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Data Lake for the Platform for Analytical Models in Epidemiology (PAMEpi)

DOI

Table of contents

General info

Each folder in this directory contains all the descriptions for building a data lake that can enable studies on a specific infectious disease. Each folder has four subfolders: Data Collection, Data Curation, Data Description, and Data ETL.

  • Data Collection: contains the scripts for downloading data from open sources and updating when new versions are available in their original system (source).

  • Data Curation: contains the scripts for data harmonisation and cleansing for each data set. The scripts may change over time due to changes detected after the record update.

  • Data Description: we provide codes to perform basic data analysis and data validation.

  • Data ETL: we provide codes to format data for modelling and visualization.

Installation

Currently the library is on production, so the easiest way to use is clone our repository or copy the functions available in this directory.

Dependencies

Models were implemented using Python > 3.5 and depend on libraries such as Pandas, SciPy, Numpy, Matplotlib, etc. For the full list of dependencies as well libraries versions check requirements.txt inside each folder.

License

MIT License

Citing the directory

Platform For Analytical Modelis in Epidemiology. (2022). GitHub directory: https://github.com/PAMepi/PAMepi_scripts_datalake.git. PAMepi/PAMepi_scripts_datalake: v1.0.0 (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.6384641

Note that in each folder you will find a doi linked to the dataset processed by the team, which can be cited in your work.

Support

This study was financed by

* Bill and Melinda Gates Foundation and Minderoo Foundation HDR UK, through the Grand Challenges ICODA COVID-19 Data Science, with reference number 2021.0097 * Fiocruz Innovation Promotion Program - Innovative ideas and products - COVID-19, orders and strategies INOVA-FIOCRUZ, with reference Number VPPIS-005-FIO-20-2-40.

References

[1] Platform for Analytical Models in Epidemiology - PAMEpi (2020).

[2] Platform for Analytical Models in Epidemiology - PAMEpi-Covid-19: Data (2020).

About

This directory builds the data architecture of the PAMEpi. It describes which data is collected, how it is stored, arranged, integrated, and put to use for analyses, modelling and visualization.

Topics

covid-19data-sciencepandaspython

Resources

Readme
MIT license
Activity
Custom properties

Stars

2 stars

Watchers

4 watching

Forks

0 forks
Report repository

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 Data Lake for the Platform for Analytical Models in Epidemiology (PAMEpi)
DOI
Table of contents
General info
Each folder in this directory contains all the descriptions for building a data lake that can enable studies on a specific infectious disease. Each folder has four subfolders: Data Collection, Data Curation, Data Description, and Data ETL.
  • Data Collection: contains the scripts for downloading data from open sources and updating when new versions are available in their original system (source).
  • Data Curation: contains the scripts for data harmonisation and cleansing for each data set. The scripts may change over time due to changes detected after the record update.
  • Data Description: we provide codes to perform basic data analysis and data validation.
  • Data ETL: we provide codes to format data for modelling and visualization.
Installation
Currently the library is on production, so the easiest way to use is clone our repository or copy the functions available in this directory.
Dependencies
Models were implemented using Python > 3.5 and depend on libraries such as Pandas, SciPy, Numpy, Matplotlib, etc. For the full list of dependencies as well libraries versions check requirements.txt inside each folder.
License
MIT License
Citing the directory
Platform For Analytical Modelis in Epidemiology. (2022). GitHub directory: https://github.com/PAMepi/PAMepi_scripts_datalake.git. PAMepi/PAMepi_scripts_datalake: v1.0.0 (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.6384641
Note that in each folder you will find a doi linked to the dataset processed by the team, which can be cited in your work.
Support
This study was financed by
* Bill and Melinda Gates Foundation and Minderoo Foundation HDR UK, through the Grand Challenges ICODA COVID-19 Data Science, with reference number 2021.0097 * Fiocruz Innovation Promotion Program - Innovative ideas and products - COVID-19, orders and strategies INOVA-FIOCRUZ, with reference Number VPPIS-005-FIO-20-2-40.

