Monkeypox Clinical Diagnosis Analysis

This repository contains data and R code which are supplements to:

Gaspard Mande, Innocent Akonda, Anja De Weggheleire, Isabel Brosius, Laurens Liesenborghs, Emmanuel Bottieau, Noam Ross, Guy -Crispin Gembu, Robert Colebunders, Erik Verheyen, Ngonda Dauly, Herwig Leirs, Anne Laudisoit (2022),Enhanced surveillance of monkeypox in Bas-Uélé, Democratic Republic of Congo: the limitations of symptom-based case definitions International Journal of Infectious Diseases https://doi.org/10.1016/j.ijid.2022.06.060.

Please cite that paper, and/or the Zenodo data reference (https://doi.org/10.5281/zenodo.6574450) when using data or referring to this study.

Repository Structure and Reproducibility

• data/datbase_MPX_final_948_deidentified.xls contains data from the study and a data dictionary describing all variables. Data are de-indentified; variables collected but removed to anonymize data are described in the data dictionary

  Note that because the analysis uses identifiable data, the full pipeline cannot be run with the posted data. Partial data, not including unique combinations of variables that would be identifiable, is available upon request.

• R/ contains functions used in this analysis.

• reports/ contains literate code for R Markdown reports generated in the analysis

• outputs/ contains compiled reports and figures.

• This project uses the {targets} framework to organize build steps for analysis pipeline. The steps are defined in the _targets.R file and the workflow can be executed by running run.R via source("run.R") in your R terminal or Rscript run.R in your system shell. The schematic figure below summarizes the steps. (It uses mermaid.js syntax and should display as a graph on GitHub. It can also we viewed by pasting the code into https://mermaid.live.)

graph LR
  subgraph legend
    x7420bd9270f8d27d([""Up to date""]):::uptodate --- x5b3426b4c7fa7dbc([""Started""]):::started
    x5b3426b4c7fa7dbc([""Started""]):::started --- xbf4603d6c2c2ad6b([""Stem""]):::none
  end
  subgraph Graph
    x608f26fc87c17c04(["bas_corrplot"]):::uptodate --> xea144c390a1e3213(["corrplot_file"]):::uptodate
    xe22e80ea1c77ed8b(["bas_train_prepped"]):::uptodate --> x12e75493b9005333(["bas_validate_prepped"]):::uptodate
    xc9200d108e1b2a66(["bas_validate"]):::uptodate --> x12e75493b9005333(["bas_validate_prepped"]):::uptodate
    x2a8bb2bae1240fcd(["bas_excel"]):::uptodate --> x4b217d550d08ada0(["bas_data"]):::uptodate
    x3e4c5a69e5aaafdc(["bas_split"]):::uptodate --> xc9200d108e1b2a66(["bas_validate"]):::uptodate
    x4b217d550d08ada0(["bas_data"]):::uptodate --> x1bf6c3824c366cb1(["bas_cleaned"]):::uptodate
    xdb35712610fbc604(["bas_linear_model"]):::uptodate --> x79fe21176be90f97(["bas_lm_coefplot"]):::uptodate
    xb8aa5e15e9f1f7b2(["bas_train"]):::uptodate --> xe22e80ea1c77ed8b(["bas_train_prepped"]):::uptodate
    x1bf6c3824c366cb1(["bas_cleaned"]):::uptodate --> x3e4c5a69e5aaafdc(["bas_split"]):::uptodate
    x3e4c5a69e5aaafdc(["bas_split"]):::uptodate --> xb8aa5e15e9f1f7b2(["bas_train"]):::uptodate
    xdb35712610fbc604(["bas_linear_model"]):::uptodate --> x1e7dc8900c0252af(["model_diagnostics"]):::uptodate
    xb8aa5e15e9f1f7b2(["bas_train"]):::uptodate --> x1e7dc8900c0252af(["model_diagnostics"]):::uptodate
    xe22e80ea1c77ed8b(["bas_train_prepped"]):::uptodate --> x1e7dc8900c0252af(["model_diagnostics"]):::uptodate
    xc9200d108e1b2a66(["bas_validate"]):::uptodate --> x1e7dc8900c0252af(["model_diagnostics"]):::uptodate
    x12e75493b9005333(["bas_validate_prepped"]):::uptodate --> x1e7dc8900c0252af(["model_diagnostics"]):::uptodate
    x79fe21176be90f97(["bas_lm_coefplot"]):::uptodate --> xf8bd9369e68bca9a(["lm_coefplot_file"]):::uptodate
    x1bf6c3824c366cb1(["bas_cleaned"]):::uptodate --> x608f26fc87c17c04(["bas_corrplot"]):::uptodate
    xe22e80ea1c77ed8b(["bas_train_prepped"]):::uptodate --> xdb35712610fbc604(["bas_linear_model"]):::uptodate
    x6e52cb0f1668cc22(["readme"]):::started --> x6e52cb0f1668cc22(["readme"]):::started
  end
  classDef uptodate stroke:#000000,color:#ffffff,fill:#354823;
  classDef started stroke:#000000,color:#000000,fill:#DC863B;
  classDef none stroke:#000000,color:#000000,fill:#94a4ac;
  linkStyle 0 stroke-width:0px;
  linkStyle 1 stroke-width:0px;
  linkStyle 20 stroke-width:0px;

• This project requires R 4.2.0. This poject uses the {renv} framework to record R package dependencies and versions. Packages used are recorded in renv.lock and code used to manage dependencies is in renv/ and other files in the root project directory. On starting an R session in the working directory, run renv::restore() to install R package dependencies.
  • The package also requires cmdstan to be installed. (Version 2.29.2 was used). If not already installed, run cmdstanr::install_cmdstan(version = "2.29.2") after renv::restore()