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"
Science Score: 23.0%
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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○DOI references
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✓Academic publication links
Links to: zenodo.org -
○Academic email domains
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○Institutional organization owner
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○Scientific vocabulary similarity
Low similarity (11.8%) to scientific vocabulary
Keywords
lima
peru
population
prevalence
serological-surveys
workflow
Last synced: 6 months ago
·
JSON representation
Repository
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"
Basic Info
- Host: GitHub
- Owner: avallecam
- Language: R
- Default Branch: main
- Homepage: https://www.thelancet.com/journals/eclinm/article/PIIS2589-5370(21)00081-X/fulltext
- Size: 384 KB
Statistics
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 2
Topics
lima
peru
population
prevalence
serological-surveys
workflow
Created over 5 years ago
· Last pushed over 4 years ago
Metadata Files
Readme
README.Rmd
---
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
```
# covid_seroprev
[](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/).
Owner
- Name: Andree Valle Campos
- Login: avallecam
- Kind: user
- Location: Lima, Perú
- Website: https://avallecam.github.io/
- Twitter: avallecam
- Repositories: 3
- Profile: https://github.com/avallecam
pron: él/he/his, peruano, tusán.
GitHub Events
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Last synced: 6 months ago
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- Total issue authors: 0
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- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
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- Pull requests: 0
- Average time to close issues: N/A
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- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
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- Bot issues: 0
- Bot pull requests: 0