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TZA 2016-20 #452

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eclee25 opened this issue May 15, 2023 · 22 comments
Open

TZA 2016-20 #452

eclee25 opened this issue May 15, 2023 · 22 comments

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@eclee25
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eclee25 commented May 15, 2023

No description provided.

@QLLZ
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QLLZ commented Jun 6, 2023

Data pull:
HASH: 6772ea9da4f43ddc3da11c494a573af2ca3dd3c8
config

@QLLZ
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QLLZ commented Jun 7, 2023

Model run:
HASH: 6772ea9da4f43ddc3da11c494a573af2ca3dd3c8

@javierps
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One chained failed to warmup, the other three OK.

Suggestion: reject. Need to work on initialization.

@eclee25
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eclee25 commented Jun 15, 2023

One chain failed initialization and others ok.

Opinion: Reject and rerun after investigating initialization and with higher sfrac_thresh_border to remove some high rate cells in N border

@eclee25
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eclee25 commented Jun 16, 2023

Opinion: Reject and rerun on dev with drop_multiyear_adm0: yes. After sfrac branch merge, run with higher sfrac_thresh_border: 0.25

@QLLZ
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QLLZ commented Jun 22, 2023

Updated config

@QLLZ
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QLLZ commented Jun 22, 2023

Data pull:
HASH fe4f075699e84b71f1c0fe3de31eb9ebbb380d32

@QLLZ
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QLLZ commented Jun 22, 2023

64G is not enough for data pull.

plan: rerun with 100G

@QLLZ
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QLLZ commented Jun 22, 2023

rerunning with 100G (same HASH as fe4f075699e84b71f1c0fe3de31eb9ebbb380d32

@QLLZ
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QLLZ commented Jun 22, 2023

Model runnng:
HASH: fe4f075699e84b71f1c0fe3de31eb9ebbb380d32

@QLLZ
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QLLZ commented Jun 26, 2023

Country data report

@javierps
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Suspicious border pixel with very high rates/cases in northern border

@QLLZ
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QLLZ commented Jul 24, 2023

Config

Data pull & Model run:

HASH: 211913e

@QLLZ
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QLLZ commented Jul 25, 2023

country data report

@QLLZ
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QLLZ commented Jul 27, 2023

2019 modeled case are slightly overestimated. Convergency looks good.

@eclee25
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eclee25 commented Aug 4, 2023

I think there are sometimes 2 national annual estimates in Table 6 because the obs actually represent Zanzibar and I think we manually changed ZNZ to admin 0 in some places for plotting purposes -- (not sure how the cdr is pulling the admin level now). (Same issue occurs in TZA 2011-15 cdr). There are lots of national annual obs in Table 6 with varying tfracs and I think we could consider removing some of them so that the annual estimates are not artificially lowered.

Temp Approve - could consider rerunning without lower tfrac (but above 0.65) national full annual obs

@javierps
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Sep 2023 Production run: convergence OK. Rhats mostly OK, some have very large Rhats. These seem to be in zanzibar, to investigate further.

@eclee25
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eclee25 commented Sep 19, 2023

Action Required - investigate large Rhats and rerun cdr to see if there are imputed observations in 2019 and 2020

We don't think imputation gets triggered if at least one of Mainland or ZNZ has an admin 0. Could change it so that ZNZ is no treated as admin 0 as one possible solution

@eclee25
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eclee25 commented Sep 26, 2023

Second Action Required - In Table 6, it looks like the national observations for Mainland and Zanzibar have the same values in OC 20109 and OC 21025 (You can tell there are different estimates for Mainland and Zanzibar because they have different predicted values). We should audit these two observations -- it is suspicious that they have the same exact number of cases.

Investigation: In OCs 21019 and 21025 there is a phantom for AFR::Tanzania because there are subnational cases that are all reported in AFR::TZA::Mainland and presumably if you read through the AFRO reports the subnational smaller tfrac obs are getting reported on the Mainland only

Decision: We decided to keep both observations in the OCs

@eclee25
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eclee25 commented Sep 27, 2023

Decision: Test whether the no-mixture config enables better model fit and reduces Rhat issues.

@eclee25
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eclee25 commented Nov 9, 2023

After removing the admin 0 assignment for TZA Mainland and ZNZ, the model convergence and w estimate issues were resolved, even when using a mixture sd_w prior. There was one incorrect multi-year observation (censored) that was underestimated but that data has now been fixed in the database.

Rerun with updated observation

@eclee25
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eclee25 commented Nov 10, 2023

The multi-year observation is no longer present and the convergence and estimates look good. Approve

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