HopkinsIDD / cholera-mapping-pipeline

Formerly part of cholera-taxonomy. The map creation scripts, packages, and file structure
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KEN 2016-20 #412

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 (except sd_w), fits, and match to GAM input look good. Some Rhat issues at admin 1 & 2 levels.

Opinion: Approve

QLLZ commented 1 year ago

Config

Data pull(32G):

HASH: 211913e0eb7d570ed62c48bc1ae9ecd6671a6cbc

QLLZ commented 1 year ago

Model run:

HASH: 211913e0eb7d570ed62c48bc1ae9ecd6671a6cbc

QLLZ commented 1 year ago

Failed 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

rho and sd_w traceplots are not converged and they are having a mild effect on the w traceplots as well. The ID-45 model that was run on dev_dagar_fix seems to perform a bit better than this model and I think the only difference between the two is that the standard model run has drop_censored_adm0: yes and drop_censored_adm0_thresh: 2. However the national annual estimates seem to be quite between these two model runs.

Temp Approve - could consider changing this back to the ID-45 settings or changing to no-mixture sd_w prior to see if it helps settle the estimates into the lower range. Could also consider increasing the censoring threshold to reduce the number of lower tfrac full annual observations

eclee25 commented 1 year ago

ID-61 showed that the no-mixture sd_w prior improved convergence in this model. Use the no-mixture sd_w prior with all other standard settings (even though this model has subnational data)

QLLZ commented 1 year ago

Data pull, model run:

HASH: 05f598b95b5d42ac0049963f8a0b7e04d6f1dbd7

javierps commented 1 year ago

Autocor in rho, std_w and ws OK. All Rhats OK.

Suggestion: Accept.

eclee25 commented 1 year ago

Many conflicting annual obs - ok. Agree with J. Approve