Package: r4pde 0.2.1

r4pde: Companion to R for Plant Disease Epidemiology Book

Datasets and utility functions to support the book "R for Plant Disease Epidemiology" (R4PDE). It includes functions for quantifying disease, assessing spatial patterns, and modeling plant disease epidemics based on weather predictors. These tools are intended for teaching and research in plant disease epidemiology. 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_0.2.1.tar.gz
r4pde_0.2.1.zip(r-4.7)r4pde_0.2.1.zip(r-4.6)r4pde_0.2.1.zip(r-4.5)
r4pde_0.2.1.tgz(r-4.6-any)r4pde_0.2.1.tgz(r-4.5-any)
r4pde_0.2.1.tar.gz(r-4.7-any)r4pde_0.2.1.tar.gz(r-4.6-any)
r4pde_0.2.1.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:

On CRAN:

Conda:

botanical-epidemiologydata-analysisdata-analysis-repidemicsrlang

5.65 score 6 stars 114 scripts 257 downloads 44 exports 96 dependencies

Last updated from:4c52d497ee. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK274
source / vignettesOK284
linux-release-x86_64OK267
macos-release-arm64OK131
macos-oldrel-arm64OK137
windows-develOK609
windows-releaseOK189
windows-oldrelOK642
wasm-releaseOK152

Exports:AFSDaugment_functional_pcaautoplot.r4pde_functional_pcaBPLcompare_curvesCompMuCenscount_subareascount_subareas_randomdiagnose_curvesDSIDSI2fit_gradientsfunctional_contrastfunctional_curvesfunctional_distancesfunctional_instabilityfunctional_pcafunctional_pca_clustersfunctional_resistancefunctional_summaryget_brdwgdget_era5get_fpca_eigenfunctionsget_fpca_scoresget_fpca_varianceget_nasapowerjoin_countoruns_testoruns_test_boustrophedonoruns_test_byrowcolplot_AFSDplot_curvesplot_dendrogramplot_diagnosticsplot_dspplot_dsp_rank_heatmapplot_functional_instabilityrank_dspreconstruct_curvessimulate_dsp_datasuggest_ktheme_r4pdewindowpanewindowpane_tests

Dependencies:abindaskpassbackportsbitbit64bootbroomcarcarDataclicliprcolorspacecowplotcpp11crayoncrulcurlDerivdoBydplyrfarverforecastFormulafracdiffgenericsggplot2gluegtablehmshttpcodehttrigraphisobandjsonlitelabelinglatticelifecyclelme4lmtestlubridatemagrittrMASSMatrixMatrixModelsmgcvmicrobenchmarkmimeminqamodelrnasapowernlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigprettyunitsprogresspurrrquantregR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreadrreformulasrlangS7scalesSparseMstringistringrsurvivalsysterratibbletidyrtidyselecttimechangetimeDatetriebeardtzdburcaurltoolsutf8vctrsviridisLitevroomwithryyjsonrzoo

Readme and manuals

Help Manual

Help pageTopics
Analysis of foci structure and dynamics (AFSD)AFSD
Augment functional PCAaugment_functional_pca
BlastWheat datasetBlastWheat
Binary Power Law Analysis for Spatial Disease PatternsBPL
BudBlightSoybean datasetBudBlightSoybean
Compare epidemic curves using GAM smoothing, functional distances, clustering, and optional permutation/bootstrappingcompare_curves
Survival analysis for quantitative ordinal scale dataCompMuCens
Count the Number of Ones in Subareas of a Matrixcount_subareas
Random Subgrid Sampling of a Binary Matrixcount_subareas_random
Diagnostic tools for functional epidemic curve modelsdiagnose_curves
DidymellaWatermelon datasetDidymellaWatermelon
Calculate the Disease Severity Index (DSI) (class for each unit)DSI
Calculate the Disease severity Index (DSI) (frequency of each class)DSI2
FHBWheat datasetFHBWheat
FHBWheatBrazil datasetFHBWheatBrazil
Fit Gradient Models to Datafit_gradients
Functional Contrast (Disease Suppression Profiles)functional_contrast
Fit genotype-specific epidemic trajectories using GAMfunctional_curves
Compute pairwise functional distances and cluster curvesfunctional_distances
Normalized functional instability from compare_curves outputfunctional_instability functional_instability.functional_curves functional_instability.functional_dsp
Functional principal component analysis of disease progress curvesfunctional_pca functional_pca.functional_curves functional_pca.functional_dsp
Cluster curves based on FPCA scoresfunctional_pca_clusters
Compute functional resistance and stability-adjusted functional resistancefunctional_resistance
Summarize Disease Suppression Profilesfunctional_summary
FusariumBanana datasetFusariumBanana
Fetch BR-DWGD Data for Multiple Locationsget_brdwgd
Fetch ERA5 Data from Open-Meteo for Multiple Locationsget_era5
Get FPCA eigenfunctionsget_fpca_eigenfunctions
Get FPCA scoresget_fpca_scores
Get FPCA variance explainedget_fpca_variance
Fetch NASA POWER Data for Multiple Locations with a Progress Barget_nasapower
Test for Spatial Join Count Statisticsjoin_count
Runs Testoruns_test
Boustrophedon Run Test for Binary Matrixoruns_test_boustrophedon
Runs Test for Each Row and Column of a Binary Matrixoruns_test_byrowcol
Plot ASFDplot_AFSD
Plot environment-adjusted epidemic curves by clusterplot_curves plot_curves.functional_distances plot_curves.functional_dsp plot_curves.r4pde_compare_curves
Plot functional dendrogram of epidemic curvesplot_dendrogram
Plot diagnostics for functional epidemic curve modelsplot_diagnostics
Plot Disease Suppression Profilesplot_dsp
Plot DSP Rankings Heatmapplot_dsp_rank_heatmap
Plot method for functional instability resultsplot_functional_instability
Plot functional_curvesplot.functional_curves
Plot method for compare_curves objectsplot.r4pde_compare_curves
Plot functional PCA resultsautoplot.r4pde_functional_pca plot.r4pde_functional_pca
Print functional_curvesprint.functional_curves
Print functional_distancesprint.functional_distances
Print functional_resistanceprint.functional_resistance
Print method for curve diagnosticsprint.r4pde_curve_diagnostics
Print method for suggest_kprint.suggest_k
Rank Treatments based on Functional DSP Descriptorsrank_dsp
Reconstruct curves using specified FPCA componentsreconstruct_curves
RustSoybean datasetRustSoybean
#' Simulate Disease Suppression Profile Datasimulate_dsp_data
SpatialAggregated datasetSpatialAggregated
SpatialRandom datasetSpatialRandom
Suggest GAM smoothing parameters for epidemic curve modelssuggest_k
Custom ggplot2 theme based on cowplot::theme_half_opentheme_r4pde
WhiteMoldSoybean datasetWhiteMoldSoybean
Window Pane for Epidemiological Analysiswindowpane
Windowpane Tests for Correlation Analysiswindowpane_tests