"source": [
"## 1. Extract data from Colombia\n",
"\n",
"To extract data from Colombia, use the `Extractor` class from the `socio4health` library. As in the publication, extract the Colombian National Population and Housing Census 2018 (**CNPV 2018**) dataset from the Colombian Nacional Administration of Statistics (**DANE**) website. The dataset is available at: https://microdatos.dane.gov.co/index.php/catalog/643/related-materials.\n",
"\n",
"The `Extractor` class requires the following parameters:\n",
"- `input_path`: The `URL` or local path to the data source.\n",
"- `down_ext`: A list of file extensions to download. This can include `.CSV`, `.csv`, `.zip`, etc.\n",
"- `output_path`: The local path where the extracted data will be saved.\n",
"- `key_words`: A list of keywords to filter the files to be downloaded. In this case, we are only interested in the file `14045.zip`, which contains the data at the desired level of granularity (census block level or \"Manzana\").\n",
"- `depth`: The depth of the directory structure to traverse when downloading files. A depth of `0` means only the files in the specified directory will be downloaded.\n",
"\n"
]
},
{
"metadata": {
"ExecuteTime": {
"end_time": "2025-09-23T14:51:31.155788Z",
"start_time": "2025-09-23T14:49:52.219994Z"
}
},
"cell_type": "code",
"source": [
"col_online_extractor = Extractor(input_path=\"https://microdatos.dane.gov.co/index.php/catalog/643/related-materials\",\n",
" down_ext=['.cpg', '.dbf', '.prj','.sbn', '.sbx', '.shx', '.shp', '.zip'],\n",
" output_path=\"../CNVP2018\",\n",
" key_words=[\"14045.zip\"],\n",
" depth=0)\n",
"col_CNPV = col_online_extractor.s4h_extract()"
],
"id": "99cb294462133ad7",
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"2025-09-23 09:49:52,233 - INFO - ----------------------\n",
"2025-09-23 09:49:52,235 - INFO - Starting data extraction...\n",
"2025-09-23 09:49:52,236 - INFO - Extracting data in online mode...\n",
"2025-09-23 09:49:52,236 - INFO - Scraping URL: https://microdatos.dane.gov.co/index.php/catalog/643/related-materials with depth 0\n",
"2025-09-23 09:49:56,948 - INFO - Spider completed successfully for URL: https://microdatos.dane.gov.co/index.php/catalog/643/related-materials\n",
"2025-09-23 09:49:56,950 - INFO - Downloading files to: ../CNVP2018\n",
"Downloading files: 0%| | 0/1 [00:00, ?it/s]2025-09-23 09:50:07,974 - INFO - Successfully downloaded: 14045.zip\n",
"Downloading files: 100%|██████████| 1/1 [00:11<00:00, 11.02s/it]\n",
"2025-09-23 09:50:07,986 - INFO - Processing (depth 0): 14045.zip\n",
"2025-09-23 09:50:15,101 - INFO - Extracted: 383d6920_MGN_NivelManzana_Integrado_CNPV_MGN_ANM_MANZANA.cpg\n",
"2025-09-23 09:50:17,199 - INFO - Extracted: 383d6920_MGN_NivelManzana_Integrado_CNPV_MGN_ANM_MANZANA.dbf\n",
"2025-09-23 09:50:17,204 - INFO - Extracted: 383d6920_MGN_NivelManzana_Integrado_CNPV_MGN_ANM_MANZANA.prj\n",
"2025-09-23 09:50:17,219 - INFO - Extracted: 383d6920_MGN_NivelManzana_Integrado_CNPV_MGN_ANM_MANZANA.sbn\n",
"2025-09-23 09:50:17,227 - INFO - Extracted: 383d6920_MGN_NivelManzana_Integrado_CNPV_MGN_ANM_MANZANA.sbx\n",
"2025-09-23 09:50:17,862 - INFO - Extracted: 383d6920_MGN_NivelManzana_Integrado_CNPV_MGN_ANM_MANZANA.shp\n",
"2025-09-23 09:50:17,886 - INFO - Extracted: 383d6920_MGN_NivelManzana_Integrado_CNPV_MGN_ANM_MANZANA.shx\n",
"Processing files: 0%| | 0/7 [00:00, ?it/s]2025-09-23 09:50:17,904 - WARNING - Unsupported extension: .cpg\n",
"2025-09-23 09:50:17,906 - WARNING - Unsupported extension: .shx\n",
"2025-09-23 09:50:17,909 - WARNING - Unsupported extension: .dbf\n",
"2025-09-23 09:50:17,917 - WARNING - Unsupported extension: .prj\n",
"Processing files: 71%|███████▏ | 5/7 [01:13<00:29, 14.60s/it]2025-09-23 09:51:31,124 - WARNING - Unsupported extension: .sbn\n",
"Processing files: 86%|████████▌ | 6/7 [01:13<00:11, 11.41s/it]2025-09-23 09:51:31,132 - WARNING - Unsupported extension: .sbx\n",
"Processing files: 100%|██████████| 7/7 [01:13<00:00, 10.46s/it]\n",
"2025-09-23 09:51:31,136 - INFO - Successfully processed 7/7 files\n",
"2025-09-23 09:51:31,141 - INFO - Extraction completed successfully.\n"
]
}
],
"execution_count": 3
},
{
"metadata": {
"ExecuteTime": {
"end_time": "2025-09-23T14:51:49.753740Z",
"start_time": "2025-09-23T14:51:44.728006Z"
}
},
"cell_type": "code",
"source": "col_CNPV[0]",
"id": "ad028a6de2823c88",
"outputs": [
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\n", "| \n", " | variable_name | \n", "type | \n", "size | \n", "question | \n", "description | \n", "value | \n", "
