Package index • breedtools

Choose a design

Start from the number of entries and the field space you have.

design_options(): Suggest trial layouts from the number of entries and available field space
augmented_row_column_capacity(): Calculate augmented row-column design capacity
augmented_row_column_layouts(): List the analyzable layouts of an augmented row-column field
augmented_prep_parameters(): Feasible parameters for augmented p-rep constructions

Unreplicated entries plus replicated checks in rows, columns and blocks (Federer, Nair and Raghavarao 1975; Piepho and Williams 2016).

augmented_row_column_design(): Generate an augmented row-column field design
plot_augmented_row_column_design(): Plot an augmented row-column design grid
analyze_augmented_row_column_design(): Analyze an augmented row-column design
print(<augmented_row_column_analysis>): Print augmented row-column analysis

Multi-location partially replicated designs (Williams, Piepho and Whitaker 2011).

augmented_prep_design(): Generate an augmented p-rep design
augmented_prep_concurrence(): Calculate pairwise concurrence for a p-rep design
plot_augmented_prep_design(): Plot an augmented p-rep design grid
analyze_augmented_prep_design(): Analyze an augmented p-rep design
analyze_augmented_prep_two_stage(): Two-stage analysis of a multi-location augmented p-rep trial
print(<augmented_prep_analysis>): Print augmented p-rep analysis
print(<augmented_prep_two_stage>): Print a two-stage p-rep analysis

Fully replicated spatial designs (Williams, John and Whitaker 2006).

resolvable_row_column_design(): Generate a resolvable (spatial) row-column design
resolvable_row_column_efficiency(): Efficiency of a resolvable row-column design
plot_resolvable_row_column_design(): Plot a resolvable row-column design
analyze_resolvable_row_column(): Analyze a resolvable row-column trial with RC, LV + RC or AR + RC models
print(<resolvable_row_column_analysis>): Print a resolvable row-column analysis

Trait plots, outliers, two-stage and single-stage analysis of several trials, and the values to store from them.

plot_trait(): Plot a trait: distribution and field map
find_outliers(): Find outliers in trait data (IQR rule)
remove_outliers(): Remove outliers from trait data (IQR rule)
analyze_two_stage(): Two-stage analysis of a multi-location trial, for any design
analyze_single_stage(): Single-stage analysis of several trials
compare_first_stage(): Compare raw and first-stage adjusted values
first_stage_values(): First-stage plot values from an analysis
second_stage_values(): Second-stage genotype values from analyses
prediction_accuracy(): Accuracy of adjusted means against known values
print(<two_stage_analysis>): Print a two-stage analysis
print(<single_stage_analysis>): Print a single-stage analysis

Verify a design and record a checklist of what was tested.

Log in through BrAPI, list programs, folders and locations, and check names before designing.

breedbase_login(): Log in to a Breedbase server
breedbase_programs() breedbase_folders() breedbase_locations(): List breeding programs, folders and locations in Breedbase
breedbase_check(): Check names in Breedbase before building a design
breedbase_statistics(): List the statistic terms of Breedbase (SGNSTAT ontology)
breedbase_adjusted_trait(): Find or create the Breedbase trait for adjusted values
breedbase_refresh(): Refresh the Breedbase phenotype cache

Convert agricolae designs, preview the payload, and save trials with their plots.

prepare_breedbase_trial(): Prepare an agricolae design and trial information for Breedbase
as_breedbase_design(): Convert an agricolae field book for saving to Breedbase
save_breedbase(): Save a design to Breedbase
breedbase_trial_plots(): Read the plots of a trial saved in Breedbase
phenotype_template(): Phenotyping template with the Breedbase plot names of a design

Read and save phenotypic data, first-stage plot values and second-stage analyses.

breedbase_phenotypes(): Read phenotypic data of trials from Breedbase
save_breedbase_phenotypes(): Save phenotypic data to Breedbase
save_breedbase_first_stage(): Save first-stage results to Breedbase as a trait of the field plots
save_breedbase_analysis(): Save analysis results to Breedbase as an analysis
add_breedbase_analysis_values(): Add results to an analysis that is already in Breedbase

Read Breedbase phenotype files, test homogeneity of error variances (Hartley’s Fmax) and group environments by GxE (Lin 1982).

read_breedbase_file(): Read phenotype or design data from Excel, CSV, or tab-delimited files
read_breedbase_excel(): Read a Breedbase Excel phenotype file
prepare_breedbase_pheno(): Prepare Breedbase phenotype data for multi-environment analysis
run_breedbase_variance_check(): Run Breedbase multi-location phenotype variance check
run_environment_stratification(): Run Lin-style environment stratification
run_breedbase_environment_stratification(): Run Lin-style environment stratification from a Breedbase phenotype file
read_locations(): Load location coordinates
map_environment_groups(): Create a map of environment groups

analyze_environment_anova(): Run individual ANOVA by environment
analyze_one_environment(): Analyze one environment using ANOVA
hartley_fmax_test(): Hartley Fmax test for residual variance homogeneity
hartley_critical_sim(): Simulate Hartley Fmax critical value
make_environment_groups(): Test all compatible environment groups using Hartley Fmax
get_compatible_groups(): Get compatible environment groups
get_maximal_groups(): Select maximal compatible environment groups
harmonic_mean(): Calculate harmonic mean

prepare_environment_stratification_data(): Prepare phenotype data for Lin environment stratification
detect_design(): Detect field trial design for environment stratification
prepare_design_factors(): Prepare design factors
calculate_environment_stratification_anova(): Calculate design-aware ANOVA
lin_group_environments(): Group environments using Lin-style GE compatibility testing
lin_test_group(): Test one Lin environment group
lin_ss_ge(): Calculate Lin genotype-by-environment sum of squares
lin_error_mse(): Calculate residual error MSE for a Lin environment group
complete_environment_info(): Complete environment metadata
add_environment_metadata(): Add environment metadata to result table
add_pairwise_environment_metadata(): Add environment metadata to pairwise Lin results
environment_summary_by_group(): Summarize environment names by group

breedtools breedtools-package: breedtools: design, analysis and 'Breedbase' storage of plant breeding trials