opensafely / post-covid-gastrointestinal

post-covid-gastrointestinal

This is the code and configuration for post-covid-gastrointestinal.

You can run this project via Gitpod in a web browser by clicking on this badge:

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Details of the purpose and any published outputs from this project can be found at the link above.

The contents of this repository MUST NOT be considered an accurate or valid representation of the study or its purpose. This repository may reflect an incomplete or incorrect analysis with no further ongoing work. The content has ONLY been made public to support the OpenSAFELY open science and transparency principles and to support the sharing of re-usable code for other subsequent users. No clinical, policy or safety conclusions must be drawn from the contents of this repository.

Repository navigation

• If you are interested in how we defined our code lists, look in the codelists folder.

• Analyses scripts are in the analysis directory:

  • If you are interested in how we defined our variables, we use study definition scripts to define three cohorts: pre-vaccination, vaccinated and unvaccinated. Study start dates (i.e., index) and end dates differ by cohort and are all described in the protocol. Hence, we have a study definition for each; these are written in python. Extracted data is then combined to create our final cohorts, in the preprocess data script.
  • This directory also contains all the R scripts that process, describe, and analyse the extracted data.

• The lib/ directory contains a list of active analyses.

• The project.yaml defines run-order and dependencies for all the analysis scripts. This file should not be edited directly. To make changes to the yaml, edit and run the create_project.R script which generates all the actions.

Manuscript

This manuscript is currently being drafted.

Code

The project.yaml defines project actions, run-order and dependencies for all analysis scripts. This file should not be edited directly. To make changes to the yaml, edit and run the create_project.R script instead. Project actions are then run securely using OpenSAFELY Jobs. Details of the purpose and any published outputs from this project can be found at this link as well.

Below is a description of each action in the project.yaml with arguments denoted by {arg} in the action name:

To be completed.

Output

consort_*.csv

Variable	Description
Description	criterion applied to cohort
N	number of people in the cohort after criterion applied time
removed	number of people removed due to criterion being applied

table1_*.csv

Variable	Description
Characteristic	patient characteristic under consideration
Subcharacteristic	patient sub characteristic under consideration
N (%)	number of people with characteristic, alongside % of total
COVID-19 diagnoses	number of people with characteristic and COVID-19

table2_*.csv

Variable	Description
name	unique identifier for analysis
cohort	cohort used for the analysis
exposure	exposure used for the analysis
outcome	outcome used for the analysis
analysis	string to identify whether this is the ‘main’ analysis or a subgroup
unexposed_person_days	number of person days before or without exposure in the analysis
unexposed_events	number of unexposed people with the outcome in the analysis
exposed_person_days	number of person days after exposure in the analysis
exposed_events	number of exposed people with the outcome in the analysis
total_person_days	number of person days in the analysis
total_events	number of people with the outcome in the analysis
day0_events	number of people with the exposure and outcome on the same day
total_exposed	number of people with the exposure in the analysis
sample_size	number of people in the analysis

venn_*.csv

Variable	Description
outcome	outcome under consideration
only_snomed	outcome identified in primary care only
only_hes	outcome identified in secondary care only
only_death	outcome identified in death registry only
snomed_hes	outcome identified in primary and secondary care
snomed_death	outcome identified in primary care and death registry
hes_death	outcome identified in secondary care and death registry
snomed_hes_death	outcome identified in primary care, secondary care, and death registry
total_snomed	total outcomes identified in primary care
total_hes	total outcomes identified in secondary care
total_death	total outcomes identified in death registry
total	total outcomes identified
cohort	cohort under consideration

model_output.csv

Variable	Description
name	unique identifier for analysis
cohort	cohort used for the analysis
outcome	outcome used for the analysis
analysis	string to identify whether this is the ‘main’ analysis or a subgroup
error	captured error message if analysis did not run
model	string to identify whether the model adjustment
term	string to identify the term in the analysis
lnhr	log hazard ratio for the analysis
se_lnhr	standard error for the log hazard ratio for the analysis
hr	hazard ratio for the analysis
conf_low	lower confidence limit for the analysis
conf_high	higher confidence limit for the analysis
N_total	total number of people in the analysis
N_exposed	total number of people with the exposure in the analysis
N_events	total number of people with the outcome following exposure in the analysis
person_time_total	total person time included in the analysis
outcome_time_median	median time to outcome following exposure
strata_warning	string to identify strata variables that may cause model faults
surv_formula	survival formula for the analysis

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Read more at OpenSAFELY.org.

Licences

As standard, research projects have a MIT license.