Report automation with OfficeR and Flextable
PHE ePoster Library. Puleston R. Apr 10, 2019; 257465; 15247
Dr. Richard Puleston
Dr. Richard Puleston
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Abstract Report automation with OfficeR and FlextableThe core offer for the Field Service includes providing regular reports to our internal and external stakeholders on the key infectious diseases themes that we monitor (e.g. tuberculosis (TB) and healthcare associated infections (HCAI)). The generation of these reports can be very involved, requiring extensive data manipulation, generation of summary tables and figures (including maps) and their insertion into the draft document, commentary and final formatting. By definition these reports are repeated regularly and therefore are resource intensive for the service to produce. Given the ongoing challenges with decreasing resources, in the Field Service team East Midlands we have investigated and implemented steps to make the generation of these reports more efficient and reproducible using R software. Many R users will be familiar with the Markdown package that allows the automated generation of reports, but the outputs are not fully formatted and do not allow the production of Excel workbooks. They may be less familiar with the OfficeR and Flextable packages which allow fully formatted Word, Excel and Powerpoint products to be generated. In this presentation we will demonstrate how we have automated (using OfficeR, Flextable and Markdown) the monthly production of HCAI reports (Excel workbooks), the TB annual report, our weekly influenza like illness and infectious intestinal disease reports and generated Powerpoint presentations, so providing efficiency and accuracy gains for our team. We are also using R much more extensively in our routine work for example in the manipulation of sexual health data and in outbreak investigations and may touch on these too. Funding Core PHE funding
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