References
[1] Platform for Analytical Models in Epidemiology - PAMEpi (2020).
[2] Platform for Analytical Models in Epidemiology - PAMEpi-Covid-19: Data (2020).
About
This directory builds the data architecture of the PAMEpi. It describes which data is collected, how it is stored, arranged, integrated, and put to use for analyses, modelling and visualization.
Topics
covid-19data-sciencepandaspython
Resources
Readme
MIT license
Activity
Custom properties
Stars
2 stars
Watchers
4 watching
Forks
0 forks
Report repository
Releases
Packages
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, 'i');
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 Data Lake for the Platform for Analytical Models in Epidemiology (PAMEpi)
DOI
Table of contents
General info
Each folder in this directory contains all the descriptions for building a data lake that can enable studies on a specific infectious disease. Each folder has four subfolders: Data Collection, Data Curation, Data Description, and Data ETL.
  • Data Collection: contains the scripts for downloading data from open sources and updating when new versions are available in their original system (source).
  • Data Curation: contains the scripts for data harmonisation and cleansing for each data set. The scripts may change over time due to changes detected after the record update.
  • Data Description: we provide codes to perform basic data analysis and data validation.
  • Data ETL: we provide codes to format data for modelling and visualization.
Installation
Currently the library is on production, so the easiest way to use is clone our repository or copy the functions available in this directory.
Dependencies
Models were implemented using Python > 3.5 and depend on libraries such as Pandas, SciPy, Numpy, Matplotlib, etc. For the full list of dependencies as well libraries versions check requirements.txt inside each folder.
License
MIT License
Citing the directory
Platform For Analytical Modelis in Epidemiology. (2022). GitHub directory: https://github.com/PAMepi/PAMepi_scripts_datalake.git. PAMepi/PAMepi_scripts_datalake: v1.0.0 (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.6384641
Note that in each folder you will find a doi linked to the dataset processed by the team, which can be cited in your work.
Support
This study was financed by
* Bill and Melinda Gates Foundation and Minderoo Foundation HDR UK, through the Grand Challenges ICODA COVID-19 Data Science, with reference number 2021.0097 * Fiocruz Innovation Promotion Program - Innovative ideas and products - COVID-19, orders and strategies INOVA-FIOCRUZ, with reference Number VPPIS-005-FIO-20-2-40.

References
[1] Platform for Analytical Models in Epidemiology - PAMEpi (2020).
[2] Platform for Analytical Models in Epidemiology - PAMEpi-Covid-19: Data (2020).
About
This directory builds the data architecture of the PAMEpi. It describes which data is collected, how it is stored, arranged, integrated, and put to use for analyses, modelling and visualization.
Topics
covid-19data-sciencepandaspython
Resources
Readme
MIT license
Activity
Custom properties
Stars
2 stars
Watchers
4 watching
Forks
0 forks
Report repository
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Packages
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Repository files navigation
 Data Lake for the Platform for Analytical Models in Epidemiology (PAMEpi)
DOI
Table of contents
General info
Each folder in this directory contains all the descriptions for building a data lake that can enable studies on a specific infectious disease. Each folder has four subfolders: Data Collection, Data Curation, Data Description, and Data ETL.
  • Data Collection: contains the scripts for downloading data from open sources and updating when new versions are available in their original system (source).
  • Data Curation: contains the scripts for data harmonisation and cleansing for each data set. The scripts may change over time due to changes detected after the record update.
  • Data Description: we provide codes to perform basic data analysis and data validation.
  • Data ETL: we provide codes to format data for modelling and visualization.
Installation
Currently the library is on production, so the easiest way to use is clone our repository or copy the functions available in this directory.
Dependencies
Models were implemented using Python > 3.5 and depend on libraries such as Pandas, SciPy, Numpy, Matplotlib, etc. For the full list of dependencies as well libraries versions check requirements.txt inside each folder.
License
MIT License
Citing the directory
Platform For Analytical Modelis in Epidemiology. (2022). GitHub directory: https://github.com/PAMepi/PAMepi_scripts_datalake.git. PAMepi/PAMepi_scripts_datalake: v1.0.0 (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.6384641
Note that in each folder you will find a doi linked to the dataset processed by the team, which can be cited in your work.
Support
This study was financed by
* Bill and Melinda Gates Foundation and Minderoo Foundation HDR UK, through the Grand Challenges ICODA COVID-19 Data Science, with reference number 2021.0097 * Fiocruz Innovation Promotion Program - Innovative ideas and products - COVID-19, orders and strategies INOVA-FIOCRUZ, with reference Number VPPIS-005-FIO-20-2-40.

