HopkinsIDD / cholera-mapping-pipeline

Formerly part of cholera-taxonomy. The map creation scripts, packages, and file structure
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LBR 2011-15 #413

Open eclee25 opened 1 year ago

QLLZ commented 1 year ago

Data pull: HASH: 6772ea9da4f43ddc3da11c494a573af2ca3dd3c8 config

QLLZ commented 1 year ago

Model run: HASH: 6772ea9da4f43ddc3da11c494a573af2ca3dd3c8

QLLZ commented 1 year ago

Country data report

eclee25 commented 1 year ago

Poor sd_w convergence and questionable w convergence with many Rhats exceeding threshold. Not much subnational data seems to be available. Maps and fits seem okay for what is there, and I think the convergence issues are related to lack of subnational data.

Opinion: Needs further investigation of data comparison report before potential Approve

javierps commented 1 year ago

From figure 3 there seems that there is not subnational data here, so not surprising this is happening.

If not more data available then don't think things can be much better than this.

eclee25 commented 1 year ago

No subnational obs

Opinion: Temp Approve and rerun with spatial_effect: no

QLLZ commented 1 year ago

Updated config Data pull and model run: HASH: f56d5a942b106ad7750b9be31c0456cefa5b6dc7

javierps commented 1 year ago

OK.

No w run.

QLLZ commented 1 year ago

Config

Data pull:

HASH: 211913e0eb7d570ed62c48bc1ae9ecd6671a6cbc

Data pull failed log file

QLLZ commented 1 year ago

Data pull and model run (dev_taxdat_funs_fix branch):

HASH: 31f14227cd28a9824db72b7a6c45b0d65652872e

QLLZ commented 1 year ago

country data report

QLLZ commented 1 year ago

Population are slightly underestimated. Other results look good.

Suggestion: accept if population is acceptable.

eclee25 commented 1 year ago

No subnat data, no-W model. Some Rhat issues in genquant outputs but this makes sense. All other diags look good. Approve.

javierps commented 11 months ago

Sep 2023 Production run: convergence issues, Rhats OK.

Suggestion: investigate further.

eclee25 commented 11 months ago

After removing the unused parameters from sampling, all diags look good. Approve