HopkinsIDD / cholera-mapping-pipeline

Formerly part of cholera-taxonomy. The map creation scripts, packages, and file structure
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BDI 2011-15 #375

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

sd_w, od_param, and w did not converge and Rhats look bad. While the national annual observation fits seem ok, output case maps seem much too large. The warmup and sampling times are much too short (on the order of 20 seconds each).

Opinion: Investigate what went wrong with the warmup and sampling or simply try rerunning.

eclee25 commented 1 year ago

Opinion: @javierps notes that only 2011 subnational data was available and it was censored. This caused errors with convergence. New data was found for 2014-2015 at the district level. Rerun is on hold while we enter this.

eclee25 commented 1 year ago

OC 21375 added new 2014-15 subnational data. Make a new config and rerun with spatial_effect: yes and drop_censored_adm0: yes and drop_censored_adm0_thresh: 2

eclee25 commented 1 year ago

Original round will be tested on dev_dagar_fix branch as part of ptc ID 45

eclee25 commented 1 year ago

ptc ID 45 on dev_dagar_fix looks good now that more subnational data exists. Opinion: Approve

QLLZ commented 1 year ago

Config

Data pull & Model run:

HASH: 211913e0eb7d570ed62c48bc1ae9ecd6671a6cbc

QLLZ commented 1 year ago

country data report

QLLZ commented 1 year ago

Modeled cases look good. Convergency looks good. Population comparison looks good.

eclee25 commented 1 year ago

All diagnostics look good. Opinion: Approve

QLLZ commented 1 year ago

Data pull, model run:

HASH: 05f598b95b5d42ac0049963f8a0b7e04d6f1dbd7

javierps commented 1 year ago

Sep 2023 Production run: all OK.

Suggestion: accept.

eclee25 commented 1 year ago

Approve