AR2R0 |
Title Calculate basic reproduction number from attack rate |
clean_labels |
Standardise labels |
empirical_incubation_dist |
Extract empirical incubation period distribution from linelist data |
fit_discrete |
Fit discretised distributions using ML |
fit_disc_gamma |
Fit discretised distributions using ML |
fit_gamma_incubation_dist |
Fit discrite gamma distribution to incubation periods |
gamma_log_likelihood |
Reparameterise Gamma distributions |
gamma_mucv2shapescale |
Reparameterise Gamma distributions |
gamma_shapescale2mucv |
Reparameterise Gamma distributions |
hash_names |
Anonymise data using scrypt |
lm2R0_sample |
Transform a growth rate into a reproduction number |
R02AR |
Title Calculate attack rate from basic reproduction number |
R02herd_immunity_threshold |
Title Calculate herd immunity threshold from basic reproduction number |
r2R0 |
Transform a growth rate into a reproduction number |
sim_linelist |
Simulate simple linelist data |