covid19.analytics

2.1.3.3

Load and Analyze Live Data from the COVID-19 Pandemic

0packages depend

5.2Kdownloads / year

20.0%test coverage

11/13checks pass

Overview

About

Maintained by Marcelo PonceFirst published 2020-04-0612 releasesCRAN page ↗GitHub ↗

Load and analyze updated time series worldwide data of reported cases for the Novel Coronavirus Disease (COVID-19) from different sources, including the Johns Hopkins University Center for Systems Science and Engineering (JHU CSSE) data repository https://github.com/CSSEGISandData/COVID-19, "Our World in Data" https://github.com/owid/ among several others. The datasets reporting the COVID-19 cases are available in two main modalities, as a time series sequences and aggregated data for the last day with greater spatial resolution. Several analysis, visualization and modelling functions are available in the package that will allow the user to compute and visualize total number of cases, total number of changes and growth rate globally or for an specific geographical location, while at the same time generating models using these trends; generate interactive visualizations and generate Susceptible-Infected-Recovered (SIR) model for the disease spread.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("covid19.analytics", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("mponce0/covid19.analytics")

Development version from mponce0/covid19.analytics. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-covid19.analytics

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-covid19.analytics

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-covid19.analytics

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 8.2 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.04

20.0%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-07-15
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-07-14
11 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-06-27
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-21
10 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-06-09
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-06-08
11 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
9 OK · 5 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 6,113 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 86%
Documented parameters: 100%
Return-value docs: 39%
References docs: 0%

Downloads

5.2K

CRAN downloads in the past year

Rank #10,226 · ~14/day · ~432/mo

Releases R versions

Daily download trend is not available in this view yet.

34030 days

1.1K90 days

5.2K1 year

Compare downloads with other packages →

Also on220 r2u32 autocran34 c2d4u

Repository

GitHub ↗ mponce0/covid19.analytics

35Stars

11Forks

4Open issues

0Open PRs

9Releases

12,840Commits

3Contributors

rcovid19covid19-datancov2019sars-cov-2

License GPL-2.0 · 12,840 commits · Last activity 2022-08-18 · 0% stars, 30d

Stars over time

2025-03-24 · 342026-07-07 · 35

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 1 family in the upstream repository

Checks run against github.com/mponce0/covid19.analytics on 2026-07-19.

Continuous integration (2)

GitHub ActionsTravis CI

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

21 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (15)

readxl ape rentrez curl plotly htmlwidgets deSolve gplots pheatmap shiny shinydashboard shinycssloaders DT dplyr collapsibleTree

LinkingTo (0)

none

Suggests (6)

knitr devtools roxygen2 markdown rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 7,527 (66%)Rd 3,382 (30%)Other 464 (4%)Vignettes 20 (0%)Shell 20 (0%)

Code characteristics

Cyclomatic complexity: 3.0 median / 37 max
Test cases: 8 / 0.04 per code line

Test coverage

Line coverage

20%

Expression

17.5%

Tests / Examples

20.0% / 28% ex

Functions

77 41 exported

Complexity

5.8 avg / 37 max

Call network

77 nodes / 167 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

77 functions

Function	Cyclo	Coverage
X.covid19.genomic.data exp	2	0%
c19.NP_fasta.data exp	8	0%
c19.NPs.data exp	15	0%
c19.fasta.data exp	8	0%
c19.genomic.data exp	9	0%
c19.ptree.data exp	11	0%

People & History

People (0)

Author records are not tracked yet for this package.

Listed in earlier versions (2)

Marcelo Ponce

no longer listed · 1.0 to 2.1.3.3

Amit Sandhel

no longer listed · 2.0 to 2.1.3.3

Package Timeline

12 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
2.1.3.3Latest
2023-10-15 · current release · diff ↗
2.1.3.2
2023-10-10 · diff ↗
unarchivedReturned to CRAN
2023-10-10
archivedRemoved from CRAN
2023-10-08
repeated policy violation On Internet access
2.1.3.1
2023-05-25 · diff ↗
R
R 4.3.0 released · 2023-04-21
2.1.3
2022-08-18 · diff ↗
R
R 4.2.0 released · 2022-04-22
2.1.2
2022-04-06 · diff ↗
2.1.1
2021-09-14 · diff ↗
R
R 4.1.0 released · 2021-05-18
2.1
2021-03-23 · diff ↗
2.0
2020-09-28 · diff ↗

Show 8 earlier events

unarchivedReturned to CRAN
2020-09-28
archivedRemoved from CRAN
2020-09-16
policy violation On Internet access, first warned on May 2
1.1.1
2020-07-13 · diff ↗
1.1
2020-05-03 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.0.1
2020-04-13 · diff ↗
1.0
2020-04-06
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2020-04-06
Total releases: 12 / 6 yrs
License: GPL (>= 2) OSI
Download size: 3.6 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Epidemiology

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