Learn R Programming

r4pde

An R package developed as a companion to the book R for Plant Disease Epidemiology. It provides access to a suite of specialized R functions and datasets tailored for teaching and analyzing plant disease epidemiology. This package supports researchers, students, and practitioners by offering tools for disease quantification, spatial analysis and predictive modeling.

Installation

The development version of {r4pde} is available from GitHub. To install it along with its dependencies (including Bioconductor packages), use the pak package:

if (!requireNamespace("pak", quietly = TRUE)) install.packages("pak")
pak::pkg_install("emdelponte/r4pde")

Alternatively, using remotes:

if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")
remotes::install_github("emdelponte/r4pde")

Note: The package depends on Icens, which is available from Bioconductor. Both pak and remotes will install it automatically if needed.

Reporting Issues

Please report any bugs or issues via the GitHub issue tracker.

License and Citation

  • This package is released under the MIT license.
  • To cite the package, please use:
citation("r4pde")

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Version

Install

install.packages('r4pde')

Version

0.1.0

License

MIT + file LICENSE

Issues

Pull Requests

Stars

Forks

Maintainer

Emerson M. Del Ponte

Last Published

July 2nd, 2025

Functions in r4pde (0.1.0)

plot_AFSD

Plot ASFD
theme_r4pde

Custom ggplot2 theme based on cowplot::theme_half_open
oruns_test

Runs Test
join_count

Test for Spatial Join Count Statistics
oruns_test_boustrophedon

Boustrophedon Run Test for Binary Matrix
DSI2

Calculate the Disease severity Index (DSI) (frequency of each class)
oruns_test_byrowcol

Runs Test for Each Row and Column of a Binary Matrix
DidymellaWatermelon

DidymellaWatermelon dataset
get_nasapower

Fetch NASA POWER Data for Multiple Locations with a Progress Bar
fit_gradients

Fit Gradient Models to Data
windowpane_tests

Windowpane Tests for Correlation Analysis
windowpane

Window Pane for Epidemiological Analysis
AFSD

Analysis of foci structure and dynamics (AFSD)
FHBWheat

FHBWheat dataset
CompMuCens

Survival analysis for quantitative ordinal scale data.
DSI

Calculate the Disease Severity Index (DSI) (class for each unit)
BPL

Binary Power Law Analysis for Spatial Disease Patterns
FusariumBanana

FusariumBanana dataset
WhiteMoldSoybean

WhiteMoldSoybean dataset
SpatialRandom

SpatialRandom dataset
BlastWheat

BlastWheat dataset
count_subareas

Count the Number of Ones in Subareas of a Matrix
count_subareas_random

Random Subgrid Sampling of a Binary Matrix
BudBlightSoybean

BudBlightSoybean dataset
SpatialAggregated

SpatialAggregated dataset
RustSoybean

RustSoybean dataset