Introducing best practice for reproducibility in government

There is an appetite to improve the reproducibility of quantitative analysis undertaken across government. Our team supports conversion of regular publications into Reproducible Analytical Pipelines (RAP). To achieve this, we developed a roadmap to work with analysts in our organisation and help them transform their pipelines and build their skills. An audit of the current RAP status of all regular pipelines assisted in resource allocation and planning. The maturity of a RAP is evaluated on 7 criteria required to reach a minimum viable product (MVP) and 7 additional advanced criteria as outlined by the Analysis Function (AF). We use a combination of hands-on pair-coding with analysis teams, regular and ad hoc code reviews, and training sessions to convert existing pipelines into RAPs, while simultaneously upskilling the analysts. We have also developed guidance and training documentation to share internally and externally. Currently, out of 73 regular publications, 12 have reached the MVP, with an average score of 4.36 out of 7. This scoring is reassessed monthly, allowing us to track the progress in real-time. Self-assessment of technical skills increased by between 43% and 89% and 97% said their understanding of RAP principals improved because of the training and 77% said they are now able to implement best practice into their work. By working with the pipeline owners instead of just refactoring the code directly, we are ensuring business resilience. The in-depth knowledge of the pipeline and skills required to maintain it are present within the analysis team. Publishing our methods, documentation and tools facilitates adoption of RAP for those without a dedicated RAP team. We are on track to convert all our regular publications into RAPs and move to “RAP by default”, in line with the AF RAP Strategy. This will improve the reproducibility, quality, efficiency, transparency, and trustworthiness of analysis within government. We hope other organisations can learn from our methods

Vaccine effectiveness for prevention of covid-19 related hospital admission during pregnancy in England during the alpha and delta variant dominant periods of the SARS-CoV-2 pandemic: population based cohort study

OBJECTIVE: To estimate vaccine effectiveness for preventing covid-19 related hospital admission in individuals first infected with the SARS-CoV-2 virus during pregnancy compared with those of reproductive age who were not pregnant when first infected with the virus. DESIGN: Population based cohort study. SETTING: Office for National Statistics Public Health Data Asset linked dataset, providing national linked census and administrative data in England, 8 December 2020 to 31 August 2021. PARTICIPANTS: 815 477 females aged 18-45 years (mean age 30.4 years) who had documented evidence of a first SARS-CoV-2 infection in the NHS Test and Trace or Hospital Episode Statistics data. MAIN OUTCOME MEASURES: Hospital admission where covid-19 was recorded as the primary diagnosis. Cox proportional hazards models, adjusted for calendar time of infection, sociodemographic factors, and pre-existing health conditions related to uptake of the covid-19 vaccine and risk of severe covid-19 outcomes, were used to estimate vaccine effectiveness as the complement of the hazard ratio for hospital admission for covid-19. RESULTS: Compared with pregnant individuals who were not vaccinated, the adjusted rate of hospital admission for covid-19 was 77% (95% confidence interval 70% to 82%) lower for pregnant individuals who had received one dose and 83% (76% to 89%) lower for those who had received two doses of vaccine. These estimates were similar to those found in the non-pregnant group: 79% (77% to 81%) for one dose and 83% (82% to 85%) for two doses of vaccine. Among those who were vaccinated >90 days before infection, having two doses of vaccine was associated with a greater reduction in risk than one dose. CONCLUSIONS: Covid-19 vaccination was associated with reduced rates of hospital admission in pregnant individuals infected with the SARS-CoV-2 virus, and the reduction in risk was similar to that in non-pregnant individuals. Waning of vaccine effectiveness occurred more quickly after one than after two doses of vaccine

Vaccine effectiveness for prevention of covid-19 related hospital admission during pregnancy in England during the alpha and delta variant dominant periods of the SARS-CoV-2 pandemic:population based cohort study

Objective To estimate vaccine effectiveness for preventing covid-19 related hospital admission in individuals first infected with the SARS-CoV-2 virus during pregnancy compared with those of reproductive age who were not pregnant when first infected with the virus. Design Population based cohort study. Setting Office for National Statistics Public Health Data Asset linked dataset, providing national linked census and administrative data in England, 8 December 2020 to 31 August 2021. Participants 815 477 females aged 18-45 years (mean age 30.4 years) who had documented evidence of a first SARS-CoV-2 infection in the NHS Test and Trace or Hospital Episode Statistics data. Main outcome measures Hospital admission where covid-19 was recorded as the primary diagnosis. Cox proportional hazards models, adjusted for calendar time of infection, sociodemographic factors, and pre-existing health conditions related to uptake of the covid-19 vaccine and risk of severe covid-19 outcomes, were used to estimate vaccine effectiveness as the complement of the hazard ratio for hospital admission for covid-19. Results Compared with pregnant individuals who were not vaccinated, the adjusted rate of hospital admission for covid-19 was 77% (95% confidence interval 70% to 82%) lower for pregnant individuals who had received one dose and 83% (76% to 89%) lower for those who had received two doses of vaccine. These estimates were similar to those found in the non-pregnant group: 79% (77% to 81%) for one dose and 83% (82% to 85%) for two doses of vaccine. Among those who were vaccinated >90 days before infection, having two doses of vaccine was associated with a greater reduction in risk than one dose. Conclusions Covid-19 vaccination was associated with reduced rates of hospital admission in pregnant individuals infected with the SARS-CoV-2 virus, and the reduction in risk was similar to that in non-pregnant individuals. Waning of vaccine effectiveness occurred more quickly after one than after two doses of vaccine

Vaccine effectiveness for prevention of covid-19 related hospital admission during pregnancy in England during the alpha and delta variant dominant periods of the SARS-CoV-2 pandemic: population based cohort study

Objective To estimate vaccine effectiveness for preventing covid-19 related hospital admission in individuals first infected with the SARS-CoV-2 virus during pregnancy compared with those of reproductive age who were not pregnant when first infected with the virus. Design Population based cohort study. Setting Office for National Statistics Public Health Data Asset linked dataset, providing national linked census and administrative data in England, 8 December 2020 to 31 August 2021. Participants 815 477 females aged 18-45 years (mean age 30.4 years) who had documented evidence of a first SARS-CoV-2 infection in the NHS Test and Trace or Hospital Episode Statistics data. Main outcome measures Hospital admission where covid-19 was recorded as the primary diagnosis. Cox proportional hazards models, adjusted for calendar time of infection, sociodemographic factors, and pre-existing health conditions related to uptake of the covid-19 vaccine and risk of severe covid-19 outcomes, were used to estimate vaccine effectiveness as the complement of the hazard ratio for hospital admission for covid-19. Results Compared with pregnant individuals who were not vaccinated, the adjusted rate of hospital admission for covid-19 was 77% (95% confidence interval 70% to 82%) lower for pregnant individuals who had received one dose and 83% (76% to 89%) lower for those who had received two doses of vaccine. These estimates were similar to those found in the non-pregnant group: 79% (77% to 81%) for one dose and 83% (82% to 85%) for two doses of vaccine. Among those who were vaccinated >90 days before infection, having two doses of vaccine was associated with a greater reduction in risk than one dose. Conclusions Covid-19 vaccination was associated with reduced rates of hospital admission in pregnant individuals infected with the SARS-CoV-2 virus, and the reduction in risk was similar to that in non-pregnant individuals. Waning of vaccine effectiveness occurred more quickly after one than after two doses of vaccine.</p

Effect of Antiplatelet Therapy on Survival and Organ Support–Free Days in Critically Ill Patients With COVID-19

International audienc