ZAF 2011-15 - Githubissues

HopkinsIDD / cholera-mapping-pipeline

Formerly part of cholera-taxonomy. The map creation scripts, packages, and file structure

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ZAF 2011-15 #455

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 failed: log file

QLLZ commented 1 year ago

Country data report

In this report, there are no plots of

Variance of cases in gam input per grid cell
Variance of rates per 100000 in gam input per grid cell

because there are few data, so each t, sx, and sy in gam input only has one y value. variance is unable to be estimated.

for gam input cases plot, it's not in log scale because all the observations are 0.

javierps commented 1 year ago

Very small number of cases. This causes issues in convergence.

Suggestion: reject and create a new model with no w.

eclee25 commented 1 year ago

Poor convergence in rho and sd_w due to small case counts.

Opinion: Temp Approve and rerun with spatial_effect: no

QLLZ commented 1 year ago

Updated config Data pull: HASH: f56d5a942b106ad7750b9be31c0456cefa5b6dc7

QLLZ commented 1 year ago

model run

HASH f56d5a942b106ad7750b9be31c0456cefa5b6dc7

eclee25 commented 1 year ago

Some slight apparent divergences in the middle of sampling but otherwise ok.

QLLZ commented 1 year ago

Config

Data pull & Model run:

HASH: 211913e0eb7d570ed62c48bc1ae9ecd6671a6cbc

QLLZ commented 1 year ago

Failed data pull 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

Results look good.

Suggestion: accept.

eclee25 commented 1 year ago

Almost all 0s, no-W model. Diags look good. Approve

QLLZ commented 1 year ago

Data pull failed in prepare_stan_input step: https://github.com/HopkinsIDD/cholera-mapping-reports/blob/Sep_2023_nocovar_production_runs/sbatch_logs/country_data_reports/errors/Sep2023_no_w_109364_0.log

eclee25 commented 1 year ago

Merged in branches related to minor fixes in the UN population adjustment and admin 0 clipping precision which resolve and speed up the data pull and grid-shape computations.

Rerun no-W model on dev to finalize.

eclee25 commented 1 year ago

Due to errors in the output shapefile ordering, we reran this model as a production run on dev_fix_unpop_new which seems to have resolved the issue.

Approve