Tools for Quantitative Plant Disease Epidemiology
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Documentation for package ‘r4pde’ version 0.2.2
Help Pages
| AFSD | Analysis of foci structure and dynamics (AFSD) |
| augment | Augment generic for functional objects |
| augment.functional_rate | Augment functional_rate |
| augment_functional_pca | Augment functional PCA |
| augment_functional_rate | Augment functional_rate (alias) |
| autoplot.r4pde_functional_pca | Plot functional PCA results |
| BlastWheat | BlastWheat dataset |
| BPL | Binary Power Law Analysis for Spatial Disease Patterns |
| BudBlightSoybean | BudBlightSoybean dataset |
| CompMuCens | Survival analysis for quantitative ordinal scale data |
| count_subareas | Count the Number of Ones in Subareas of a Matrix |
| count_subareas_random | Random Subgrid Sampling of a Binary Matrix |
| diagnose_curves | Diagnostic tools for functional epidemic curve models |
| DidymellaWatermelon | DidymellaWatermelon dataset |
| DSI | Calculate the Disease Severity Index (DSI) (class for each unit) |
| DSI2 | Calculate the Disease severity Index (DSI) (frequency of each class) |
| FHBWheat | FHBWheat dataset |
| FHBWheatBrazil | FHBWheatBrazil dataset |
| fit_gradients | Fit Gradient Models to Data |
| 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 fitted functional disease curves |
| functional_instability.functional_curves | Normalized functional instability from fitted functional disease curves |
| functional_instability.functional_dsp | Normalized functional instability from fitted functional disease curves |
| functional_pca | Functional principal component analysis of disease progress curves |
| functional_pca.functional_curves | Functional principal component analysis of disease progress curves |
| functional_pca.functional_dsp | Functional principal component analysis of disease progress curves |
| functional_pca_clusters | Cluster curves based on FPCA scores |
| functional_rate | Instantaneous Disease Progress Rates from Functional Curves |
| functional_resistance | Compute functional resistance and stability-adjusted functional resistance |
| functional_summary | Summarize Disease Suppression Profiles |
| functional_suppression_profiles | Functional suppression profiles of disease control treatments |
| FusariumBanana | FusariumBanana dataset |
| get_brdwgd | Fetch BR-DWGD Data for Multiple Locations |
| get_era5 | Fetch ERA5 Data from Open-Meteo for Multiple Locations |
| get_fpca_eigenfunctions | Get FPCA eigenfunctions |
| get_fpca_scores | Get FPCA scores |
| get_fpca_variance | Get FPCA variance explained |
| get_nasapower | Fetch NASA POWER Data for Multiple Locations with a Progress Bar |
| 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.functional_curves | Plot functional_curves |
| plot.functional_rate | Plot functional_rate curves and rates |
| plot.functional_suppression_profiles | Plot functional suppression profiles |
| plot.functional_suppression_profiles_list | Plot a list of functional suppression profiles |
| plot.r4pde_functional_pca | Plot functional PCA results |
| plot_AFSD | Plot ASFD |
| plot_curves | Plot environment-adjusted epidemic curves by cluster |
| plot_curves.functional_distances | Plot environment-adjusted epidemic curves by cluster |
| plot_curves.functional_dsp | Plot environment-adjusted epidemic curves by cluster |
| plot_dendrogram | Plot functional dendrogram of epidemic curves |
| plot_diagnostics | Plot diagnostics for functional epidemic curve models |
| 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_rate | Print a functional_rate object |
| print.functional_resistance | Print functional_resistance |
| print.functional_suppression_profiles | Print functional suppression profiles |
| print.functional_suppression_profiles_list | Print a list of functional suppression profiles |
| print.r4pde_curve_diagnostics | Print method for curve diagnostics |
| print.suggest_k | Print method for suggest_k |
| 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 |
| rank_dsp | Rank Treatments based on Functional DSP Descriptors |
| reconstruct_curves | Reconstruct curves using specified FPCA components |
| RustSoybean | RustSoybean dataset |
| simulate_dsp_data | #' Simulate Disease Suppression Profile Data |
| SpatialAggregated | SpatialAggregated dataset |
| SpatialRandom | SpatialRandom dataset |
| suggest_k | Suggest GAM smoothing parameters for epidemic curve models |
| summary.functional_rate | Summarize a functional_rate object |
| summary.functional_suppression_profiles | Summarize functional suppression profiles |
| summary.functional_suppression_profiles_list | Summarize a list of functional suppression profiles |
| theme_r4pde | Custom ggplot2 theme based on cowplot::theme_half_open |
| WhiteMoldSoybean | WhiteMoldSoybean dataset |
| windowpane | Window Pane for Epidemiological Analysis |
| windowpane_tests | Windowpane Tests for Correlation Analysis |