References
[1] Platform for Analytical Models in Epidemiology - PAMEpi (2020).
[2] Platform for Analytical Models in Epidemiology - PAMEpi-Covid-19: Data (2020).
About
This directory builds the data architecture of the PAMEpi. It describes which data is collected, how it is stored, arranged, integrated, and put to use for analyses, modelling and visualization.
Topics
covid-19data-sciencepandaspython
Resources
Readme
MIT license
Activity
Custom properties
Stars
2 stars
Watchers
4 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
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, 'i');
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 Data Lake for the Platform for Analytical Models in Epidemiology (PAMEpi)
DOI
Table of contents
General info
Each folder in this directory contains all the descriptions for building a data lake that can enable studies on a specific infectious disease. Each folder has four subfolders: Data Collection, Data Curation, Data Description, and Data ETL.
  • Data Collection: contains the scripts for downloading data from open sources and updating when new versions are available in their original system (source).
  • Data Curation: contains the scripts for data harmonisation and cleansing for each data set. The scripts may change over time due to changes detected after the record update.
  • Data Description: we provide codes to perform basic data analysis and data validation.
  • Data ETL: we provide codes to format data for modelling and visualization.
Installation
Currently the library is on production, so the easiest way to use is clone our repository or copy the functions available in this directory.
Dependencies
Models were implemented using Python > 3.5 and depend on libraries such as Pandas, SciPy, Numpy, Matplotlib, etc. For the full list of dependencies as well libraries versions check requirements.txt inside each folder.
License
MIT License
Citing the directory
Platform For Analytical Modelis in Epidemiology. (2022). GitHub directory: https://github.com/PAMepi/PAMepi_scripts_datalake.git. PAMepi/PAMepi_scripts_datalake: v1.0.0 (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.6384641
Note that in each folder you will find a doi linked to the dataset processed by the team, which can be cited in your work.
Support
This study was financed by
* Bill and Melinda Gates Foundation and Minderoo Foundation HDR UK, through the Grand Challenges ICODA COVID-19 Data Science, with reference number 2021.0097 * Fiocruz Innovation Promotion Program - Innovative ideas and products - COVID-19, orders and strategies INOVA-FIOCRUZ, with reference Number VPPIS-005-FIO-20-2-40.

References
[1] Platform for Analytical Models in Epidemiology - PAMEpi (2020).
[2] Platform for Analytical Models in Epidemiology - PAMEpi-Covid-19: Data (2020).
About
This directory builds the data architecture of the PAMEpi. It describes which data is collected, how it is stored, arranged, integrated, and put to use for analyses, modelling and visualization.
Topics
covid-19data-sciencepandaspython
Resources
Readme
MIT license
Activity
Custom properties
Stars
2 stars
Watchers
4 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
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 Data Lake for the Platform for Analytical Models in Epidemiology (PAMEpi)
DOI
Table of contents
General info
Each folder in this directory contains all the descriptions for building a data lake that can enable studies on a specific infectious disease. Each folder has four subfolders: Data Collection, Data Curation, Data Description, and Data ETL.
  • Data Collection: contains the scripts for downloading data from open sources and updating when new versions are available in their original system (source).
  • Data Curation: contains the scripts for data harmonisation and cleansing for each data set. The scripts may change over time due to changes detected after the record update.
  • Data Description: we provide codes to perform basic data analysis and data validation.
  • Data ETL: we provide codes to format data for modelling and visualization.
Installation
Currently the library is on production, so the easiest way to use is clone our repository or copy the functions available in this directory.
Dependencies
Models were implemented using Python > 3.5 and depend on libraries such as Pandas, SciPy, Numpy, Matplotlib, etc. For the full list of dependencies as well libraries versions check requirements.txt inside each folder.
License
MIT License
Citing the directory
Platform For Analytical Modelis in Epidemiology. (2022). GitHub directory: https://github.com/PAMepi/PAMepi_scripts_datalake.git. PAMepi/PAMepi_scripts_datalake: v1.0.0 (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.6384641
Note that in each folder you will find a doi linked to the dataset processed by the team, which can be cited in your work.
Support
This study was financed by
* Bill and Melinda Gates Foundation and Minderoo Foundation HDR UK, through the Grand Challenges ICODA COVID-19 Data Science, with reference number 2021.0097 * Fiocruz Innovation Promotion Program - Innovative ideas and products - COVID-19, orders and strategies INOVA-FIOCRUZ, with reference Number VPPIS-005-FIO-20-2-40.

