seed mixed up with seeding_cases in run.R

[skyehersh]

Hello, think I found a minor variable misuse issue. Here are lines 362 and 363 in run.R when pars is defined:

S_0 = population - seed,
E1_0 = seed,

It seems that these call for seeding_cases instead of seed, as line 298 says:

parameters$seeding_cases <- pars$E1_0.

Found this when passing a seed greater than my population size to calibrate(), which threw the following error:

Error in init_check_explicit(init, population, seeding_cases) : 
  population size is not large enough in each age bracket

[richfitz]

@OJWatson - can you try running things with:

options(warnPartialMatchAttr=TRUE,
        warnPartialMatchDollar=TRUE,
        warnPartialMatchArgs=TRUE)

and it will likely flush out the root cause of this

[OJWatson]

Yup will try and get round to this today :)