r4pde

r4pde provides tools for quantitative plant disease epidemiology. It started as the companion package to the book R for Plant Disease Epidemiology and now also implements methods from recent research on the functional analysis of disease progress curves. It is aimed at researchers, students and practitioners who analyse field and greenhouse disease data.

What the package does

Area	What you can do	Main functions
Disease progress curves (functional analysis)	Fit smooth, design-adjusted disease progress curves with GAMs; estimate instantaneous rates; compare and cluster whole trajectories; rank resistance and quantify stability across environments	functional_curves(), functional_rate(), functional_distances(), functional_pca(), functional_resistance(), functional_instability(), diagnose_curves()
Disease management	Build Disease Suppression Profiles (DSP) for fungicides or other control measures relative to an untreated check, summarise and rank them	functional_contrast(), functional_summary(), functional_suppression_profiles(), rank_dsp(), plot_dsp()
Spatial epidemiology	Test for aggregation (ordinary runs, join counts, binary power law), analyse foci (AFSD), count subareas, fit dispersal gradients	oruns_test(), join_count(), BPL(), AFSD(), count_subareas(), fit_gradients()
Disease quantification	Compute disease severity indices from ordinal scales and compare treatments on censored ordinal data	DSI(), DSI2(), CompMuCens()
Weather and environment	Download daily weather (NASA POWER, ERA5, BR-DWGD) and build window-pane variables for weather–disease models	get_nasapower(), get_era5(), get_brdwgd(), windowpane(), windowpane_tests()
Datasets	Real epidemiological datasets used in the book and in the examples	BudBlightSoybean, RustSoybean, FHBWheat, WhiteMoldSoybean, SpatialAggregated, …

The reference page lists every function by family.

Installation

Install the stable release from CRAN:

install.packages("r4pde")

The development version is on GitHub. To install it with its dependencies (including Bioconductor packages), use pak:

if (!requireNamespace("pak", quietly = TRUE)) install.packages("pak")
# pak::pkg_install("emdelponte/r4pde")
install.packages("r4pde", repos = c('https://emdelponte.r-universe.dev', 'https://cloud.r-project.org'))

Or with remotes:

if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")
# remotes::install_github("emdelponte/r4pde")
install.packages("r4pde", repos = c('https://emdelponte.r-universe.dev', 'https://cloud.r-project.org'))

Learning more

• Book: R for Plant Disease Epidemiology explains the epidemiological concepts and uses this package throughout.
• Vignette: Functional analysis of disease progress curves walks through the full workflow, from fitting curves to resistance and stability across environments.
• Website: emdelponte.github.io/r4pde has the function reference and the changelog.
• Methods: many functions follow Madden, Hughes and van den Bosch (2007), The Study of Plant Disease Epidemics (doi:10.1094/9780890545058).

Reporting issues

Please report bugs or suggest features on the GitHub issue tracker. A small reproducible example helps a lot.

License and citation

r4pde is released under the MIT license. To cite it, run:

citation("r4pde")