HopkinsIDD / cholera-mapping-pipeline

Formerly part of cholera-taxonomy. The map creation scripts, packages, and file structure
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MWI 2016-20 #426

Open eclee25 opened 1 year ago

QLLZ commented 1 year ago

Data pull: HASH: 10db6c83d6486774d3148785df24b3145f375bb2 config

QLLZ commented 1 year ago

reran the initial values data after the new updates on initial values HASH: 6772ea9da4f43ddc3da11c494a573af2ca3dd3c8

QLLZ commented 1 year ago

Model run: HASH: 6772ea9da4f43ddc3da11c494a573af2ca3dd3c8

QLLZ commented 1 year ago

Prestan report

Country data report

eclee25 commented 1 year ago

Convergence, maps, Rhats, fits, match to GAM input look good. Some small sfrac cells seem to have large rates on lake border

Opinion: Approve

QLLZ commented 1 year ago

Config

Data pull:

HASH: 211913e0eb7d570ed62c48bc1ae9ecd6671a6cbc

QLLZ commented 1 year ago

Failed stan model run log file

QLLZ commented 1 year ago

Rerun on dev_u_combs_fix

HASH: e56580fa5ddab00293e31ff90139351f80ae3f6c

QLLZ commented 1 year ago

country data report

eclee25 commented 1 year ago

Diags look good but annual estimates for 2016 and 2018 seem a bit high -- This is similar to what we saw in the last round of production runs and the magnitude of the overestimation seems the same as well.

Temp Approve - someone else should review the report

javierps commented 1 year ago

Sep 2023 Production run: convergence OK, over-estimation of cases in 2018.

Suggestion: 2nd opinion.

eclee25 commented 1 year ago

Continued overestimation in 2016 & 2018, similar to previous runs. sd_w and rho convergence issues could potentially be improved with a no-mixture model, but I don't think this will improve the over-estimation issue.

For Discussion - Temp Approve

Action Required: Investigate subnational sum of cases vs national case counts -- Is the subnational data suggesting that the 2016 and 2018 observations should be larger?

QLLZ commented 1 year ago

The subnational data suggests that there are around 793 cases in 2018 and around 1920 cases in 2016. These are similar to the national data (around 800 in 2018 and 1792 in 2016).

eclee25 commented 1 year ago

Discussed as a group and decided to Approve