R Observatory: Metrics for sicegar version 0.3.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

sicegar

0.3.0Package record

Analysis of Single-Cell Viral Growth Curves

0packages depend

3.2Kdownloads / year

37.2%test coverage

11/13flavors OK

Overview

About

Maintained by Johanna HardinCRAN page ↗GitHub ↗Website ↗Issues ↗

Aims to quantify time intensity data by using sigmoidal and double sigmoidal curves. It fits straight lines, sigmoidal, and double sigmoidal curves on to time vs intensity data. Then all the fits are used to make decision on which model best describes the data. This method was first developed in the context of single-cell viral growth analysis (for details, see Caglar et al. (2018) doi:10.7717/peerj.4251), and the package name stands for "SIngle CEll Growth Analysis in R".

Changes in 0.3.0

Added functionality so that the lower asymptote (h0) can be estimated freely, instead of forced to be zero.

To implement, toggle use_h0 = TRUE in fitAndCategorize() and figureModelCurves().

Set default value of threshold_t0_max_int to 1E10.
Fixed typo in object assignment of decisionList$test.sm_tmax_IntensityRatio.
Fixed typo so that now the asymptote ratio (parameterDF$finalAsymptoteIntensityRatio_Estimate) is also unnormalized, along with all other parameters.
Updated **ggplot** functions to have current syntax.
Edited grammar and spelling throughout.

From NEWS.md in the release

Install

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

install.packages("sicegar", 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("wilkelab/sicegar")

Development version from wilkelab/sicegar. 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-sicegar

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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-sicegar

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-sicegar

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

2NOTE11OK

Check messages

NOTEdependencies in R coder-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Namespace in Imports field not imported from:
  ‘dplyr’
All declared Imports should be used.

CRAN check page ↗

Slowest check: 4.2 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.3.0

READMEYes · 170 wordsVignettesYes · 7 · dynamicNEWSYes · 67% structured · mentions 0.3.0Citation fileYes · cites a publicationWebsiteYes

Help pages: 21
Examples that run: 100%20 run in a plain check
Exported functions with examples: 95%
Documented parameters: 88%
Return-value docs: 95%
Help pages citing references: 0%

Vignettes (7)

How these are measured

Downloads

3.2K

CRAN downloads in the past year

Rank #12,281 · ~9/day · ~269/mo

Releases R versions

Daily download trend is not available in this view yet.

34030 days

90390 days

3.2K1 year

Compare downloads with other packages →

Also on90 r2u5 autocran

How downloads are counted

Repository

wilkelab/sicegar ↗Organization: wilkelab

10Stars

9Forks

3Open issues

0Open PRs

4Releases

112Commits

3Commit identities

112 commits · Last activity 2021-05-08 · The default branch showed an older version (0.2.4) than CRAN on 2026-10-22

Responsiveness

How these are sampled

PRs merged (all time): 0%
Median days to close, 50 most recently updated closed issues: 50
Median days to close, 50 most recently updated closed PRs: 632

PRs over time

2026-07-11 · 12026-07-20 · 0

How these are measured

PracticesBeta

5 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/wilkelab/sicegar on 2026-10-22.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Coverage (1)

Coverage reporting (Codecov)

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Installing sicegar adds 31 packages (15 with compiled code, 19 MB of source tarballs). Heaviest: ggplot2 6.0 MB, isoband 1.5 MB, timeSeries 1.4 MB.

Depends (0)

none

Imports (5)

minpack.lm fBasics ggplot2statsdplyr

LinkingTo (0)

none

Suggests (5)

covr cowplot testthat knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (7)

Johanna Hardin

Author, Maintainer since 0.3.0 (2025) · added in 0.3.0

Samuel Butler

Author · added in 0.3.0

M. Umut Caglar

Author

Phineus Choi

Author · added in 0.3.0

Thomas Matheis

Author · added in 0.3.0

Mira Terdiman

Author · added in 0.3.0

Claus O. Wilke

Author

Previously maintained by Claus O. Wilke (0.2.3 to 0.2.4) and M. Umut Caglar (0.1 to 0.2.2).

Releases (6)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.3.0Latest
record
2025-11-15 · current release · diff ↗ ·
added 7 exports
categorize_h0, doublesigmoidalFitFormula_h0, doublesigmoidalFitFunction_h0, multipleFitFunction_h0, parameterCalculation_h0, sigmoidalFitFormula_h0, sigmoidalFitFunction_h0
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
0.2.4
record
2021-05-08 · diff ↗
R
R 4.0.0 released · 2020-04-24
unarchivedReturned to CRAN
2019-08-23
0.2.3
record
2019-08-23 · diff ↗
archivedRemoved from CRAN
2019-07-27
check problems were not corrected in time
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
0.2.2
record
2017-10-17 · diff ↗
0.2
record
2017-07-11 · diff ↗ ·
removed 6 exports
categorize_nosignal, fitFunction, lineFitFormula, lineFitFunction, numericalReCalculation, printInfectionCurves

added 5 exports
figureModelCurves, fitAndCategorize, multipleFitFunction, parameterCalculation, preCategorize

Show 3 earlier eventsHide 3 earlier events

R
R 3.4.0 released · 2017-04-21
0.1
record
2017-03-19
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2017-03-19
Total releases: 6 / 9 yrs
License: GPL-2 | GPL-3 OSI
Download size: 522 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("sicegar")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.7717/peerj.4251.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for sicegar version 0.3.0 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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