covid-rt-estimates

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Add estimates for a complete time series in each country/subnational region

9

Due to computational and storage constraints, it is not feasible to run the complete time series every day with our current resources. For this reason, we have shifted our daily...

seabbs

Currently, to obtain sample estimates, `output` in `regional_epinow_opts` attribute of `AbstractDataset` (line 71 in `R/entities/abstract-dataset.R`) must be modified in order to change the behaviour of the `EpiNow2::regional_epinow` call in `update_regional.R`....

burtonrossj

Docker image does not work as described by README

1

Docker image fails when following README instructions. Replicated the error on Mac and an AWS Sagemaker instance. ```bash sudo docker run -d --user rstudio --name covidrtestimates covidrtestimates /bin/bash bin/update-estimates.sh ```...

cslatteryjbc

Currently this is crudely implemented using `azcopy` but unfortunately it has been difficult to control folder paths included. A more robust approach to this would be very helpful for downstream...

seabbs

If there's no new data to process the summary data errors ``` 2021-01-31 21:01:47 INFO Data has not been updated since last run. If wanting to run again then remove...

joeHickson

Missing data - Saudi Arabia

2

Saudi Arabia data hasn't updated since Jan-04-2021, even though time stamp indicates current data.

josebsalazar

Evaluate switching to OSF for archiving results.

1

As the data verse solution appears to be unreliable and there is no evidence the issues will be able to be fixed it might be sensible to move to another...

seabbs

Much of the current logging is informative but not truly helpful and makes understanding errors difficult (as logging doesn't stop on error). Having two layers of logging (summary + trace)...

seabbs

Get historical reproduction numbers for Lithuania

4

Hello developers, thank you for a great analysis! I would like to get an effective reproduction numbers for Lithuania starting from 2020-02-17. Is it possible to get this kind of...

ramashka328

In R it is usual to split function loading from calling the functions (i.e `run-region-updates.R` which is currently more C or Python like). It would make sense to make all...

seabbs