Package: r4pde 0.2.3

r4pde: Tools for Quantitative Plant Disease Epidemiology

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>.

Authors:Emerson Del Ponte [aut, cre]

r4pde_0.2.3.tar.gz
r4pde_0.2.3.zip(r-4.7-any)r4pde_0.2.3.zip(r-4.6-any)r4pde_0.2.3.zip(r-4.5-any)
r4pde_0.2.3.tgz(r-4.6-any)r4pde_0.2.3.tgz(r-4.5-any)
r4pde_0.2.3.tar.gz(r-4.7-any)r4pde_0.2.3.tar.gz(r-4.6-any)
r4pde_0.2.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
r4pde/json (API)

# Install 'r4pde' in R:

install.packages('r4pde', repos = c('https://emdelponte.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/emdelponte/r4pde/issues

Pkgdown/docs site:https://emdelponte.github.io

Datasets:

BlastWheat - BlastWheat dataset
BudBlightSoybean - BudBlightSoybean dataset
DidymellaWatermelon - DidymellaWatermelon dataset
FHBWheat - FHBWheat dataset
FHBWheatBrazil - FHBWheatBrazil dataset
FusariumBanana - FusariumBanana dataset
RustSoybean - RustSoybean dataset
SpatialAggregated - SpatialAggregated dataset
SpatialRandom - SpatialRandom dataset
WhiteMoldSoybean - WhiteMoldSoybean dataset

On CRAN:

botanical-epidemiology data-analysis data-analysis-r epidemics rlang

6.78 score 7 stars 124 scripts 523 downloads 47 exports 96 dependencies

Last updated from:1e27267baa. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	243
source / vignettes	OK	243
linux-release	OK	243
macos-release	OK	196
macos-oldrel	OK	142
windows-devel	OK	217
windows-release	OK	161
windows-oldrel	OK	182
wasm-release	OK	145

Exports:AFSD augment augment_functional_pca augment_functional_rate autoplot.r4pde_functional_pca BPL CompMuCens count_subareas count_subareas_random diagnose_curves DSI DSI2 fit_gradients 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 get_nasapower join_count oruns_test oruns_test_boustrophedon oruns_test_byrowcol plot_AFSD plot_curves plot_dendrogram plot_diagnostics plot_dsp plot_dsp_rank_heatmap plot_functional_instability rank_dsp reconstruct_curves simulate_dsp_data suggest_k theme_r4pde windowpane windowpane_tests

Dependencies:abind askpass backports bit bit64 boot broom car carData cli clipr cluster colorspace cowplot cpp11 crayon crul curl Deriv doBy dplyr farver forecast Formula fracdiff generics ggplot2 glue gtable hms httpcode httr igraph isoband jsonlite labeling lattice lifecycle lme4 lmtest lubridate magrittr MASS Matrix MatrixModels mgcv mime minqa modelr nasapower nlme nloptr nnet numDeriv openssl pbkrtest pillar pkgconfig prettyunits progress purrr quantreg R6 rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack readr reformulas rlang S7 scales SparseM stringi stringr survival sys terra tibble tidyr tidyselect timechange timeDate triebeard tzdb urca urltools utf8 vctrs viridisLite vroom withr yyjsonr zoo

Functional analysis of plant disease progress curves

Introduction | Example Data: Soybean Bud Blight | 1. Fitting Disease Progress Curves: functional_curves() | 2. Instantaneous Velocity and Growth Phenotypes: functional_rate() | 3. Whole-Trajectory Distances and Clustering: functional_distances() | 4. Orthogonal Trajectory Decomposition: functional_pca() | 5. Functional Resistance Profiling: functional_resistance() | 6. Environmental Instability: functional_instability() | Summary

