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idem-lab / conmat

Create Contact Matrices from Population Data
https://idem-lab.github.io/conmat/dev/
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Add small example datasets for use in examples #164

Open njtierney opened 3 months ago

njtierney commented 3 months ago

E.g.,

Instead of doing

polymod_setting_data <- get_polymod_setting_data()

polymod_setting_data_small <- polymod_setting_data %>%
  lapply(FUN = function(x) x %>% filter(age_from <= 20, age_to <= 20)) |> 
  new_setting_data()

Just have a couple of smaller datasets

See how small I can make it but still be useful?

This way the examples can all run as well

njtierney commented 3 months ago

Even better, write a function that does this:

library(conmat)
new_polymod_setting_data <- function(
    countries = c(
      "Belgium", 
      "Finland", 
      "Germany", 
      "Italy", 
      "Luxembourg", 
      "Netherlands",
      "Poland", 
      "United Kingdom"
      ),
    age_limit = 20
    ){
  polymod_setting_data <- get_polymod_setting_data(countries = countries)

  polymod_setting_data_clipped <- lapply(
      polymod_setting_data,
      \(x) dplyr::filter(x, age_from <= age_limit, age_to <= age_limit)) |> 
    new_setting_data() 

  polymod_setting_data_clipped
}

polymod_30 <- new_polymod_setting_data(age_limit = 30)
summary(polymod_30$home)
#>    setting             age_from      age_to      contacts       participants  
#>  Length:961         Min.   : 0   Min.   : 0   Min.   : 0.000   Min.   : 72.0  
#>  Class :character   1st Qu.: 7   1st Qu.: 7   1st Qu.: 2.000   1st Qu.: 86.0  
#>  Mode  :character   Median :15   Median :15   Median : 5.000   Median :122.0  
#>                     Mean   :15   Mean   :15   Mean   : 6.984   Mean   :116.3  
#>                     3rd Qu.:23   3rd Qu.:23   3rd Qu.:10.000   3rd Qu.:142.0  
#>                     Max.   :30   Max.   :30   Max.   :54.000   Max.   :159.0

Created on 2024-07-02 with reprex v2.1.0

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