COVID19 Spain cases
Data
All raw data is directly downloaded from Ministerio de Sanidad website, which daily updates the statistics from the COVID19 epidemy. The downloaded archives are PDF files that are transformed into csv files in order to better analyze them.
Repo Structure
.
├── data
│ ├── csv_agedata
│ ├── csv_data
│ ├── final_data
│ ├── info_data
│ └── pdf_data
├── imgs
├── notebooks
└── src
Data structure
data
├── csv_agedata
│ ├── COVID_es_[DATE].csv
├── csv_data
│ ├── COVID_es_[DATE].csv
├── final_data
│ └── dataCOVID19_es.csv
├── info_data
│ ├── PoblaciónCCAA.csv
│ ├── death_rate.csv
│ └── poblacio?\201n_edades.csv
└── pdf_data
├── Actualizacion_[XX]_COVID-19.pdf
- Original data are gathered in
data/pdf_data - csvs from original data by date are gathered in
data/csv_data(Cases) anddata/agecsv_data(Total per age) info_datacontains extra data from sources such as Instituto Nacional de Estadísticafinal_datacontains the csv filedataCOVID19_es.csvwhich is daily updated.- By default all special characters included in PDF tables are removed. If there are inconsistencies in the data on a certain date, please review the table footer of the corresponding PDF.
FINAL DATA (dictionary)
| Column | Meaning |
|---|---|
| CCAA | Spanish Autonomous community |
| fecha | Date |
| casos | Cases |
| nuevos | Number of new cases compared to the previous day |
| IA | Cumulative incidence |
| Hospitalizados | Number of hospitalized patients |
| HospitalizadosNuevos | Number of hospitalized patients |
| UCI | Number of patients requiring Intensive care unit assistance |
| UCINuevos | Number of new patients requiring Intensive care unit assistance |
| muertes | Number of deaths |
| muertesNuevos | Number of new deaths |
| curados | Number of healed patients |
| curadosNuevos | Number of new healed patients |
| PCR | Polymerase chain reaction |
| testrap | Total quick tests performed |
| postestrap | Total positive quick tests |
| posTOTAL | Total positive tests |
AGE DATA (dictionary)
| Column | Meaning |
|---|---|
| age | Age range |
| fecha | date |
| Conf{V} | Confirmed cases |
| Hosp{V} | Hospitalized patients |
| Hosp{V}% | Hospitalized patients (%) |
| UCI{V} | Patients requiring Intensive care unit assistance |
| UCI{V}% | Patients requiring Intensive care unit assistance (%) |
| Fall{V} | Deaths |
| Fall{V}% | Deaths (%) |
| Let{V} | Mortality (%) |
| Variable {V} | Meaning |
|---|---|
| Total {T} | Total |
| Mujer {M} | Woman |
| Hombre {H} | Man |
Scripts
The src folder contains the scripts to get the data download_pdf.py & get_pdf_today.py, to transform pdf to csv pdf_to_csv.py or get_age_tab.py and to get dataCOVID19_es.csv file > join_data.py.
Notebooks
The notebooks folder contains some examples of epidemologic models such as SIRModel.ipynb, SEIRModel.ipynb or LogisticCurve.ipynb.
Contribute
Feel free to contact me or make a pull-request if you want to change/add anything.
Special thanks to Pedro Vélez and covid-19-stats for their contribution to this repo