Data

Tools

Indexes

Applications

Experiments

Open Source Science

nCov2019

:microbe: Exploring COVID-19 data

https://github.com/yulab-smu/ncov2019

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: aps.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.6%) to scientific vocabulary

Keywords

covid-19 covid-api covid-data covid-virus covid19-data covid19-tracker sars-cov-2
Last synced: 9 months ago · JSON representation

Repository

:microbe: Exploring COVID-19 data

Basic Info
Statistics
  • Stars: 19
  • Watchers: 5
  • Forks: 7
  • Open Issues: 0
  • Releases: 0
Topics
covid-19 covid-api covid-data covid-virus covid19-data covid19-tracker sars-cov-2
Created over 5 years ago · Last pushed over 3 years ago
Metadata Files
Readme License

README.md

nCov2019: An R package for exploring COVID-19 statistics

The package was developed since Jan. 2020 and originally hosted on GuangchuangYu/nCov2019. This repo contains an up-to-date version with data from new sources (from worldometers and JHUCSSE) and new data types (vaccine and therapeutics data).

:house: Data Sources

Fetching data using API provided by disease.sh

Find out more on the vignette vignette.

:writing_hand: Authors

Guangchuang YU and Tianzhi Wu

https://yulab-smu.top

If you use nCov2019, please cite the following article:

Wu T, Hu E, Ge X*, Yu G*. 2021. nCov2019: an R package for studying the COVID-19 coronavirus pandemic. PeerJ 9:e11421 https://doi.org/10.7717/peerj.11421

:arrow_double_down: Installation

Get the development version from github:

``` r

install.packages("remotes")

remotes::install_github("YuLab-SMU/nCov2019") ```

:beginner: Usages

  • res <- query() to query 5 types of statistics
    • global summary,
    • latest data
    • historical data
    • vaccine data
    • therapeutic data
  • x <- res$global to access global summary data
    • summary(x) will return global overview
    • x$affectedCountries will return total affected countries,(other 20 types of statistics is available)
  • y <- res$latest or y <- res$historical to access latest or historical data
    • y["global"] will return all countries' statistics
    • y[country] will return country level statistics
    • For countries in China, UK, Australia, Canada ,Denmark , France and Netherlands, provincial data is also available and y[country,province] will return statistics data of the selected province
  • z <- res$vaccine or y <- res$therapeutics to access vaccine or therapeutic data
    • summary(z) will return the summary of their trial phase
    • z["all"] will return all candidate
    • z[ID="id1"] each vaccine or therapeutics candidate has an id, this will return detail description of the selected candidate (e.g., "id1")
  • plot() to present data on map
  • dashboard() to open Shiny app dashboard

:art: Example

Run the script example.R in R using source("example.R"), will produce the following figure:

:book: Documents

:chart_with_upwards_trend: Shiny Apps that use nCov2019

:sparkling_heart: Collected in resource list

Owner

  • Name: Bioinformatics Group @ SMU
  • Login: YuLab-SMU
  • Kind: organization
  • Email: gcyu1@smu.edu.cn
  • Location: Guangzhou

Research group led by Prof. Guangchuang Yu in School of Basic Medical Sciences, Southern Medical University

GitHub Events

Total
Last Year

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 51
  • Total Committers: 5
  • Avg Commits per committer: 10.2
  • Development Distribution Score (DDS): 0.392
Past Year
  • Commits: 4
  • Committers: 2
  • Avg Commits per committer: 2.0
  • Development Distribution Score (DDS): 0.25
Top Committers
Name Email Commits
Guangchuang Yu g****u@g****m 31
timze t****e@t****n 12
timze216 7****9@q****m 4
timze t****e@t****n 3
Chun-Hui Gao g****l@g****m 1
Committer Domains (Top 20 + Academic)
timzedemac-mini.lan: 1 qq.com: 1 timzes-mac-mini.lan: 1

Issues and Pull Requests

Last synced: almost 3 years ago

All Time
  • Total issues: 1
  • Total pull requests: 7
  • Average time to close issues: 2 months
  • Average time to close pull requests: about 1 hour
  • Total issue authors: 1
  • Total pull request authors: 3
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • covidresearchanalysis (1)
Pull Request Authors
  • timze216 (5)
  • GuangchuangYu (1)
  • gaospecial (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 506 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 4
  • Total maintainers: 1
cran.r-project.org: nCov2019

Exploring 'COVID'-19 Statistics

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 506 Last month
Rankings
Forks count: 10.1%
Stargazers count: 12.9%
Average: 20.5%
Downloads: 24.1%
Dependent repos count: 25.5%
Dependent packages count: 29.8%
Maintainers (1)
guangchuangyu@gmail.com
Last synced: almost 2 years ago

Dependencies

DESCRIPTION cran
  • R >= 3.6.0 depends
  • RColorBrewer * imports
  • downloader * imports
  • ggplot2 * imports
  • jsonlite * imports
  • DT * suggests
  • cowplot * suggests
  • dplyr * suggests
  • ggplotify * suggests
  • ggrepel * suggests
  • grDevices * suggests
  • knitr * suggests
  • magick * suggests
  • maps * suggests
  • plotly * suggests
  • prettydoc * suggests
  • remotes * suggests
  • reshape2 * suggests
  • rmarkdown * suggests
  • shadowtext * suggests
  • shiny * suggests
  • shinyBS * suggests
  • shinycssloaders * suggests
  • shinydashboard * suggests
  • tidyr * suggests
  • utils * suggests