R Observatory: Metrics for epifitter version 1.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

epifitter

1.0.0Package record

Analysis and Simulation of Plant Disease Progress Curves

0packages depend

20.4Kdownloads / year

60.3%test coverage

13/13flavors OK

Overview

About

Maintained by Kaique dos S. AlvesCRAN page ↗GitHub ↗Website ↗Issues ↗

Tools for analysis, visualization, and simulation of plant disease progress curves. Includes functions to calculate area-under-the-curve summaries, fit and compare exponential, monomolecular, logistic, and Gompertz models using linear or nonlinear regression, work with single or multiple epidemics, and produce 'ggplot2'-based visualizations. Also includes an experimental powdery mildew dataset for reproducible teaching and research workflows. See Madden, Hughes, and van den Bosch (2007) doi:10.1094/9780890545058 for background on the epidemiological methods.

Changes in 1.0.0

Highlights

Modernized the fitting workflow with shared input validation, more informative error messages, and improved grouped-model ergonomics.
Refreshed the documentation site with updated articles, improved accessibility, dark mode support, and a clearer visual style for figures.
Added a formal package citation, a vignette built around the bundled PowderyMildew dataset, and expanded regression tests for area summaries and model fitting.
Corrected area-under-the-curve handling for repeated assessment times and strengthened defaults for nonlinear fitting workflows.

--------------------------------------------------------------------------------

From NEWS.md in the release

Install

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

install.packages("epifitter", 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("AlvesKS/epifitter")

Development version from AlvesKS/epifitter. 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-epifitter

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-epifitter

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-epifitter

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

13OK

CRAN check page ↗

Slowest check: 2.3 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-04-14
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.0

READMEYes · 336 wordsVignettesYes · 5 · dynamicNEWSYes · 100% structured · mentions 1.0.0Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 20 (1 internal)includes a package overview page
Examples that run: 100%13 run in a plain check
Exported functions with examples: 75%
Documented parameters: 94%
Return-value docs: 100%
Help pages citing references: 20%

Vignettes (5)

Area-under-the-curve summaries HTML
Getting started with epifitter HTML
Model fitting workflows HTML
Simulation workflows HTML
Working with the PowderyMildew dataset HTML

How these are measured

Downloads

20.4K

CRAN downloads in the past year

Rank #5,540 · ~56/day · ~1.7K/mo

Releases R versions

Daily download trend is not available in this view yet.

63630 days

1.5K90 days

20.4K1 year

Compare downloads with other packages →

Also on110 r2u5 autocran68 c2d4u

How downloads are counted

Repository

alvesks/epifitter ↗Account: AlvesKS

7Stars

4Forks

1Open issues

3Open PRs

0Releases

54Commits

2Commit identities

54 commits · Last activity 2026-06-20 · 0% stars, 30d · Default branch at 1.0.1, ahead of CRAN 1.0.0 (checked 2026-10-11)

Responsiveness

How these are sampled

PRs merged (all time): 75%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 172

Stars over time

2025-01-29 · 52026-07-11 · 7

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/alvesks/epifitter on 2026-10-11.

Governance and community (1)

Code of conduct

Docs source (2)

pkgdown

GitHub Pages site last deployed 2026-06-20

pkgdown site last built 2026-05-17

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Installing epifitter adds 67 packages (41 with compiled code, 54 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 4.1

Imports (10)

DescTools cowplot deSolve dplyr ggplot2 magrittr minpack.lmstatstibble tidyr

LinkingTo (0)

none

Suggests (4)

knitr rmarkdown lemon testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (3)

Kaique dos S. Alves

Author, Maintainer since 0.1.0 (2020)

Emerson M. Del Ponte

Author

Adam H. Sparks

Author · added in 1.0.0

Releases (4)

Pick two releases to compare their code metrics.

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
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
1.0.0Latest
record
2021-06-14 · current release · diff ↗ ·
removed 1 export
pattern:^[[:alpha:]]+

added 16 exports
AUDPC, AUDPC_2_points, AUDPS, expo_fun, fit_lin, fit_multi, fit_nlin, fit_nlin2, gompi_fun, logi_fun, mono_fun, plot_fit, sim_exponential, sim_gompertz, sim_logistic, sim_monomolecular
0.3.0
record
2021-06-14 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.2.0
record
2020-11-26 · diff ↗
0.1.0
record
2020-10-29
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-10-29
Total releases: 4 / 6 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1
Bundled data: 11 KB / 1 file
Download size: 140 KB

Appears in task views

Agricultural Science Epidemiology

Cite

Cite this package

Run in R for the authors' entry:

citation("epifitter")

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

It points to 10.1186/s42483-021-00098-7.

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 epifitter version 1.0.0 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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