Usar {incidence2} y {dplyr} para adaptar datos de casos con {EpiNow2} y {cfr}

casos_a_incidencia.R

``` r
if(!require("pak")) install.packages("pak")

new_packages <- c(
  "incidence2",
  "outbreaks",
  "tidyverse"
)

pak::pkg_install(new_packages)

library(incidence2)
library(outbreaks)
library(tidyverse)

# base de datos de casos (tambien llamada linelist)
mers_korea_2015$linelist %>% as_tibble()
#> # A tibble: 162 × 15
#>    id      age age_class sex   place_infect   reporting_ctry loc_hosp dt_onset  
#>    <chr> <int> <chr>     <fct> <fct>          <fct>          <fct>    <date>    
#>  1 SK_1     68 60-69     M     Middle East    South Korea    Pyeongt… 2015-05-11
#>  2 SK_2     63 60-69     F     Outside Middl… South Korea    Pyeongt… 2015-05-18
#>  3 SK_3     76 70-79     M     Outside Middl… South Korea    Pyeongt… 2015-05-20
#>  4 SK_4     46 40-49     F     Outside Middl… South Korea    Pyeongt… 2015-05-25
#>  5 SK_5     50 50-59     M     Outside Middl… South Korea    365 Yeo… 2015-05-25
#>  6 SK_6     71 70-79     M     Outside Middl… South Korea    Pyeongt… 2015-05-24
#>  7 SK_7     28 20-29     F     Outside Middl… South Korea    Pyeongt… 2015-05-21
#>  8 SK_8     46 40-49     F     Outside Middl… South Korea    Seoul C… 2015-05-26
#>  9 SK_9     56 50-59     M     Outside Middl… South Korea    Pyeongt… NA        
#> 10 SK_10    44 40-49     M     Outside Middl… China          Pyeongt… 2015-05-21
#> # ℹ 152 more rows
#> # ℹ 7 more variables: dt_report <date>, week_report <fct>, dt_start_exp <date>,
#> #   dt_end_exp <date>, dt_diag <date>, outcome <fct>, dt_death <date>


mers_incidence <- mers_korea_2015$linelist %>%
  # transformar de linelist a incidencia usando {incidence2}
  incidence2::incidence(
    date_index = "dt_onset",
    complete_dates = TRUE
  ) %>%
  # seleccionar y renonmbrar columnas usando {dplyr} para {EpiNow2}
  dplyr::select(date = date_index, confirm = count)

mers_incidence
#>          date confirm
#> 1  2015-05-11       1
#> 2  2015-05-12       0
#> 3  2015-05-13       0
#> 4  2015-05-14       0
#> 5  2015-05-15       0
#> 6  2015-05-16       0
#> 7  2015-05-17       1
#> 8  2015-05-18       1
#> 9  2015-05-19       0
#> 10 2015-05-20       5
#> 11 2015-05-21       6
#> 12 2015-05-22       2
#> 13 2015-05-23       4
#> 14 2015-05-24       2
#> 15 2015-05-25       3
#> 16 2015-05-26       1
#> 17 2015-05-27       2
#> 18 2015-05-28       1
#> 19 2015-05-29       3
#> 20 2015-05-30       5
#> 21 2015-05-31      10
#> 22 2015-06-01      16
#> 23 2015-06-02      11
#> 24 2015-06-03       7
#> 25 2015-06-04      12
#> 26 2015-06-05       9
#> 27 2015-06-06       7
#> 28 2015-06-07       7
#> 29 2015-06-08       6
#> 30 2015-06-09       1
#> 31 2015-06-10       6
#> 32 2015-06-11       3
#> 33 2015-06-12       0
#> 34 2015-06-13       2
#> 35 2015-06-14       0
#> 36 2015-06-15       1
```

<sup>Created on 2024-07-11 with [reprex v2.1.0](https://reprex.tidyverse.org)</sup>