Tools for Quantitative Plant Disease Epidemiology
Overview
Tools for quantitative plant disease epidemiology, including functional analysis of disease progress curves, spatial epidemiology, disease quantification, and weather-driven epidemic analysis. The package also serves as an educational resource and companion to the book "R for Plant Disease Epidemiology" (R4PDE). Several functions are based on classical and contemporary methods, including those discussed in Laurence V. Madden, Gareth Hughes, and Frank van den Bosch (2007) doi:10.1094/9780890545058.
New functions
- Added
functional_rate(): Estimates instantaneous rates of plant disease progress (\eqn{S'(t) = dS(t)/dt}) and associated uncertainty from epidemic trajectories fitted byfunctional_curves(). Supports response and link scale derivatives via GAM linear predictor matrix differences, handles boundary conditions without extrapolation, accounts for zero-epidemic curves and negative rates, and computes key rate phenotypes (\eqn{r_{max}}, \eqn{t_{r_{max}}}, growth duration, cumulative positive growth, and growth windows). Includes S3 methods:print(),summary(),plot(), andaugment().
Bug fixes and improvements
functional_curves(): Fixed smooth term label inspection during prediction so that.unitexperimental unit and block random effects are correctly identified and supplied topredict.gam().
From NEWS.md in the release
Install
Health
- OK13 OK2026-08-05
- NOTE12 OK, 1 NOTE2026-08-01
- OK13 OK2026-06-09
- ERROR12 OK, 1 ERROR2026-06-08
- OK14 OK2026-03-10
Documentation
- Help pages
- 75
- Examples that run
- 50%9 run in a plain check (1 of them under a condition) · 1 only when donttest examples are enabled (R CMD check --as-cran) · 8 never run
- Exported functions with examples
- 38%
- Documented parameters
- 100%
- Return-value docs
- 85%
- Help pages citing references
- 4%
Downloads
Repository
- PRs merged (all time)
- 100%
- Median days to close, 50 most recently updated closed issues
- 132
- Median days to close, 50 most recently updated closed PRs
- 0
Stars over time
Forks over time
Releases over time
Issues over time
Commits over time
4 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/emdelponte/r4pde on 2026-10-11.
Dependencies
Code & Tests
Datasets
People & History
Pick two releases to compare their code metrics.
- 0.2.2Latest2026-09-07 · current release · diff ↗ ·
added 30 exports
augment, augment_functional_pca, augment_functional_rate, autoplot.r4pde_functional_pca, diagnose_curves, functional_contrast, functional_curves, functional_distances, functional_instability, functional_pca, functional_pca_clusters, functional_rate, functional_resistance, functional_summary, functional_suppression_profiles, get_brdwgd, get_era5, get_fpca_eigenfunctions, get_fpca_scores, get_fpca_variance, plot_curves, plot_dendrogram, plot_diagnostics, plot_dsp, plot_dsp_rank_heatmap, plot_functional_instability, rank_dsp, reconstruct_curves, simulate_dsp_data, suggest_k - RR 4.6.0 released · 2026-04-24
- 0.1.02025-07-02
- RR 4.5.0 released · 2025-04-11
Package metadata
- First published
- 2025-07-02
- Total releases
- 2 / 1 yrs
- License
- MIT + file LICENSE OSI
- Minimum R
- ≥ 4.1.0
- Bundled data
- 29 KB / 10 files
- Download size
- 510 KB
Cite
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