Envirotyping for Quantitative Genetics and Plant Breeding

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Documentation for package ‘EnvRtype’ version 0.1.3

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package README

Help Pages

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_envirome	Coerce a Simulated Envirome Diversity Matrix to a Plain Matrix
as.matrix.sim_W	Coerce a Simulated Envirome 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.default	Extract the Correlation Among Environments
env_cor.matrix	Extract the Correlation Among Environments
env_cor.sim_envirome	Extract the Correlation Among Environments
env_cor.sim_met	Extract the Correlation Among Environments
env_cor.sim_W	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_pca	PCA of Interval-Resolved Environmental Indices
env_pca_biplot	Environments in Principal Component Space
env_pca_scree	Scree Plot of Environmental PCA
env_pc_associate	Correlate Environmental PCs with a Per-Environment Variable
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
G2F_2014_17	Genome to Fields (G2F) GxE panel (2014-2017)
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_met	Diagnostic Plot for a Simulated MET
plot.sim_W	Diagnostic Plot for a Simulated Envirome
plot_planting_window	Plot genotype performance across candidate planting dates
print.kernel_set	Print a kernel set
print.scan_untested_envs	Print a Scan of Untested Environments
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.sim_W	Print a Simulated Envirome
print.soil_gmm	Print a soil_gmm object
print.T_matrix	Print an Envirotype (T) Matrix
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
show_phenology	List Built-in Phenology Templates
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
sim_W	Simulate an Envirome with a Known Relationship to an Environment Correlation
sim_W_grid	Sweep Envirome Size and Quality (Power Analysis)
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.
T_matrix	Envirotype Frequency Matrix, Ready for the Kernel Pipeline
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
W_matrix	Build the Matrix of Environmental Covariables for Reaction Norm