|---|---|---|---|---|---|---|
| 0 | \n", "COD_DANE_A | \n", "Text | \n", "22.0 | \n", "Código de manzana concatenado (departamento, m... | \n", "NaN | \n", "NaN | \n", "
| 1 | \n", "DPTO_CCDGO | \n", "Text | \n", "2.0 | \n", "Código del departamento | \n", "NaN | \n", "NaN | \n", "
| 2 | \n", "MPIO_CCDGO | \n", "Text | \n", "3.0 | \n", "Código del municipio | \n", "NaN | \n", "NaN | \n", "
| 3 | \n", "MPIO_CDPMP | \n", "Text | \n", "5.0 | \n", "Código concatenado que identifica al municipio | \n", "NaN | \n", "NaN | \n", "
| 4 | \n", "CLAS_CCDGO | \n", "Text | \n", "1.0 | \n", "Código de la clase 1 cabecera municipal, 2 cen... | \n", "NaN | \n", "NaN | \n", "
| ... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
| 101 | \n", "TP51_13_ED | \n", "Double | \n", "NaN | \n", "Conteo de personas donde el nivel educativo de... | \n", "Ninguno | \n", "NaN | \n", "
| 102 | \n", "TP51_99_ED | \n", "Double | \n", "NaN | \n", "Conteo de personas donde el nivel educativo de... | \n", "Sin información | \n", "NaN | \n", "
| 103 | \n", "CD_LC_CM | \n", "Text | \n", "10.0 | \n", "Código de la localidad o comuna | \n", "NaN | \n", "NaN | \n", "
| 104 | \n", "NMB_LC_CM | \n", "Text | \n", "50.0 | \n", "Nombre de la localidad o comuna | \n", "NaN | \n", "NaN | \n", "
| 105 | \n", "TP_LC_CM | \n", "Text | \n", "20.0 | \n", "Descripción de tipo localidad o comuna o corre... | \n", "NaN | \n", "NaN | \n", "
106 rows × 6 columns
\n", "| \n", " | variable_name | \n", "type | \n", "size | \n", "question | \n", "description | \n", "value | \n", "possible_answers | \n", "question_en | \n", "description_en | \n", "possible_answers_en | \n", "category | \n", "
|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", "VERSION | \n", "Long Integer | \n", "NaN | \n", "año de la información geográfica | \n", "NaN | \n", "NaN | \n", "NaN | \n", "year of geographical information | \n", "NaN | \n", "NaN | \n", "Identification | \n", "
| 1 | \n", "CTNENCUEST | \n", "Double | \n", "NaN | \n", "cantidad de encuestas cnpv 2018 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "Number of CNPV 2018 surveys | \n", "NaN | \n", "NaN | \n", "Identification | \n", "
| 2 | \n", "TP3_1_SI | \n", "Double | \n", "NaN | \n", "cantidad de encuestas que reportaron estar en ... | \n", "NaN | \n", "NaN | \n", "NaN | \n", "number of surveys that reported to be in ethni... | \n", "NaN | \n", "NaN | \n", "Identification | \n", "
| 3 | \n", "TP3A_RI | \n", "Double | \n", "NaN | \n", "cantidad de encuestas que reportaron estar en ... | \n", "resguardo indígena | \n", "NaN | \n", "NaN | \n", "number of surveys that reported to be in ethni... | \n", "Indigenous shelter | \n", "NaN | \n", "Identification | \n", "
| 4 | \n", "TP3B_TCN | \n", "Double | \n", "NaN | \n", "cantidad de encuestas que reportaron estar en ... | \n", "tccn | \n", "NaN | \n", "NaN | \n", "number of surveys that reported to be in ethni... | \n", "TCCN | \n", "NaN | \n", "Identification | \n", "
| ... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
| 101 | \n", "DATO_ANM | \n", "Text | \n", "50.0 | \n", "nombre capa anonimizada | \n", "NaN | \n", "NaN | \n", "NaN | \n", "Anonymity layer name | \n", "NaN | \n", "NaN | \n", "Identification | \n", "
| 102 | \n", "NMB_LC_CM | \n", "Text | \n", "50.0 | \n", "nombre de la localidad o comuna | \n", "NaN | \n", "NaN | \n", "NaN | \n", "locality or commune name | \n", "NaN | \n", "NaN | \n", "Identification | \n", "
| 103 | \n", "TP27_PERSO | \n", "Double | \n", "NaN | \n", "número de personas | \n", "NaN | \n", "NaN | \n", "NaN | \n", "number of people | \n", "NaN | \n", "NaN | \n", "Identification | \n", "
| 104 | \n", "DENSIDAD | \n", "Double | \n", "NaN | \n", "número promedio de habitantes en la manzana qu... | \n", "NaN | \n", "NaN | \n", "NaN | \n", "Average number of inhabitants in the apple liv... | \n", "NaN | \n", "NaN | \n", "Identification | \n", "
| 105 | \n", "AREA | \n", "Double | \n", "NaN | \n", "área de la manzana en metros cuadrados (sistem... | \n", "NaN | \n", "NaN | \n", "NaN | \n", "Apple area in square meters (Magna_Colombia_bo... | \n", "NaN | \n", "NaN | \n", "Identification | \n", "
106 rows × 11 columns
\n", "| \n", " | Unmatched ddfs variable | \n", "Unmatched dict_df variables | \n", "
|---|---|---|
| 0 | \n", "COD_RDTM | \n", "None | \n", "
| 1 | \n", "FILENAME | \n", "None | \n", "
| 2 | \n", "GEOMETRY | \n", "None | \n", "
| 3 | \n", "SHAPE_AREA | \n", "None | \n", "
| 4 | \n", "SHAPE_LENG | \n", "None | \n", "