**README**
Here, you will find all data necessary to recreate the figures and tables of the main manuscript and supplement for the 2-year neurological and psychiatric risk trajectories of SARS-CoV-2 infection.
Each RDS file contains an R object that contains the results for the comparison of neurological and psychiatric sequelae between cohorts.
Four of the RDS files contain results for the main comparisons between COVID-19 and a matched cohort of patients infected with another respiratory infection:
**OSF_2y_trajectories_all.rds** contains the results for the whole cohorts (n=1,284,437 patients in each cohort)
**OSF_2y_trajectories_children.rds** contains the results for the cohorts of children (n=185,748 patients in each cohort)
**OSF_2y_trajectories_adults.rds** contains the results for the cohorts of adults (n=856,588 patients in each cohort)
**OSF_2y_trajectories_older_adults.rds** contains the results for the cohorts of older adults (n=242,101 patients in each cohort)
Once loaded, the variable contains a list with the following fields:
`outcomeNames`: a vector of outcome names. Note that when both first and first+recurrent outcome are investigated, the results in the main manuscript focus on _first_ diagnosis only. For instance, the results for cognitive deficit in the manuscript corresponds to "Cognitive deficit (first)" which is outcome 38 (`outcomeNames[38]` is `'Cognitive deficit (first)'`).
`outcomes`: a list of the same length as `outcomeNames` which contains the results for each outcome (i.e. it is a list of lists). For instance, `outcomes[[38]]` contains the results for cognitive deficit. Each outcome contains the following fields:
- `HR_6m`: the HR at 6 months
- `HR_6m_CI`: the 95% CI of the HR at 6 months
- `HR_6m_p`: the p-value of the HR at 6 months
- `risk_horizon`: the risk horizon (in days); set to infinite if > 730 days.
- `time_equal_incidence`: the time to equal incidence
- `KM`: a list that contains the data for the Kaplan-Meier curves and its confidence interval
- `HRt`: a list that contains the data for the time-varying HR.
`cohort1`: the name of the first cohort (set to 'COVID-19')
`cohort2`: the name of the first cohort (set to 'Other respiratory infection')
As an illustration, the following lines of code would plot the KM curves for cognitive deficit (outcome 33) for the whole cohorts (corresponding to Figure 1E of the main manuscript):
`res=readRDS('OSF_2y_trajectories_all.rds')`
`plot(res$outcomes[[38]]$HRt$time,res$outcomes[[38]]$HRt$value,type='l')`
Similarly, this data can be used to plot curves not presented in the paper. For instance, the time-varying HR for cognitive deficit among _children_ can be plotted as follows:
`res=readRDS('OSF_2y_trajectories_children.rds')`
`plot(res$outcomes[[38]]$HRt$time,res$outcomes[[38]]$HRt$value,type='l')`
The other three RDS files contain results for the comparisons between SARS-CoV-2 variants:
**OSF_alpha_variant.rds** contains the results for the comparison of those diagnosed just after vs. just before the emergence of the alpha variant.
**OSF_delta_variant.rds** contains the results for the comparison of those diagnosed just after vs. just before the emergence of the delta variant.
**OSF_omicron_variant.rds.rds** contains the results for the comparison of those diagnosed just after vs. just before the emergence of the omicron variant.
Once loaded in R, the variables are structured in the exact same way as above, except that time-varying hazard ratios (and hence risk horizon and time to equal incidence) are not reported for this analysis.
