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mrc-ide / squire

SEIR transmission model of COVID-19. Documentation at:
https://mrc-ide.github.io/squire/
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Calibrate crashing #142

Open flitaiff opened 3 years ago

flitaiff commented 3 years ago

Hi there,

When trying to run ´calibrate´ with data from Brazil, it crashes with:

Running Grid Search... Error in dnbinom(data, k, mu = mu, log = TRUE) : Non-numeric argument to mathematical function`

Tried different combinations of parameters with no success.

out <- calibrate(
      data = Brasil[1:30,],
      R0_min = 1,
      R0_max = 5,
      R0_step = 0.1,
      first_start_date = "2020-02-22",
      last_start_date = "2020-02-23",
      day_step = 1,
      replicates = 100,
      n_particles = 10000,
      country = "Brazil"
    )

head(Brasil) X date deaths cases 1 1 2020-02-25 0 0 2 2 2020-02-26 0 1 3 3 2020-02-27 0 1 4 4 2020-02-28 0 1 5 5 2020-02-29 0 2 6 6 2020-03-01 0 2

The object "Brasil" is attached.

Would you please tell me what is going on?

Brasil.zip