References
[1] Platform for Analytical Models in Epidemiology - PAMEpi (2020).
[2] Platform for Analytical Models in Epidemiology - PAMEpi-Covid-19: Data (2020).
About
This directory builds the data architecture of the PAMEpi. It describes which data is collected, how it is stored, arranged, integrated, and put to use for analyses, modelling and visualization.
Topics
covid-19data-sciencepandaspython
Resources
Readme
MIT license
Activity
Custom properties
Stars
2 stars
Watchers
4 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
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GitHub - PAMepi/PAMepi_scripts_datalake: This directory builds the data architecture of the PAMEpi. It describes which data is collected, how it is stored, arranged, integrated, and put to use for analyses, modelling and visualization. · GitHub
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Repository files navigation
 Data Lake for the Platform for Analytical Models in Epidemiology (PAMEpi)
DOI
Table of contents
General info
Each folder in this directory contains all the descriptions for building a data lake that can enable studies on a specific infectious disease. Each folder has four subfolders: Data Collection, Data Curation, Data Description, and Data ETL.
  • Data Collection: contains the scripts for downloading data from open sources and updating when new versions are available in their original system (source).
  • Data Curation: contains the scripts for data harmonisation and cleansing for each data set. The scripts may change over time due to changes detected after the record update.
  • Data Description: we provide codes to perform basic data analysis and data validation.
  • Data ETL: we provide codes to format data for modelling and visualization.
Installation
Currently the library is on production, so the easiest way to use is clone our repository or copy the functions available in this directory.
Dependencies
Models were implemented using Python > 3.5 and depend on libraries such as Pandas, SciPy, Numpy, Matplotlib, etc. For the full list of dependencies as well libraries versions check requirements.txt inside each folder.
License
MIT License
Citing the directory
Platform For Analytical Modelis in Epidemiology. (2022). GitHub directory: https://github.com/PAMepi/PAMepi_scripts_datalake.git. PAMepi/PAMepi_scripts_datalake: v1.0.0 (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.6384641
Note that in each folder you will find a doi linked to the dataset processed by the team, which can be cited in your work.
Support
This study was financed by
* Bill and Melinda Gates Foundation and Minderoo Foundation HDR UK, through the Grand Challenges ICODA COVID-19 Data Science, with reference number 2021.0097 * Fiocruz Innovation Promotion Program - Innovative ideas and products - COVID-19, orders and strategies INOVA-FIOCRUZ, with reference Number VPPIS-005-FIO-20-2-40.

References
[1] Platform for Analytical Models in Epidemiology - PAMEpi (2020).
[2] Platform for Analytical Models in Epidemiology - PAMEpi-Covid-19: Data (2020).
About
This directory builds the data architecture of the PAMEpi. It describes which data is collected, how it is stored, arranged, integrated, and put to use for analyses, modelling and visualization.
Topics
covid-19data-sciencepandaspython
Resources
Readme
MIT license
Activity
Custom properties
Stars
2 stars
Watchers
4 watching
Forks
0 forks
Report repository
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GitHub - PAMepi/PAMepi_scripts_datalake: This directory builds the data architecture of the PAMEpi. It describes which data is collected, how it is stored, arranged, integrated, and put to use for analyses, modelling and visualization. · GitHub
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 Data Lake for the Platform for Analytical Models in Epidemiology (PAMEpi)
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Table of contents
General info
Each folder in this directory contains all the descriptions for building a data lake that can enable studies on a specific infectious disease. Each folder has four subfolders: Data Collection, Data Curation, Data Description, and Data ETL.
  • Data Collection: contains the scripts for downloading data from open sources and updating when new versions are available in their original system (source).
  • Data Curation: contains the scripts for data harmonisation and cleansing for each data set. The scripts may change over time due to changes detected after the record update.
  • Data Description: we provide codes to perform basic data analysis and data validation.
  • Data ETL: we provide codes to format data for modelling and visualization.
Installation
Currently the library is on production, so the easiest way to use is clone our repository or copy the functions available in this directory.
Dependencies
Models were implemented using Python > 3.5 and depend on libraries such as Pandas, SciPy, Numpy, Matplotlib, etc. For the full list of dependencies as well libraries versions check requirements.txt inside each folder.
License
MIT License
Citing the directory
Platform For Analytical Modelis in Epidemiology. (2022). GitHub directory: https://github.com/PAMepi/PAMepi_scripts_datalake.git. PAMepi/PAMepi_scripts_datalake: v1.0.0 (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.6384641
Note that in each folder you will find a doi linked to the dataset processed by the team, which can be cited in your work.
Support
This study was financed by
* Bill and Melinda Gates Foundation and Minderoo Foundation HDR UK, through the Grand Challenges ICODA COVID-19 Data Science, with reference number 2021.0097 * Fiocruz Innovation Promotion Program - Innovative ideas and products - COVID-19, orders and strategies INOVA-FIOCRUZ, with reference Number VPPIS-005-FIO-20-2-40.

References
[1] Platform for Analytical Models in Epidemiology - PAMEpi (2020).
[2] Platform for Analytical Models in Epidemiology - PAMEpi-Covid-19: Data (2020).
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This directory builds the data architecture of the PAMEpi. It describes which data is collected, how it is stored, arranged, integrated, and put to use for analyses, modelling and visualization.
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