dsfsi / covid19africa Goto Github PK

This data looks like its out dated I dont see recent cases for south africa, I only see about 554 cases @vukosim or the data is available here, if it here which file is the correct one?

Have a list that can be updated daily with updated cases.

• Useful for visualisation
• Useful for situational awareness.

You can use the WHO situational reports (linked in /data/) to assist. How do we automatically extract from situational reports pdfs?

We need some help with a description of line list sources for African countries. You can see sources of data we have put here https://github.com/dsfsi/covid19africa/tree/master/data

And then use it to help fill in this spreadsheet. https://docs.google.com/spreadsheets/d/1XcOZAe43A8uezREyd9Kz4kYKu_LYShOq0KY_RNo7UU0/edit?usp=sharing

I used JHU dataset to a create dashboard using MS power bi. The dataset consist of FIPS, Admin2,Province_State, Country_Region, Last_Update, Lat, Long_, Confirmed,Deaths, Recovered, Active, Combined_Key, Incidence_Rate, Case-Fatality_Ratio.
I am suggesting that such can be added to the github repo, and such folder can be named as covid19 africa daily report; for example South Africa case will be
South Africa | 2020-06-19 04:33:17 | -30.5595 | 22.9375 | 83890 | 1737 | 44920 | 37233 | South Africa | 141.44638837917344 | 2.070568601740374 respectively. The FIPS, Admin2, Province_State are empty.
If such dataset is added it will be easy to create a dashboard for Africa and more collaboration can be done.
The link to the dashboard preview can be found here

line list – a table summarizing information about people who are infected, dead, recovered etc. The table would include demographic and location information. Such a dataset would help us understand how COVID19 transmission in Africa is similar or different to what’s being observed in other regions of the world.

This would be part of a broader effort focused on collating COVID19 data globally. We need volunteers ASAP to help in this effort. The data will be made publicly available and volunteers will be acknowledged.

See https://github.com/dsfsi/covid19africa/blob/master/data/line-list-africa.csv

Hello, I just thought I'd share this project I did in me free time:
https://sacovidmap.netlify.com/

My code is open source so anyone who who's working on anything related may use as much of it as they want:
https://github.com/webdevan/covid-map

Disclaimer: I'm not a scientist, so use this at your own risk.

I'm using the cumulative cases CSVs in this repo and should update automatically when new data is merged (if the structure changes my map will break!). I might submit an issue to discuss how we can structure the data in a way that can scale (because it is likely to keep expanding and evolving so getting some standards and structure going would be helpful).

Anyway, just wanted to put this out there so that people can use it, and if there's any feedback let me know.

Error picked up by @JosseyMikka must be fixed.

Add data sources for African Country Cases

Edit the https://github.com/dsfsi/covid19africa/blob/master/data/README.md with your resources

How to fork and submit changes https://opensource.com/article/19/7/create-pull-request-github

Hi There,

Wondering why you don't use John Hopkins data and build onto it? They have done (are doing) a tremendous work to pull together a fairly solid data.

If you need inspiration on presenting the data, here is my try: virus-corona.herokuapp.com

Cheers,
Louis

The who_covid_19_sit_rep_time_series_africa.csv data which is the time Series Data for confirmed cases only exist. I think we should add the Deaths and Recovered Time Series data as well.

I was wondering if there is an idea of incorporating number of tests done per day per country in the current dataset.

I am not sure how it could be integrated in the current line-list files but adding a column 'num_tests' could be an idea.

alternatively a separate line-list with: date, num_tests, positives could handle it.

Thank you,
Million

Hi all,

I'm involved in the Wellcome Open Research Fund project - afrimapr - which is creating R building blocks to make health data in Africa more visible through mapping. This resource might be useful for others to build scripts/maps/apps with. It's in very early stages of development.

Please see https://www.lstmed.ac.uk/news-events/news/open-data-and-software-to-support-the-covid-19-response-in-africa and our website at http://afrimapr.org. We're currently working to make health facilities (from open data i.e. WHO and healthsites.io ) building blocks in R.

If you have any ideas about how this may be useful to you or others, please get in touch.

Hi there,

Super cool project you have here! As the list of countries in the dashboard grows, it'll be hard to have all in the same page. One possible idea to would be to have a selector for which countries to display. I did something like this for a similar project using a textbox and comparing user input to what countries are in the database.

I am not sure what is powering the dashboard, but if it's something like Python/Plotly, I'd be happy to share actual code to do this.

Stay safe and keep going strong! 💪

Hello,
Your dataset was added to CoronaWhy (https://www.coronawhy.org/) Data Lake on Dataverse as a piece of common COVID-19 data https://datasets.coronawhy.org/dataset.xhtml?persistentId=doi:10.5072/FK2/XZCZOC
Would you be willing to help with the maintenance of your dataset in Dataverse, e.g. adding the relevant metadata and keeping the dataset up-to-date? That will help to make the dataset findable and accessible for the medical science community.

I've been uploading the time series data for a while, but for the past five days i've been having conflicts issues, i do follow this process is this link. I've tried a lot of things but it's not still working. What other things can i do.

BU Health has made available a file with early case information for many African countries.

Tasks:

• For countries that are not on yet available on the repo, create a line list in the CSV format we use.
• For countries that are already on the line list, validate.

File https://github.com/dsfsi/covid19africa/blob/master/data/staging/2020.04.01.20050203-2.xlsx

line list templates https://github.com/dsfsi/covid19africa/tree/master/data/templates

If you are concentrating on a specific country, PLEASE list yourself below to avoid duplication of work

Problem description

We would like to do the following analysis per African country:

1. Visualise the daily and cumulative cases since the first reported case
2. Calculate the relative risk of infection with COVID-19 by age group
3. Analyse the distribution of the infection by gender and age
4. Analyze the change in the status of those who were affected over time (ie, "recovered", "ICU", "treatment" etc)

Current bottlenecks

Most of the data collected are not complete. For example, in most countries, there is a large chunk of missing data it the gender and age fields of the individuals who have tested positive.

Also for most countries, the current state of the individuals is unknown. So when new deaths occur it is hard to identify which individual in passed away.

In most countries only the first few cases that are reported on in detail, however this makes it hard to track the progression of the diseases via age and gender down the down

If taking this up

Please help with validating the data for the country you have chosen

We do not have analysis notebooks as yet. See README in notebooks/ for ideas.