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Home Page: https://www.monkeypox.global.health
License: MIT License
Monkeypox summary report
Home Page: https://www.monkeypox.global.health
License: MIT License
Since outbreak_associated is no longer included in Nextstrain TSV download, use clade membership B.1 as the primary indicator of outbreak, as well as include the two A.2 genomes from USA.
Flag outliers in new data.
Create www.monkeypox.global.health/archives.html which will have list of all reports
Consider expanding Figure 4 legend to include the following:
"Figure 4: Age and gender distribution of monkeypox confirmed cases in 2022. X% of confirmed cases include sufficient metadata to be included in this figure. Of these cases, X% include reported age ranges that span multiple age categories. Under such circumstances, counts are evenly distributed among the categories that capture the reported age range. "
I have the lines of code to calculate these percentages.
@Mougk thoughts?
Originally posted by @tvarrelman in globaldothealth/monkeypox#79 (comment)
Can't do it in the usual UI as there's no pull request to reference, so here's the points I observed.
monkeypox-report/src/test_build.py
Line 105 in b09edfd
monkeypatch
to substitute requests.get
here, or any problem accessing GitHub will make the test runner exit.Line 79 in b09edfd
if __name__ == '__main__'
so that you can also test unhappy paths.monkeypox-report/src/test_build.py
Line 132 in b09edfd
n_countries_suspected_only
is 1 because it correctly counted those, not because it actually used the same logic for n_countries_discarded
? My preference would be to introduce functions that calculate the summary statistics separately and test that they work correctly, which might help with:Line 166 in b09edfd
Line 225 in b09edfd
Line 243 in b09edfd
monkeypox-report/src/test_build.py
Line 169 in b09edfd
raise ValueError
) case isn't tested.Line 268 in b09edfd
test_build.py
that seems to mostly generate dictionaries with random content that are used in a two-line test file. Could that be replaced with a constant dictionary, maybe loaded from json or yaml?monkeypox-report/src/figures/genomics.py
Line 30 in b09edfd
I ran the following command
michael@plex:~/code/globalhealth-monkeypox-report$ poetry run python src/build.py bucket
I get the following error, why?
botocore.exceptions.NoCredentialsError: Unable to locate credentials
Figure Legend 1A could be improved. suggestion: a) make smaller, b) put under the Map and horizontal c) Potentially have a zoom for Europe now that there are many lines between European countries.
Fig 1A shows the travel history. At present, there is a lot of travel within Europe which causes overlapping lines. It would be nice to have a zoom out box below the current figure which shows data within Europe only.
Number of countries in text (n = 62) not the same than in figure 1B. Should be consistent. There were some that have discarded cases (perhaps change sentence to: "In X countries suspected or confirmed cases were reported. X confirmed transmission, X continue to have suspected cases only, and X countries discarded cases that were suspected."
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