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

Bipart network analysis

This section deals with bipart network that represents "which location has which germplasm which year".

Steps with `PPBstats`

Format the data with format_data_PPBstats()
get descriptive plot with plot()

Format the data

The format required is a data frame with the following compulsory columns as factor: "germplasm", "location", "year". Possible options are : "long", "lat" to get map representation

Note that data frame with unipart network for seed lots format can also be used.

The format of the data are checked by the function format_data_PPBstats() with the following arguments :

type : "data_network"
network_part : "bipart"
vertex_type : c("germplasm", "location")

The function returns list of igraph object^[http://igraph.org/r/] coming from igraph::graph_from_data_frame().

data(data_network_unipart_sl)
head(data_network_unipart_sl)

net_bipart = format_data_PPBstats(
  type = "data_network",
  data = data_network_unipart_sl, 
  network_part = "bipart", 
  vertex_type =  c("germplasm", "location")
  )

For bipart network, it returns a list with as many elements as year in the data as well as all years merged in the first element of the list. If no year are provided into the data, all information are merged.

names(net_bipart)

Describe the data

The different representations are done with the plot() function.

p_net = plot(net_bipart, plot_type = "network", 
                          labels_on = TRUE, labels_size = 4)
names(p_net) # one element per year, the first element with all the data
p_net$`2009`

With barplots, it represents the number of edges per vertex for each germplasm and each location.

p_bar = plot(net_bipart, plot_type = "barplot")
names(p_bar) # one element per year, the first element with all the data
p_bar = p_bar$`2005-2006-2007-2008-2009`$barplot
p_bar$germplasm
p_bar$location

Location present on the network can be displayed on a map with plot_type = "map". When using map, do not forget to use credit : Map tiles by Stamen Design, under CC BY 3.0. Data by OpenStreetMap, under ODbL.

p_map = PPBstats:::plot.data_network(net_bipart[1], plot_type = "map", labels_on = "location")
p_map$`2005-2006-2007-2008-2009`

As well as plot information regarding a variable on map with a pie with plot_type = "map" and by setting arguments data_to_pie and vec_variables:

# y1 is a quantitative variable
p_map_pies_y1 = PPBstats:::plot.data_network(net_bipart[1], data_to_pie, plot_type = "map", vec_variables = "y1")
p_map_pies_y1$`2005-2006-2007-2008-2009`

# y2 is a qualitative variable
p_map_pies_y2 = PPBstats:::plot.data_network(net_bipart[1], data_to_pie, plot_type = "map", vec_variables = "y2")
p_map_pies_y2$`2005-2006-2007-2008-2009`