Possible interface for simple fitting

[TimTaylor]

library(incidence2)
library(incidence2plus)
library(tidyr)

data(ebola_sim_clean, package = "outbreaks")
dat <- ebola_sim_clean$linelist

inci <- incidence(
  dat,
  date_index = date_of_onset,
  interval = "week",
  last_date = "2014-10-05",
  groups = gender
)
#> 3522 observations outside of [2014-04-07, 2014-10-05] were removed.

inci %>% 
  fit(model = "poisson")
#> # A tibble: 2 x 6
#>   gender model  fitted                 r `r-lower` `r-upper`
#>   <fct>  <list> <list>             <dbl>     <dbl>     <dbl>
#> 1 f      <glm>  <tibble [26 × 6]> 0.0249    0.0233    0.0265
#> 2 m      <glm>  <tibble [26 × 6]> 0.0250    0.0234    0.0267

inci %>% 
  fit(model = "poisson") %>% 
  add_doubling()
#> # A tibble: 2 x 9
#>   gender model fitted      r `r-lower` `r-upper` doubling `doubling-lower`
#>   <fct>  <lis> <list>  <dbl>     <dbl>     <dbl>    <dbl>            <dbl>
#> 1 f      <glm> <tibb… 0.0249    0.0233    0.0265     27.9             29.8
#> 2 m      <glm> <tibb… 0.0250    0.0234    0.0267     27.7             29.7
#> # … with 1 more variable: `doubling-upper` <dbl>

inci %>% 
  fit(model = "poisson") %>% 
  plot(color = "white", angle = 45, n_breaks = 4)

^{Created on 2020-09-03 by the reprex package (v0.3.0)}

[thibautjombart]

Very cool!