Issues with data files

[sbfnk]

This is a space to gather issues with the data files to help the maintainers of the Social contact data community on Zenodo keep track. If you spot any issue please add a comment below.

• CoMix social contact data (Belgium ) (https://doi.org/10.5281/zenodo.4035001) contains duplicate files names only differing by capitalisation. Suggested fix: remove obsolete files
• CoMix social contact data (Belgium ) (https://doi.org/10.5281/zenodo.4035001) contains a file comix_be_hh_extra.csv with duplicate rows, preventing it from being merged. Suggested fix: deduplicate the file (e.g. by running unique(df))
• CoMix 2.0 social contact data (https://doi.org/10.5281/zenodo.7014555) does not contain information on the country of participants (get_survey() fails on CoMiX 2.0 #53). Suggested fix: add a country column
• Social contact data for Zimbabwe (https://doi.org/10.5281/zenodo.1127693) has a household file 2017_melegaro_zimbabwe_hh_common.csv that seems to contain the information twice and therefore cannot be associated with the survey uniquely. Suggested fix: deduplicate the file (e.g. by running unique(df) which reduces the number of rows by half)
• CoMix social contact data (UK) (https://doi.org/10.5281/zenodo.4905745) has a stray column X in the files comix_uk_hh_common.csv and comix_uk_participant_common.csv which is not matching and prevents them from being merged. Suggested fix: remove the X column from these two files.

[LloydChapman]

You've already caught the issues with the UK CoMix social contact data (https://zenodo.org/records/13684044) but I thought I'd add the code here (also in #249) for the fix in case it's useful:

# Load packages
library(socialmixr)
library(data.table)
library(lubridate)
library(jsonlite)
library(countrycode)

# Download CoMiX data
comix_survey <- download_survey("https://zenodo.org/records/13684044")

remove_X_col <- function(file){
    x <- fread(file)
    if ("X" %in% names(x)){
        x[,"X":=NULL]
    }
    fwrite(x, file = file)
}

change_country_name <- function(file, old_country, new_country){
    x <- fread(file)
    if ("country" %in% names(x)){
        x[country == old_country, country := new_country]
    }
    fwrite(x, file = file)
}

remove_X_col(comix_survey[3])
remove_X_col(comix_survey[5])
change_country_name(comix_survey[5], "uk", "GB")

# Load CoMix survey data
comix <- load_survey(comix_survey, participant.age.column = "part_age")

Note that currently this doesn't get the participant's ages due to issue #249.