Rendered fromfunctional-analysis.Rmdusingknitr::rmarkdown

Last update: 2026-09-07
Started: 2026-09-07

Help page	Topics
Analysis of foci structure and dynamics (AFSD)	AFSD
Augment generic for functional objects	augment
Augment functional PCA	augment_functional_pca
Augment functional_rate (alias)	augment_functional_rate
Augment functional_rate	augment.functional_rate
BlastWheat dataset	BlastWheat
Binary Power Law Analysis for Spatial Disease Patterns	BPL
BudBlightSoybean dataset	BudBlightSoybean
Survival analysis for quantitative ordinal scale data	CompMuCens
Count the Number of Ones in Subareas of a Matrix	count_subareas
Random Subgrid Sampling of a Binary Matrix	count_subareas_random
Diagnostic tools for functional epidemic curve models	diagnose_curves
DidymellaWatermelon dataset	DidymellaWatermelon
Calculate the Disease Severity Index (DSI) (class for each unit)	DSI
Calculate the Disease severity Index (DSI) (frequency of each class)	DSI2
FHBWheat dataset	FHBWheat
FHBWheatBrazil dataset	FHBWheatBrazil
Fit Gradient Models to Data	fit_gradients
Functional Contrast (Disease Suppression Profiles)	functional_contrast
Fit genotype-specific epidemic trajectories using GAM	functional_curves
Compute pairwise functional distances and cluster curves	functional_distances
Normalized functional instability from fitted functional disease curves	functional_instability functional_instability.functional_curves functional_instability.functional_dsp
Functional principal component analysis of disease progress curves	functional_pca functional_pca.functional_curves functional_pca.functional_dsp
Cluster curves based on FPCA scores	functional_pca_clusters
Instantaneous Disease Progress Rates from Functional Curves	functional_rate
Compute functional resistance and stability-adjusted functional resistance	functional_resistance
Summarize Disease Suppression Profiles	functional_summary
Functional suppression profiles of disease control treatments	functional_suppression_profiles
FusariumBanana dataset	FusariumBanana
Fetch BR-DWGD Data for Multiple Locations	get_brdwgd
Fetch ERA5 Data from Open-Meteo for Multiple Locations	get_era5
Get FPCA eigenfunctions	get_fpca_eigenfunctions
Get FPCA scores	get_fpca_scores
Get FPCA variance explained	get_fpca_variance
Fetch NASA POWER Data for Multiple Locations with a Progress Bar	get_nasapower
Test for Spatial Join Count Statistics	join_count
Runs Test	oruns_test
Boustrophedon Run Test for Binary Matrix	oruns_test_boustrophedon
Runs Test for Each Row and Column of a Binary Matrix	oruns_test_byrowcol
Plot ASFD	plot_AFSD
Plot environment-adjusted epidemic curves by cluster	plot_curves plot_curves.functional_distances plot_curves.functional_dsp
Plot functional dendrogram of epidemic curves	plot_dendrogram
Plot diagnostics for functional epidemic curve models	plot_diagnostics
Plot Disease Suppression Profiles	plot_dsp
Plot DSP Rankings Heatmap	plot_dsp_rank_heatmap
Plot method for functional instability results	plot_functional_instability
Plot functional_curves	plot.functional_curves
Plot functional_rate curves and rates	plot.functional_rate
Plot functional suppression profiles	plot.functional_suppression_profiles
Plot a list of functional suppression profiles	plot.functional_suppression_profiles_list
Plot functional PCA results	autoplot.r4pde_functional_pca plot.r4pde_functional_pca
Print functional_curves	print.functional_curves
Print functional_distances	print.functional_distances
Print a functional_rate object	print.functional_rate
Print functional_resistance	print.functional_resistance
Print functional suppression profiles	print.functional_suppression_profiles
Print a list of functional suppression profiles	print.functional_suppression_profiles_list
Print method for curve diagnostics	print.r4pde_curve_diagnostics
Print method for suggest_k	print.suggest_k
Print summary of functional suppression profiles	print.summary.functional_suppression_profiles
Print summary of a list of functional suppression profiles	print.summary.functional_suppression_profiles_list
Rank Treatments based on Functional DSP Descriptors	rank_dsp
Reconstruct curves using specified FPCA components	reconstruct_curves
RustSoybean dataset	RustSoybean
Simulate Disease Suppression Profile Data	simulate_dsp_data
SpatialAggregated dataset	SpatialAggregated
SpatialRandom dataset	SpatialRandom
Suggest GAM smoothing parameters for epidemic curve models	suggest_k
Summarize a functional_rate object	summary.functional_rate
Summarize functional suppression profiles	summary.functional_suppression_profiles
Summarize a list of functional suppression profiles	summary.functional_suppression_profiles_list
Custom ggplot2 theme based on cowplot::theme_half_open	theme_r4pde
WhiteMoldSoybean dataset	WhiteMoldSoybean
Window Pane for Epidemiological Analysis	windowpane
Windowpane Tests for Correlation Analysis	windowpane_tests

Package: r4pde 0.2.3

r4pde: Tools for Quantitative Plant Disease Epidemiology

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Help Manual

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