functional_rate(): Estimates instantaneous rates
of plant disease progress () and associated uncertainty from epidemic
trajectories fitted by functional_curves(). Supports
response and link scale derivatives via GAM linear predictor matrix
differences, handles boundary conditions without extrapolation, accounts
for zero-epidemic curves and negative rates, and computes key rate
phenotypes (, , growth duration, cumulative positive growth, and growth
windows). Includes S3 methods: print(),
summary(), plot(), and
augment().functional_curves(): Fixed smooth term label inspection
during prediction so that .unit experimental unit and block
random effects are correctly identified and supplied to
predict.gam().functional_contrast(), functional_summary(),
plot_dsp(), rank_dsp(),
plot_dsp_rank_heatmap(), and
simulate_dsp_data().functional_curves(): Updated the GAM formula to fit
independent smooths per treatment by default
(trt + s(time, by=trt)), avoiding artifactual drops
(“caimento”) at the tails of flat curves. Added the
global_smooth parameter to allow users to opt-in to the
previous Global-Specific smoothing behavior.simulate_dsp_data(): Adjusted the amplitudes of the
simulated suppression profiles (“Early”, “Late”, “Persistent”) to
achieve exactly a 70% reduction in AUDPC compared to the unsprayed
control, representing a realistic fungicide efficacy scenario._pkgdown.yml to include the newly exported
functional PCA and DSP functions in the “Functional Analysis” reference
index, resolving site build errors.functional_curves(), functional_distances(),
functional_pca(), functional_resistance(), and
related methods.functional_pca(): Performs functional principal
component analysis on fitted disease progress curves to decompose
variation among epidemic trajectories into orthogonal temporal
components. Includes plotting and extractor functions.functional_curves(): Fits genotype-specific epidemic
trajectories using GAM, with support for genotype-level covariates.functional_distances(): Computes pairwise functional
distances among fitted curves and performs hierarchical clustering and
permutation testing.functional_resistance(): Calculates Functional
Resistance Index (FRI) and Stability-Adjusted Functional Resistance
Index (SAFRI) with support for stratified rankings and
bootstrap-supported classification.suggest_k(): Helper function to recommend GAM smoothing
parameters (k_smooth, k_trt,
k_env, gamma) based on data structure;
supports tidy-eval column names and can infer replication from a data
frame.heading_group) to adjust functional curves and resistance
rankings, allowing for better distinction between genetic resistance and
phenological escape.diagnose_curves(), plot_curves(),
and plot_dendrogram() to support the new functional
analysis object classes.functional_instability() for computing normalized
functional instability (NFI) of genotype-by-environment epidemic curves,
with optional decomposition into spatial and temporal components.plot_functional_instability() for visualizing
overall, spatial, and temporal NFI results as bar charts.get_era5() for retrieving ERA5 reanalysis weather
data via Open-Meteo API.get_brdwgd() for extracting daily weather data
from the Brazilian Daily Weather Gridded Data (BR-DWGD) NetCDF
files.r4pde package.
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