Code to reproduce results from Household Transmission of SARS-COV-2: Insights from a Population-based Serological Survey.
In the Stan/ directory are stan code for running a series of different models we compared in the analyses. Code that runs the stan models are in HHtrans_public.Rmd. Note that generated data are saved using git-lfs so if you want them locally you need to use git lfs pull.
The models are as follows:
| file name | model number | description |
|---|---|---|
| serosurvey-analysis-bq.stan | 0 | null model |
| serosurvey-analysis-bq.stan | 1 | age (infectee) |
| serosurvey-analysis-bq.stan | 2 | age (infectee), sex (infectee) |
| serosurvey-analysis-bq.stan | 3 | age (infectee), sex (infectee), age and sex interaction term (infectee) |
| serosurvey-analysis-bq-sym.stan | 4 | age (infectee), sex (infectee), symptom (infector) |
| serosurvey-analysis-bq-sym-contact.stan | 5 | age (infectee), sex (infectee), reduced extra-hh contact (infectee), symptom (infector) |
| serosurvey-analysis-bq-sym-contact.stan | 6 | age (infectee), sex (infectee), reduced extra-hh contact (infectee), extra-hh contact freq (infectee), symptom (infector) |
| serosurvey-analysis-bq-sym-infector-2049ref.stan | 7 | age (infectee), sex (infectee), symptom (infector), age (infector) |
| serosurvey-analysis-bq-sym-infector-2049ref.stan | 8 | sex (infectee), symptom (infector), age (infector) |
| serosurvey-analysis-bq-sym-infector.stan | 9 | age (infectee), sex (infectee), age (infector) |
We have included dummy data for in order to help users test the code. Data will be made available upon request by contacting azman@jhu.edu.
We have tried our best to make this code understandable and usable but please do get in touch if you spot an issue or have a question.
| Variable | Description | Type |
|---|---|---|
| Household codbar | unique Household ID | |
| codbar_entry | unique individual ID | |
| sex | sex (i.e., f or m) | binary |
| week | week of study recruitment | numeric |
| datededebut | recruitment date | date |
| IgG_Ratio | IgG reading | numeric |
| nr_personnes_rencon | How many people do you meet on average per week, outside of the people you live with on a daily basis? (i.e., 0, 1-2, 3-5, 6-10, over 10 times a week) | categorical |
| reduit_personnes_rencon | Since the epidemic, have you reduced the number of people you meet per day? (i.e., 1=yes or 0=no) | binary |
| IgG_pos | IgG_Ratio >= 1.1 or not (i.e., TRUE or FALSE) | binary |
| age_cat | age category (i.e., 5-9, 10-19, 20-49, 50-64, 65+) | categorical |
| symptom_any | whether an IgG+ individual reported fever, cough, panting, or loss of taste or smell (i.e., 1=yes, 0=no) | binary |
| debut_symptom_within2wk | whether one develops symptom within the 2 weeks prior to blood draw (i.e., 1=yes, 0=no) | binary |
| reduit_famavg | imputed reuit_personnes_rencon based on family average (i.e., 1=yes, 0=no) | binary |
| nr_personnes_rencon_famavg | imputed nr_personnes_rencon based on family average (i.e., 0, 1-2, 3-5, 6-10, over 10 times a week) | categorical |