# Project overview The PACCMan project investigated the effect of COVID-19 on hearing health. Data was collected between September 2021 and July 2022. The project was conducted by researchers from the [Manchester Centre for Audiology and Deafness](https://sites.manchester.ac.uk/mancad/) at the University of Manchester, with support from the [NIHR Clinical Research Network](https://www.nihr.ac.uk/explore-nihr/support/clinical-research-network.htm). The work was funded by [The Royal National Institute for Deaf People](https://rnid.org.uk/), [The Dowager Countess Eleanor Peel Trust](https://peeltrust.com/), The University of Manchester [COVID-19 Research Appeal Fund](https://www.manchester.ac.uk/collaborate/give/philanthropy/appeals/coronavirus-research/), and was supported by the [NIHR Manchester Biomedical Research Centre](https://www.manchesterbrc.nihr.ac.uk/). # Repository overview This repository contains materials associated with the manuscript *Pre-registered controlled comparison of auditory function reveals no difference between hospitalised adults with and without COVID-19* (Visram et al., 2023). The repository contains de-identified data from the project, as well as R code for reproducing all data processing, analyses, and figures. # Reproducibility and R info To assist with reproducibility this work is structured as an [RStudio project](https://support.rstudio.com/hc/en-us/articles/200526207-Using-Projects), meaning it is self-contained and all file paths used are relative to the project folder. ## {renv} and package versions R packages used in this project will change over time. Future versions of packages may not function in exactly the same way as the versions used in the analyses. To assist with reproducibility a [{renv}](https://rstudio.github.io/renv/articles/renv.html) lockfile (`renv.lock`) is included in this repository. Users can restore known working versions of packages using the lockfile. An introduction to {renv} can be found here: https://rstudio.github.io/renv/articles/renv.html. Session info is also included at the end of each script/document, detailing the R and package versions used. # Guide to scripts, data, and getting started ## Scripts All R code for processing data and running analyses is contained in [Quarto](https://quarto.org/) files (i.e. files ending ".qmd" in this repository). Quarto files are R Markdown files and so will run as R code in RStudio. The html files in this repository are rendered versions of the associated .qmd files, i.e. *1.0_supplementary_materials.html* is the rendered output from the code contained in *1.0_supplementary_materials.qmd*. - *1.0_supplementary_materials.qmd* contains code for all analyses and figures included in the associated publication for the project, plus a considerable amount of additional information, details on methods, and visualisations. - *0.1_paccman_preprocessing* contains code for pre-processing of data ahead of the main supplementary materials script. This code will run in the project environment but it is not necessary to do so (all its output files are already present in the repository). - *0.0_paccman_deidentify_and_process.qmd* is inlcuded only for transparency over the treatment of raw/sensitive data. It will not run in this project environment as the files it imports contain potentially sensitive/identifying information and so can not be shared publically. ## Data Processed data is in [tidy, long format](https://r4ds.had.co.nz/tidy-data.html). Analyses in the manuscript were performed on aggregated data, collapsing over ears per participant. Users interested in the unaggregated data can also find all measurements **per ear** in the data in this repository. ## Getting started Most users of this repository will be interested in the **Supplementary Materials** discussed in the associated publication. These can be accessed by opening file **1.0_supplementary_materials.html** in your browser. Users interested in specific data sets generated by the project (e.g. PTA data, or Digits-in-Noise data, for example) can access specific data in either the raw or processed (i.e. tidied) formats. To reproduce all analyses and outputs the easiest approach is to: - click on the main folder in the Files tab of this OSF repository - click “Download as zip” - Create a new project within RStudio using the (unzipped) folder you have downloaded as an existing directory. This process will replicate the contents and structure of this repository on your own computer. # How to cite this work Please cite the associated publication: A. S. Visram, I. R. Jackson, H. Guest, C. J. Plack, S. Brij, N. Chaudhuri & K. J. Munro (2023) Pre-registered controlled comparison of auditory function reveals no difference between hospitalised adults with and without COVID-19, International Journal of Audiology, DOI: 10.1080/14992027.2023.2213841 # Contact, queries & comments Comments and queries about the published article should be directed to Anisa Visram (anisa.visram@manchester.ac.uk). Comments and queries about open materials should be directed to Iain Jackson (iain.jackson@manchester.ac.uk) [1]: https://osf.io/u7r9t