Errors with regional_epinow

[CarmenTamayo]

When running regional_epinow in the transmissibility pipeline:

res_epinow2_group <- regional_epinow(dat_i_day, generation_time = generation_time, stan = stan_opts(samples = 1e3, chains = 2), rt = rt_opts(gp_on = "R0"), horizon = 0, CrIs = c(0.5, 0.95), return_output = TRUE, verbose = FALSE, logs = NULL )

The code runs but I'm getting a series of errors which result in the output not having any data for the different regions, here is an example for London, but the same error is generated for the remaining regions of the country:

INFO [2024-01-09 13:03:58] Initialising estimates for: London
ERROR [2024-01-09 13:03:58] London: 'names' attribute [1] must be the same length as the vector [0] - <-, names(ids), paste(names(type_n), "id", sep = "")
INFO [2024-01-09 13:03:59] Completed regional estimates
INFO [2024-01-09 13:03:59] Regions with estimates: 0
INFO [2024-01-09 13:03:59] Runtime error in London : London: 'names' attribute [1] must be the same length as the vector [0] - <-, names(ids), paste(names(type_n), "id", sep = "")_
INFO [2024-01-09 13:03:59] Producing summary
INFO [2024-01-09 13:03:59] No summary directory specified so returning summary output
INFO [2024-01-09 13:03:59] Errors caught whilst generating summary statistics:
INFO [2024-01-09 13:03:59] Error in .checkTypos(e, names_x): Object 'variable' not found amongst

@jamesmbaazam do you know what the problem could be? I'm sure it's easy to fix but I've been looking at the R file for epinow and I'm not sure at what point the error is happening

Thanks!

[jamesmbaazam]

Thanks for tagging me. I'll take a look tomorrow.

[jamesmbaazam]

Hi @CarmenTamayo, I think you're getting the error because you are not wrapping the generation_time object passed to the generation_time argument in a call to generation_time_opts(). So, you should have something like

regional_epinow(
	dat_i_day, 
---  generation_time = generation_time, 
+++  generation_time =  generation_time_opts(generation_time), 
	stan = stan_opts(samples = 1e3, chains = 2),
	rt = rt_opts(gp_on = "R0"),
	horizon = 0, CrIs = c(0.5, 0.95),
	return_output = TRUE,
	verbose = FALSE,
	logs = NULL
) 

[CarmenTamayo]

Sorry @jamesmbaazam for the delay- I tried and the error persists... what else could be causing this error?
thank you

[jamesmbaazam]

Hi @CarmenTamayo, sorry to hear that. I'll dig into it now. Which branch are you experiencing this issue working on?

[CarmenTamayo]

Fixed in #144