epiverse-trace / tutorials-middle

https://epiverse-trace.github.io/tutorials-middle/
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fix lognormal mispecification of mean and sd to meanlog and sdlog #94

Open avallecam opened 1 month ago

avallecam commented 1 month ago

in quantify transmissibility checkpoint https://epiverse-trace.github.io/tutorials-middle/quantify-transmissibility.html#checklist2

in inputs for first epinow run https://epiverse-trace.github.io/tutorials-middle/create-forecast.html#create-a-short-term-forecast

# Log-tranformed mean
log_mean <- EpiNow2::convert_to_logmean(mean = 2, sd = 1)

# Log-transformed std
log_sd <- EpiNow2::convert_to_logsd(mean = 2, sd = 1)

# Reporting dalay
reporting_delay_fixed <- EpiNow2::LogNormal(
  mean = log_mean,
  sd = log_sd,
  max = 10
)

# Generation time
generation_time_fixed <- EpiNow2::LogNormal(
  mean = 3.6,
  sd = 3.1,
  max = 20
)