Query interactions

Search for specific interactions using a keyword or a specific type of interactions (e.g. mutualism). If the query is a character string, then all character columns in the table are searched and the entries for which at least one partial match was found are returned. Alternatively, a named list can be used to look for an exact match in a specific column (see Details section)

Usage

search_interactions(
  query,
  type = NULL,
  expand_node = FALSE,
  verbose = TRUE,
  ...
)

Arguments

query

either a character string including a single keyword or a named list containing a custom query (see details section below). Note that if an empty character string is passed, then all datasets available are returned.

type

a character one of the interactions type available (see details). Note that query is ignored if type is used.

expand_node

a logical. Should the function returned extra information pertaining to nodes? Default is set to FALSE, which means that only the Mangal IDs of nodes are returned.

verbose

a logical. Should extra information be reported on progress?

...

further arguments to be passed to httr::GET().

Value

An object of class mgSearchInteractions, i.e. a data.frame object including interactions. All networks in which interactions are involved are also attached to the data.frame.

Details

Names of the list should match one of the column names within the table. For the interaction table, those are:

• id: unique identifier of the interaction;

• attr_id: identifier of a specific attribute;

• direction: edge direction ("directed", "undirected" or "unknown");

• network_id: Mangal network identifier;

• node_from: node id which the interaction end to;

• node_to: node to which the interaction end to;

• type: use argument type instead.

Note that for lists with more than one element, only the first element is used, the others are ignored. The type of interactions (argument type) currently available are the following

• "competition";

• "amensalism";

• "neutralism";

• "commensalism";

• "mutualism";

• "parasitism";

• "predation";

• "herbivory";

• "symbiosis";

• "scavenger";

• "detritivore".

References

• https://mangal.io/#/

• https://mangal-interactions.github.io/mangal-api/#taxonomy

Examples

# \donttest{
 df_inter <- search_interactions(type = "competition", verbose = FALSE)
 # Get all networks containing competition
 competition_networks <- get_collection(df_inter, verbose = FALSE)
#> Processing id: 105 	1/1  

#>                                                                              

#> Processing id: 105 	1/1  

#>                                                                              

#> Processing id: 105 	1/1  

#>                                                                              

#> Processing id: 105 	1/1  

#>                                                                              

#> Processing id: 119 	1/1  

#>                                                                              

#> Processing id: 139 	1/1  

#>                                                                              

 df_net_926 <- search_interactions(list(network_id = 926), verbose = FALSE)
# }