Data-Science-Brigade / modelo-epidemiologico-sc

Bayesian epidemiological model, with a focus on the state of Santa Catarina and its micro and macroregions. https://arxiv.org/abs/2104.01133

MIT License

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🐛 Allow single region runs + Some Bugfixes #27

Closed jonjoncardoso closed 3 years ago

jonjoncardoso commented 3 years ago

Changes

Allow a single region to be fitted
In practice, EpidemicStart was always set 1 because of the way the data was being filtered and preprocessed. So, I adjusted the preprocessing so that the epidemic in each location starts 30 days before the 10-death mark, therefore removing the necessity of the EpidemicStart from the STAN model
Generate the Serial Interval distribution on the code, instead of using the legacy polynomial inherited by the original Flaxman et al model

How to validate this PR

Clone this branch
Rebuild the library. Tip: If you are starting the environment on RStudio, run the command:
```
setwd("epiCata")
devtools::build()
devtools::install(upgrade="never")
setwd("../")
```
Run the model for just a single region, say SC_MAC_GRANDE_FLORIANOPOLIS

NataliaDelCoco commented 3 years ago

Realizei testes com run_model, run_regions, run_health_regions e run_state_and_one_region.R em modos DEBUG e DEVELOP. Em todos os casos, obtive o mesmo erro:

Error in exit("Allowed locations not implemented yet") : could not find function "exit"
Calls: run_model_with_opt
Execution halted

jonjoncardoso commented 3 years ago

Realizei testes com run_model, run_regions, run_health_regions e run_state_and_one_region.R em modos DEBUG e DEVELOP. Em todos os casos, obtive o mesmo erro:
Error in exit("Allowed locations not implemented yet") : could not find function "exit"
Calls: run_model_with_opt
Execution halted

Hmmmm, talvez eu tenha esquecido de mudar algo nos scripts. Checo amanhã primeira coisa pela manhã

jonjoncardoso commented 3 years ago

@NataliaDelCoco tenta rodar de novo, dessa vez com esse script novo dedicado a single-regionsm (commit https://github.com/Data-Science-Brigade/modelo-epidemiologico-sc/commit/3c859924fc5930edda788573b027d1a7359bb941) ?

Rscript run_single_region.R -m FULL -r "2021-06-07"

NataliaDelCoco commented 3 years ago

Agora funcionou direitinho!