G2F_2014_17             Genome to Fields (G2F) GxE panel (2014-2017)
T_matrix                Envirotype Frequency Matrix, Ready for the
                        Kernel Pipeline
W_matrix                Build the Matrix of Environmental Covariables
                        for Reaction Norm
aez_default_url         Default GAEZ Download URL
aez_legend              FAO GAEZ Agro-Ecological Zone Legend
as.data.frame.sim_met   Coerce a Simulated MET to a data.frame
as.matrix.sim_W         Coerce a Simulated Envirome to a Plain Matrix
as.matrix.sim_envirome
                        Coerce a Simulated Envirome Diversity Matrix to
                        a Plain Matrix
best_planting_date      Best planting date per genotype
clay_5_15               Clay content (g/kg) from 5 to 15cm depth for
                        Nairobi, Kenya
cluster_environments    Group environments into mega-environments
                        (clusters)
coverage_summary        Summarise coverage of a scanned region
decompose_kernels       Attach spectral decompositions to a list of
                        dense kernels
env_cluster             Envirotype clustering into mega-environments
env_copula              Copula-based Dependence Indices for an
                        Environmental Covariable Matrix
env_cor                 Extract the Correlation Among Environments
env_cor_heatmap         Correlation Heatmap of Environmental Indices
env_expand              Merge an environmental covariable matrix onto a
                        phenotypic table
env_indices             Build Interval-Resolved Environmental Indices
env_kernel              Easily Building of Environmental Relatedness
                        Kernels
env_loading_curve       Seasonal Loading Curves of an Environmental PC
env_pc_associate        Correlate Environmental PCs with a
                        Per-Environment Variable
env_pca                 PCA of Interval-Resolved Environmental Indices
env_pca_biplot          Environments in Principal Component Space
env_pca_scree           Scree Plot of Environmental PCA
env_phenology           Thermal-Time Phenology: Map Daily Weather onto
                        Developmental Stages
env_risk_profile        Historical Envirotype Risk Profile Across Years
env_target_importance   Environmental drivers of phenotypic/target
                        clustering
env_typing              Environmental Typologies based on Cardinal,
                        Quantilic Limits or Data-Driven Mining
get_AEZ                 Retrieve FAO GAEZ Agro-Ecological Zone
                        Classification for Sites
get_bioclim             WorldClim Bioclimatic Variables at Trial Sites
get_climate_scenario    Future-Climate Envirotyping from CMIP6
                        Downscaled Scenarios
get_elevation           Elevation at Trial Sites from WorldClim 2.1
get_kernel              Envirotype-informed Kernels for
                        Multi-Environment Genomic Prediction
get_soil                Collect Soil Features from SoilGrids (250 m)
get_soil_resumable      Crash-Resilient Wrapper for get_soil()
get_spatial             Extract Point Estimates from Raster Files
get_weather             Easily Collect Worldwide Daily Weather Data
get_weather_hourly      Day/Night Partitioned Hourly Weather from NASA
                        POWER
get_weather_resumable   Crash-Resilient Wrapper for get_weather()
grid_scan               Scan many sites in memory-bounded chunks
kernel_cv               k-fold cross-validation predictive ability
                        (out-of-sample)
kernel_model            Kernel Models for Predicting Phenotypes across
                        Multi-Environment Conditions
kernel_model_clustered
                        Fit kernel_model() informed by an
                        environment-cluster table
kernel_model_mc         Multi-chain fit with convergence diagnostics
                        (Gelman-Rubin R-hat, ESS)
maizeG                  Maize Genomic Relationship Matrix (GRM)
maizeWTH                Maize Weather Data
maizeYield              Maize Phenotypic Data Set
map_scan                Map scanned predictions, or training-network
                        coverage
param_atmospheric       Estimate Atmospheric Parameters Related to
                        Evapotranspiration
param_radiation         Estimate Basic Solar-Radiation Parameters
param_temperature       Estimate Thermal Parameters
phenology_templates     List Built-in Phenology Templates
planting_window_table   Tabulate scan predictions against planting date
plot.sim_W              Diagnostic Plot for a Simulated Envirome
plot.sim_met            Diagnostic Plot for a Simulated MET
plot_planting_window    Plot genotype performance across candidate
                        planting dates
print.T_matrix          Print an Envirotype (T) Matrix
print.kernel_set        Print a kernel set
print.scan_untested_envs
                        Print a Scan of Untested Environments
print.sim_W             Print a Simulated Envirome
print.sim_envirome      Print a Simulated Envirome Diversity Matrix
print.sim_markers       Print a Simulated Marker Matrix
print.sim_met           Print a Simulated Multi-Environment Trial
print.soil_gmm          Print a soil_gmm object
processWTH              Enrich a get_weather() Output with Derived
                        Parameters
project_risk            Compare Envirotype Risk Between Baseline and a
                        Climate Scenario
read_progress_log       Inspect the Progress Log of a Checkpointed Run
restart_from_log        Resume an Interrupted get_weather() or
                        get_soil() Run
scan_spatial_table      Join scan predictions to coordinates
scan_untested_envs      Predict Trained Genotypes at Untested
                        Environments Without Refitting
sim_W                   Simulate an Envirome with a Known Relationship
                        to an Environment Correlation
sim_W_grid              Sweep Envirome Size and Quality (Power
                        Analysis)
sim_envirome            Simulate an Envirome with a Controllable
                        Environmental Diversity
sim_markers             Simulate a Marker Matrix with a Controllable
                        Genetic Diversity
sim_met                 Simulate a Multi-Environment Trial with a Known
                        Genetic Architecture
sim_met_C               Simulate a q x q Genetic Correlation Among
                        Environments
soil_classification     Delineate Soil Zones with a Gaussian Mixture
                        Model
summaryWTH              Basic Summary Statistics for Environmental Data
summary_water_balance   Summarise Water-Balance Output by Environment
                        or Growth Stage
tpe_weights             Target Population of Environments (TPE) Weights
truncate_gxe_kernel     Truncate the GxE kernel to its structural rank.
undecompose_kernels     Drop cached decompositions
varcomp_summary         Validated variance components, heritabilities
                        and genetic correlation.
water_balance           Daily Soil Water Balance and Crop Water-Stress
                        Indices
