filter countries in Africa with social contact survey data

filter_continent_contacts.R

library(socialmixr)
library(countrycode)
library(tidyverse)

# Get all countries names and... regex!!
all_countries <- countrycode::codelist

# Filter countries in the Africa continent
africa_countries <- all_countries %>% 
  select(continent, country.name.en,country.name.en.regex) %>% 
  filter(continent == "Africa")

africa_countries
#> # A tibble: 59 × 3
#>    continent country.name.en          country.name.en.regex         
#>    <chr>     <chr>                    <chr>                         
#>  1 Africa    Algeria                  "algeria"                     
#>  2 Africa    Angola                   "angola"                      
#>  3 Africa    Benin                    "benin|dahome"                
#>  4 Africa    Botswana                 "botswana|bechuana"           
#>  5 Africa    Burkina Faso             "burkina|\\bfaso|upper.?volta"
#>  6 Africa    Burundi                  "burundi"                     
#>  7 Africa    Cameroon                 "cameroon"                    
#>  8 Africa    Cape Verde               "verde"                       
#>  9 Africa    Central African Republic "\\bcentral.african.rep"      
#> 10 Africa    Chad                     "\\bchad"                     
#> # ℹ 49 more rows

# Create a single string reprex
africa_reprex <- africa_countries %>% 
  # slice_tail(n = 2) %>% 
  pull(country.name.en.regex) %>% 
  paste(collapse = "|")

# Filter countries in Africa with social contact survey data
socialmixr::list_surveys() %>% 
  as_tibble() %>% 
  mutate(location = str_to_lower(title)) %>% 
  filter(str_detect(
    location,
    africa_reprex, 
    negate = FALSE # change to TRUE to double check excluding by accident
  )) %>% 
  select(title, url)
#> # A tibble: 4 × 2
#>   title                                                             url         
#>   <chr>                                                             <chr>       
#> 1 Social contact data for Zimbabwe                                  https://doi…
#> 2 Social contact data for Zambia and South Africa (CODA dataset)    https://doi…
#> 3 Social contact data for IDPs in Somaliland (2019)                 https://doi…
#> 4 Social contact data for the BHDSS and FWHDSS in the Gambia (2022) https://doi…

# Get one country survey using the URL
gambia_survey <- socialmixr::get_survey(
  survey = "https://doi.org/10.5281/zenodo.13101862"
)
#> Using Social contact data for the BHDSS and FWHDSS in the Gambia (2022). To cite this in a publication, use the 'get_citation()' function

# Load contact matrix from survey
socialmixr::contact_matrix(
  survey = gambia_survey,
  countries = "Gambia",
  age.limits = c(0,20,40),
  symmetric = TRUE
)
#> Removing participants that have contacts without age information. To change this behaviour, set the 'missing.contact.age' option
#> $matrix
#>       contact.age.group
#>          [0,20)  [20,40)      40+
#>   [1,] 9.523684 3.188249 1.598430
#>   [2,] 6.356374 4.630573 2.195776
#>   [3,] 5.940886 4.093441 3.116197
#> 
#> $demography
#>    age.group population proportion  year
#>       <char>      <num>      <num> <int>
#> 1:    [0,20)    1116876  0.5647679  2015
#> 2:   [20,40)     560206  0.2832780  2015
#> 3:       40+     300502  0.1519541  2015
#> 
#> $participants
#>    age.group participants proportion
#>       <char>        <int>      <num>
#> 1:    [0,20)         1140 0.72106262
#> 2:   [20,40)          157 0.09930424
#> 3:       40+          284 0.17963314

<sup>Created on 2024-09-19 with [reprex v2.1.1](https://reprex.tidyverse.org)</sup>