https://github.com/avallecam/covid_seroprev

Analysis code for the article: "SARS-CoV-2 prevalence associated to low socioeconomic status and overcrowding in an LMIC megacity: A population-based seroepidemiological survey in Lima, Peru"
https://github.com/avallecam/covid_seroprev

lima peru population prevalence serological-surveys workflow

Last synced: 4 months ago
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Analysis code for the article: "SARS-CoV-2 prevalence associated to low socioeconomic status and overcrowding in an LMIC megacity: A population-based seroepidemiological survey in Lima, Peru"

• Host: GitHub
• URL: https://github.com/avallecam/covid_seroprev
• Owner: avallecam
• Created: 2020-10-07T00:44:18.000Z (about 5 years ago)
• Default Branch: main
• Last Pushed: 2021-07-07T15:56:31.000Z (over 4 years ago)
• Last Synced: 2025-03-02T21:45:58.357Z (9 months ago)
• Topics: lima, peru, population, prevalence, serological-surveys, workflow
• Language: R
• Homepage: https://www.thelancet.com/journals/eclinm/article/PIIS2589-5370(21)00081-X/fulltext
• Size: 384 KB
• Stars: 1
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.Rmd

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README

          
---

output: github_document

---

```{r, include = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "#>"

)

```

# covid_seroprev

[![DOI](https://zenodo.org/badge/301889893.svg)](https://zenodo.org/badge/latestdoi/301889893)

The goal of `covid_seroprev` is to register the data management and statistical 

analysis workflow used for the project and manuscript: 

__"Prevalence of SARS-CoV-2 in Lima, Peru: a population-based 

seroepidemiological survey"__

## Project Workflow

### Files:

- `Encuesta ESPI_fisico.xlsx`: XLSForm used to collect data.

- `01-clean.R`: import, clean and integration of data sources. recategorize and create variables.

- `06-prevalence.R`: estimate prevalence.

- `07-outputs.R`: create tables and figures.

- `11-sampling_comparison.R`: contrast census and sample population.

- `13-epicurve.R`: create epicurve from open data.

- `15-distributions.R`: exploratory ecdf for overcrowding.

- `16-association.R`: calculate association measurements.

### Reproducibility:

To reproduce this project from  `06-prevalence.R` onwards, you need the `uu_clean_data.rds` file stored in the `data/` folder. This data source is not available in this repository.

For reproducible workflow examples of the analysis performed in this project 

go to the:

- [serosurvey](https://avallecam.github.io/serosurvey/) R package website to generate prevalence estimates as in `06-prevalence.R`, and

- [epitidy](https://github.com/avallecam/epitidy) R package repository to calculate association measurements as in `16-association.R`.

### Required packages:

Call `renv::restore()` to reinstall all of the packages used in this project. Learn more about `renv` [here](https://rstudio.github.io/renv/).