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

Introduction

Describing the topology of networks of seed circulation is interesting since it gives insight on how exchanges are organized within a PPB programme or a Community Seed Bank[@bioversity_csb_2015][@pautasso_seed_2013]. Analysis can be done at several geographical or organizing scales, for example local, regional or national.

Two types of network are handled within PPBstats :

• unipart network where nodes are:

  • seed lots (i.e. a combinaison of a germplasm in a given location a given year) and edges are relationships such as diffusion, mixture, reproduction, crosses or selection for example.
  • locations and edges are diffusion events between locations

• bipart network where nodes are either location or germplasm

Workflow and function relations in PPBstats regarding network analysis

The workflow is very simple as only descriptive analysis can be done based on network format (Figure \@ref(fig:decision-tree-Study-network-of-seed-circulation)).

knitr::include_graphics("figures/decision-tree_Study-network-of-seed-circulation.png")

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

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

knitr::include_graphics("figures/main-functions-network.png")

| function name | description | |---|---| |format_data_PPBstats | Check and format the data to be used in PPBstats functions| | plot | Build ggplot objects to visualize output | Table: (#tab:function-descriptions-workflow-network) Main function descriptions.

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