Reschedule estimates about covid-rt-estimates HOT 16 CLOSED

Just done so again and now it's running... I'm going crazy (or drowning under multiple docker containers with similar names)

from covid-rt-estimates.

from covid-rt-estimates.

sounds like a plan - I'll kick off a UK with a -f flag to confirm it runs

from covid-rt-estimates.

excellent!

from covid-rt-estimates.

It's still failing. It has pulled the latest version of EpiNow2 v 1.2 from github which includes the signature change. I wanted to touch on versioning in the call so we can do so later.

I don't know if we can specify commit # on the project dependencies. It might be we need to back out epiforecasts/EpiNow2#74 and put it in on a 1.3 tag, updating the description here to be == v 1.2.0

Once we put the changes in here to go with epiforecasts/EpiNow2#74 / v1.3.0 then the description can be updated

from covid-rt-estimates.

I think the problem probably came about because this package was dependent on the timeout features which were V1.2 but we didn't lock and release v1.2 at that point.

from covid-rt-estimates.

yes we can gear to a commit in the remotes section.

do you have an error message?

from covid-rt-estimates.

2020-09-30 12:22:23 INFO Runtime error in London : unused arguments (warmup = 500, cores = 5, chains = 5) - EpiNow2::epinow, regional_cases, target_folder, target_date, TRUE, ...
2020-09-30 12:22:23 INFO Runtime error in North East : unused arguments (warmup = 500, cores = 5, chains = 5) - EpiNow2::epinow, regional_cases, target_folder, target_date, TRUE, ...
2020-09-30 12:22:23 INFO Runtime error in North West : unused arguments (warmup = 500, cores = 5, chains = 5) - EpiNow2::epinow, regional_cases, target_folder, target_date, TRUE, ...
2020-09-30 12:22:23 INFO Runtime error in Northern Ireland : unused arguments (warmup = 500, cores = 5, chains = 5) - EpiNow2::epinow, regional_cases, target_folder, target_date, TRUE, ...
2020-09-30 12:22:23 INFO Runtime error in Scotland : unused arguments (warmup = 500, cores = 5, chains = 5) - EpiNow2::epinow, regional_cases, target_folder, target_date, TRUE, ...
2020-09-30 12:22:23 INFO Runtime error in South East : unused arguments (warmup = 500, cores = 5, chains = 5) - EpiNow2::epinow, regional_cases, target_folder, target_date, TRUE, ...
2020-09-30 12:22:23 INFO Runtime error in South West : unused arguments (warmup = 500, cores = 5, chains = 5) - EpiNow2::epinow, regional_cases, target_folder, target_date, TRUE, ...
2020-09-30 12:22:23 INFO Runtime error in Wales : unused arguments (warmup = 500, cores = 5, chains = 5) - EpiNow2::epinow, regional_cases, target_folder, target_date, TRUE, ...
2020-09-30 12:22:23 INFO Runtime error in West Midlands : unused arguments (warmup = 500, cores = 5, chains = 5) - EpiNow2::epinow, regional_cases, target_folder, target_date, TRUE, ...

from covid-rt-estimates.

have you updated your local version of this repo? Code should be up to date in

from covid-rt-estimates.

If we specify it to bb53862614f019421da973f09aeff6f80e7f4fd1 then I think we might be ok.

root@06c94b68dc7f:/home/covid# git status
On branch master
Your branch is up to date with 'origin/master'.

nothing to commit, working tree clean

root@06c94b68dc7f:/home/covid# git pull
Already up to date.

root@06c94b68dc7f:/home/covid# git rev-parse HEAD
aaa1f2ef6cef963cedf57c6b00ce894be14ea065

from covid-rt-estimates.

I don't understand your error if your local repo is up to date.

from covid-rt-estimates.

and the epinow lib is showing latest too

install_github("epiforecasts/EpiNow2")
Skipping install of 'EpiNow2' from a github remote, the SHA1 (6fca0c88) has not changed since last install.
Use force = TRUE to force installation

from covid-rt-estimates.

local repo is showing the latest code:

   out <- regional_epinow(reported_cases = cases,
                           generation_time = location$generation_time,
                           delays = list(location$incubation_period, location$reporting_delay),
                           non_zero_points = 14, horizon = 14, burn_in = 14, samples = 4000,
                           stan_args = list(warmup = 500, cores = no_cores, 
                                            chains = ifelse(no_cores <= 4, 4, no_cores)),
                           fixed_future_rt = TRUE,  target_folder = location$target_folder,
                           return_estimates = FALSE, summary = TRUE,
                           return_timings = TRUE, future = TRUE,
                           max_execution_time = max_execution_time)

from covid-rt-estimates.

and thats mapped to the docker container? Given we don't see this issue in other implementations or in EpiNow2 tests I am at a loss if the code is not out of date.

from covid-rt-estimates.

thats from a cat in the docker container. very strange indeed.

from covid-rt-estimates.

can you run an EpiNow2 example using an interactive session?

from covid-rt-estimates.