Package index • r4pde

Disease measurement and quantification

Functions for calculating disease severity indices and survival-based censored 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)

Epidemic dynamics and functional analysis

Functions for fitting, differentiating, comparing, and classifying functional disease progress curves.

functional_curves(): Fit genotype-specific epidemic trajectories using GAM
functional_rate(): Instantaneous Disease Progress Rates from Functional Curves
functional_distances(): Compute pairwise functional distances and cluster curves
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_instability(): Normalized functional instability from fitted functional disease curves
reconstruct_curves(): Reconstruct curves using specified FPCA components
suggest_k(): Suggest GAM smoothing parameters for epidemic curve models
plot_curves(): Plot environment-adjusted epidemic curves by cluster
plot_dendrogram(): Plot functional dendrogram of epidemic curves
plot_functional_instability(): Plot method for functional instability results
diagnose_curves(): Diagnostic tools for functional epidemic curve models
plot_diagnostics(): Plot diagnostics for functional epidemic curve models
augment(): Augment generic for functional objects
augment(<functional_rate>): Augment functional_rate
augment_functional_rate(): Augment functional_rate (alias)
augment_functional_pca(): Augment functional PCA
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(<functional_rate>): Plot functional_rate curves and rates
plot(<r4pde_functional_pca>) autoplot.r4pde_functional_pca(): Plot functional PCA results
print(<functional_curves>): Print functional_curves
print(<functional_distances>): Print functional_distances
print(<functional_rate>): Print a functional_rate object
print(<functional_resistance>): Print functional_resistance
print(<r4pde_curve_diagnostics>): Print method for curve diagnostics
print(<suggest_k>): Print method for suggest_k
summary(<functional_rate>): Summarize a functional_rate object

Disease management and suppression

Tools for evaluating Disease Suppression Profiles (DSP) and treatment efficacy trajectories.

functional_contrast(): Functional Contrast (Disease Suppression Profiles)
functional_summary(): Summarize Disease Suppression Profiles
functional_suppression_profiles(): Functional suppression profiles of disease control treatments
rank_dsp(): Rank Treatments based on Functional DSP Descriptors
plot_dsp(): Plot Disease Suppression Profiles
plot_dsp_rank_heatmap(): Plot DSP Rankings Heatmap
simulate_dsp_data(): #' Simulate Disease Suppression Profile Data
plot(<functional_suppression_profiles>): Plot functional suppression profiles
plot(<functional_suppression_profiles_list>): Plot a list of functional suppression profiles
print(<functional_suppression_profiles>): Print functional suppression profiles
print(<functional_suppression_profiles_list>): Print a list of functional suppression profiles
print(<summary.functional_suppression_profiles>): Print summary of functional suppression profiles
print(<summary.functional_suppression_profiles_list>): Print summary of a list of functional suppression profiles
summary(<functional_suppression_profiles>): Summarize functional suppression profiles
summary(<functional_suppression_profiles_list>): Summarize a list of functional suppression profiles

Spatial epidemiology

Methods for spatial pattern analysis, foci dynamics, runs tests, and join-count statistics.

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
fit_gradients(): Fit Gradient Models to Data
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

Weather and environmental data

Tools for downloading and extracting gridded and station weather 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

Utilities and datasets

Package plotting theme and epidemiological research datasets.

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