Package index • r4pde

Disease Quantification

Functions for calculating disease indices and survival-based metrics.

CompMuCens(): Survival analysis for quantitative ordinal scale data
DSI(): Calculate the Disease Severity Index (DSI) (class for each unit)
DSI2(): Calculate the Disease severity Index (DSI) (frequency of each class)

Spatial analysis

Functions to detect and quantify spatial structure in disease data.

AFSD(): Analysis of foci structure and dynamics (AFSD)
BPL(): Binary Power Law Analysis for Spatial Disease Patterns
count_subareas(): Count the Number of Ones in Subareas of a Matrix
count_subareas_random(): Random Subgrid Sampling of a Binary Matrix
join_count(): Test for Spatial Join Count Statistics
oruns_test(): Runs Test
oruns_test_boustrophedon(): Boustrophedon Run Test for Binary Matrix
oruns_test_byrowcol(): Runs Test for Each Row and Column of a Binary Matrix
plot_AFSD(): Plot ASFD
windowpane(): Window Pane for Epidemiological Analysis
windowpane_tests(): Windowpane Tests for Correlation Analysis

Disease modeling

Functions for fitting gradient models and retrieving climate data.

fit_gradients(): Fit Gradient Models to Data
get_brdwgd(): Fetch BR-DWGD Data for Multiple Locations
get_era5(): Fetch ERA5 Data from Open-Meteo for Multiple Locations
get_nasapower(): Fetch NASA POWER Data for Multiple Locations with a Progress Bar

Datasets

Datasets used in the examples and analyses.

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

Miscellaneous

Utility functions for plotting and customization.

theme_r4pde(): Custom ggplot2 theme based on cowplot::theme_half_open

Functional Analysis

Functions for functional modeling and comparison of epidemic curves.

augment_functional_pca(): Augment functional PCA
compare_curves(): Compare epidemic curves using GAM smoothing, functional distances, clustering, and optional permutation/bootstrapping
functional_contrast(): Functional Contrast (Disease Suppression Profiles)
functional_curves(): Fit genotype-specific epidemic trajectories using GAM
functional_distances(): Compute pairwise functional distances and cluster curves
functional_instability(): Normalized functional instability from compare_curves output
functional_pca(): Functional principal component analysis of disease progress curves
functional_pca_clusters(): Cluster curves based on FPCA scores
functional_resistance(): Compute functional resistance and stability-adjusted functional resistance
functional_summary(): Summarize Disease Suppression Profiles
get_fpca_eigenfunctions(): Get FPCA eigenfunctions
get_fpca_scores(): Get FPCA scores
get_fpca_variance(): Get FPCA variance explained
plot(<functional_curves>): Plot functional_curves
plot(<r4pde_compare_curves>): Plot method for compare_curves objects
plot(<r4pde_functional_pca>) autoplot.r4pde_functional_pca(): Plot functional PCA results
plot_curves(): Plot environment-adjusted epidemic curves by cluster
plot_dendrogram(): Plot functional dendrogram of epidemic curves
plot_dsp(): Plot Disease Suppression Profiles
plot_dsp_rank_heatmap(): Plot DSP Rankings Heatmap
plot_functional_instability(): Plot method for functional instability results
print(<functional_curves>): Print functional_curves
print(<functional_distances>): Print functional_distances
print(<functional_resistance>): Print functional_resistance
print(<suggest_k>): Print method for suggest_k
rank_dsp(): Rank Treatments based on Functional DSP Descriptors
reconstruct_curves(): Reconstruct curves using specified FPCA components
simulate_dsp_data(): #' Simulate Disease Suppression Profile Data
suggest_k(): Suggest GAM smoothing parameters for epidemic curve models

Diagnostics

diagnose_curves(): Diagnostic tools for functional epidemic curve models
plot_diagnostics(): Plot diagnostics for functional epidemic curve models
print(<r4pde_curve_diagnostics>): Print method for curve diagnostics