In priviere/PPBstats: An R package to perform analysis found within PPB programmes

Family 1 of analysis : Compare different varieties evaluated for selection in different locations. {#family-1}

Family 1 gathers analyses that estimate entry effects. It allows to compare different entries on each location and test for significant differences among entries. Specific analysis including response to selection can also be done. The objective to compare different germplasms on each location for selection.

Decision tree

To compare different germplasms on each location for selection, different scenarios are possible (Figure \@ref(fig:decision-tree-Compare-different-varieties-evaluated-for-selection-in-different-locations-agro)) :

• classic anova (M4a, section \@ref(classic-anova)) based on on fully replicated designs (D1, section \@ref(fully-replicated)),
• spatial analysis (M4b, section \@ref(spatial-analysis)) based on row-column designs (D3, section \@ref(row-column)),
• mixed models (M5, section\@ref(ibd-model)) for incomplete blocks designs (D2, section \@ref(ibd)),
• bayesian hierarchical model intra-location (M7a, section \@ref(model-1)) based on satellite-regional farms designs (D4, section \@ref(rf-sf)).

It can be completed by organoleptic analysis (section \@ref(organoleptic)). Based on these analysis, specific objective including response to selection analysis can also be done.

knitr::include_graphics("figures/decision-tree_Compare-different-varieties-evaluated-for-selection-in-different-locations_agro.png")

Workflow and function relations in PPBstats regarding family 1 of analysis

Figure \@ref(fig:main-workflow-family-1) displays the functions and their relationships. Table \@ref(tab:function-descriptions-workflow-family-1) describes each of the main functions.

You can have more information for each function by typing ?function_name in your R session. Note that check_model(), mean_comparison() and plot() are S3 method. Therefore, you should type ?check_model, ?mean_comparison or ?plot.PPBstats to have general features and then see in details for specific functions.

knitr::include_graphics("figures/main-functions-agro-family-1.png")

| function name | description | | --- | --- | | design_experiment | Provides experimental design for the different situations corresponding to the choosen family of analysis | | format_data_PPBstats | Check and format the data to be used in PPBstats functions | | model_bh_intra-location | Run Hierarchical Bayesian intra-location model | | model_spatial | Run spatial row and column model | | model_anova | Run classic anova model | | check_model | Check if the model went well | | mean_comparisons | Get mean comparisons | | plot | Build ggplot objects to visualize output | Table: (#tab:function-descriptions-workflow-family-1) Function description.

priviere/PPBstats documentation built on May 6, 2021, 1:20 a.m.