Open mcewenkhundi opened 2 years ago
I tried your above code but the resulting graph shows a little bit of variation from the one in the book since it is missing 10 days (2014-04-07: 2014-4-16). As the estimates variable starts from 2014-04-07 in the book but following the above code, the estimates variable starts from 2014-04-17. Code does run after the adding (filter) command but it results in 10 days missing which is reflected in the graph. If anyone can help
Dear Authors,
In chapter 24, the epinow function gets an error due to missing values in the date_onset variable. I have solved this by filtering out the missing values by adding the commented line in the code below. The original data is from the linelist_cleaned.rds
Is this the correct approach or should I use the dplyr::complete function that has been used in the section https://epirhandbook.com/en/epidemic-modeling.html#epiestim to solve a similar problem?
I have pasted the error message at the bottom for your reference.
get incidence from onset dates
cases <- linelist %>%
filter(!is.na(date_onset)) %>%
group_by(date = date_onset) %>% summarise(confirm = n())
run epinow to calculate Rt
epinow_res <- epinow( reported_cases = cases, generation_time = generation_time, delays = delay_opts(incubation_period), return_output = TRUE, verbose = TRUE, horizon = 21, stan = stan_opts(samples = 750, chains = 4) )
Logging threshold set at INFO for the EpiNow2 logger Writing EpiNow2 logs to the console and: C:\Users\mkhundi\AppData\Local\Temp\Rtmps1xhoN/regional-epinow/2015-04-30.log Logging threshold set at INFO for the EpiNow2.epinow logger Writing EpiNow2.epinow logs to the console and: C:\Users\mkhundi\AppData\Local\Temp\Rtmps1xhoN/epinow/2015-04-30.log Error in seq.int(0, to0 - from, by) : 'to' must be a finite number