{"id":38654461,"url":"https://github.com/openwashdata/choleramalawi","last_synced_at":"2026-01-17T09:25:36.153Z","repository":{"id":257832142,"uuid":"867667142","full_name":"openwashdata/choleramalawi","owner":"openwashdata","description":"Data package tracking the course of the cholera epidemic in Malawi (2023-24)","archived":false,"fork":false,"pushed_at":"2024-10-16T06:58:09.000Z","size":1376,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-09-04T22:46:18.426Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://openwashdata.github.io/choleramalawi/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"cc-by-4.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/openwashdata.png","metadata":{"files":{"readme":"README.Rmd","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2024-10-04T13:46:47.000Z","updated_at":"2024-10-16T06:58:12.000Z","dependencies_parsed_at":"2024-10-16T16:14:39.258Z","dependency_job_id":"e76f3864-5624-404a-8d16-f593deecd444","html_url":"https://github.com/openwashdata/choleramalawi","commit_stats":null,"previous_names":["openwashdata/choleramalawi"],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/openwashdata/choleramalawi","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/openwashdata%2Fcholeramalawi","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/openwashdata%2Fcholeramalawi/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/openwashdata%2Fcholeramalawi/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/openwashdata%2Fcholeramalawi/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/openwashdata","download_url":"https://codeload.github.com/openwashdata/choleramalawi/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/openwashdata%2Fcholeramalawi/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28505550,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-17T06:57:29.758Z","status":"ssl_error","status_checked_at":"2026-01-17T06:56:03.931Z","response_time":85,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2026-01-17T09:25:34.747Z","updated_at":"2026-01-17T09:25:36.103Z","avatar_url":"https://github.com/openwashdata.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\nalways_allow_html: true\neditor_options: \n  markdown: \n    wrap: 72\n  chunk_output_type: console\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/README-\",\n  out.width = \"100%\",\n  message = FALSE,\n  warning = FALSE,\n  fig.retina = 2,\n  fig.align = 'center'\n)\n```\n\n# choleramalawi\n\n\u003c!-- badges: start --\u003e\n\n[![License: CC BY\n4.0](https://img.shields.io/badge/License-CC_BY_4.0-lightgrey.svg)](https://creativecommons.org/licenses/by/4.0/)\n\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13920530.svg)](https://zenodo.org/doi/10.5281/zenodo.13920530)\n\n\u003c!-- badges: end --\u003e\n\nThe goal of choleramalawi is to analyse the progress of the Cholera epidemic in Malawi (2023-24)\n\n## Installation\n\nYou can install the development version of choleramalawi from\n[GitHub](https://github.com/) with:\n\n``` {r eval=FALSE}\n# install.packages(\"devtools\")\ndevtools::install_github(\"openwashdata/choleramalawi\")\n```\n\n```{r}\n## Run the following code in console if you don't have the packages\n## install.packages(c(\"dplyr\", \"knitr\", \"readr\", \"stringr\", \"gt\", \"kableExtra\"))\nlibrary(dplyr)\nlibrary(knitr)\nlibrary(readr)\nlibrary(stringr)\nlibrary(gt)\nlibrary(kableExtra)\nlibrary(rnaturalearth)\nlibrary(rnaturalearthdata)\nlibrary(sf)\nlibrary(RColorBrewer)\n#devtools::load_all()\n```\n\nAlternatively, you can download the individual datasets as a CSV or XLSX\nfile from the table below.\n\n```{r, echo=FALSE, message=FALSE, warning=FALSE}\n\nextdata_path \u003c- \"https://github.com/openwashdata/choleramalawi/raw/main/inst/extdata/\"\n\nread_csv(\"data-raw/dictionary.csv\") |\u003e \n  distinct(file_name) |\u003e \n  dplyr::mutate(file_name = str_remove(file_name, \".rda\")) |\u003e \n  dplyr::rename(dataset = file_name) |\u003e \n  mutate(\n    CSV = paste0(\"[Download CSV](\", extdata_path, dataset, \".csv)\"),\n    XLSX = paste0(\"[Download XLSX](\", extdata_path, dataset, \".xlsx)\")\n  ) |\u003e \n  knitr::kable()\n\n```\n\n## Data\n\nThe package provides access to one dataset `choleramalawi`. It contains data on the progress of the cholera epidemic in each district of Malawi during 2022-23. The data focuses on cases and deaths for every week as well as cumulative cases and deaths.\n\n```{r}\nlibrary(choleramalawi)\n```\n\n### choleramalawi\n\nThe dataset `choleramalawi` contains data about the progress of the cholera epidemic in Malawi (2022-23).\nIt has `r nrow(choleramalawi)` observations and `r ncol(choleramalawi)` variables\n\n```{r}\ncholeramalawi |\u003e \n  head(3) |\u003e \n  gt::gt() |\u003e\n  gt::as_raw_html()\n```\n\nFor an overview of the variable names, see the following table.\n\n```{r echo=FALSE, message=FALSE, warning=FALSE}\nreadr::read_csv(\"data-raw/dictionary.csv\") |\u003e\n  dplyr::filter(file_name == \"choleramalawi.rda\") |\u003e\n  dplyr::select(variable_name:description) |\u003e \n  knitr::kable() |\u003e \n  kableExtra::kable_styling(\"striped\") |\u003e \n  kableExtra::scroll_box(height = \"200px\")\n```\n\n\n## Example\n\n```{r}\nlibrary(choleramalawi)\n\n# Top districts by total cases\n\ncholeramalawi |\u003e\n  group_by(district) |\u003e\n  summarise(total_cases = sum(cases, na.rm = TRUE)) |\u003e\n  arrange(desc(total_cases)) |\u003e\n  head(10) |\u003e\n  gt() |\u003e\n  as_raw_html()\n```\n\n```{r}\n# Plotting the number of cases over time in Lilongwe district\n\nlibrary(ggplot2)\n\ncholeramalawi |\u003e\n  filter(district == \"Lilongwe\") |\u003e\n  ggplot(aes(x = week, y = cases)) +\n  geom_line() +\n  labs(title = \"Number of cases over time in Lilongwe district\",\n       x = \"Week\",\n       y = \"Cases\")\n```\n\n```{r}\n# Plot a map of districts of Malawi colored by the number of cases\ntotal_cases_district \u003c- choleramalawi |\u003e\n  group_by(district) |\u003e\n  summarise(total_cases = sum(cases, na.rm = TRUE)) |\u003e \n  mutate(total_cases = ifelse(is.na(total_cases), 0, total_cases))\nmalawi_map \u003c- ne_states(country = \"Malawi\", returnclass = \"sf\")\n\nmalawi_map \u003c- malawi_map %\u003e%\n  left_join(total_cases_district, by = c(\"name\" = \"district\"))\n\nggplot(malawi_map) +\n  geom_sf(aes(fill = total_cases)) +\n  scale_fill_viridis_c(guide=\"none\") + \n  theme_void() +\n  labs(title = \"Cholera Cases by District in Malawi\")\n\n```\n\n\n## License\n\nData are available as\n[CC-BY](https://github.com/openwashdata/choleramalawi/blob/main/LICENSE.md).\n\n## Citation\n\nPlease cite this package using:\n\n```{r}\ncitation(\"choleramalawi\")\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fopenwashdata%2Fcholeramalawi","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fopenwashdata%2Fcholeramalawi","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fopenwashdata%2Fcholeramalawi/lists"}