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

Family 2 of analysis : Study the response of varieties under selection over several environments {#family-2}

Family 2 gathers analyses that estimate germplasm and location and interaction effects. This is to analyse the response over a network of locations. Estimation of environment and year effects is possible depending of the model. Specific analysis including migrant and residant can also be done. It allows to study the response of germplasm over several location or environments. The objectives is to study response of germplasm over several locations for selection.

Decision tree

To study response of germplasm over several locations for selection, different scenario are possible (Figure \@ref(fig:decision-tree-Study-the-response-of-varieties-under-selection-over-several-environments)) :

• AMMI and GGE (M6, sections \@ref(ammi) and \@ref(gge)) based on on fully replicated designs (D1, section \@ref(fully-replicated)),
• bayesian hierarchical model $G \times E$ (M7b, section \@ref(model-2)) based on satellite-regional farms designs (D4, section \@ref(rf-sf)),

It can be completed by specific analysis such as migrant-residant (section \@ref(migrant-residant)) which corresponds to a specific objective : study migrant and residant effect, where migrant in a location refers to a germplasm that has not been grown or selected in a given location and resident in a location refers to a germplasm that has been grown or selected in a given location.

knitr::include_graphics("figures/decision-tree_Study-the-response-of-varieties-under-selection-over-several-environments.png")

Workflow and function relations in PPBstats regarding family 2 of analysis

Figure \@ref(fig:main-workflow-family-2) displays the functions and their relationships. Table \@ref(tab:function-descriptions-workflow-family-2) 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(), biplot_data() and plot() are S3 method. Therefore, you should type ?check_model, ?mean_comparison, ?biplot_data or ?plot.PPBstats to have general features and then see in details for specific functions.

knitr::include_graphics("figures/main-functions-agro-family-2.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_GxE | Run Hierarchical Bayesian GxE model | | model_GxE | Run AMMI or GGE model | | check_model | Check if the model went well | | mean_comparisons | Get mean comparisons | | parameter_groups | Get groups of parameters based on multivariate analysis | | cross_validation_model_bh_GxE | Run complete cross validation with Hierarchical Bayesian GxE model | | predict_the_past_model_bh_GxE | predict values of germplasms in environments where they have not been grown based on Hierarchical Bayesian GxE model | | biplot_data | Compute ecovalence and format PCA results regarding $G \times E$ models | | plot | Build ggplot objects to visualize output | Table: (#tab:function-descriptions-workflow-family-2) Function description.

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