View source: R/fct_build-network.R
initialize_network | R Documentation |
Initialize a mineral-chemistry network as stand-alone network rather than for embedding into the Shiny App.
initialize_network( elements_of_interest, force_all_elements = FALSE, elements_by_redox = FALSE, restrict_to_elements = FALSE, ignore_na_redox = FALSE, age_range = c(0, 5), max_age_type = "Maximum", cluster_algorithm = "Louvain", cluster_seed = NULL, use_data_cache = TRUE )
elements_of_interest |
An array of specified elements whose minerals should be included in the network. For all elements, specify "all". |
force_all_elements |
A logical. If FALSE (default), minerals containing any of 'elements_of_interest' will be included in network. If TRUE, only minerals with full intersection of all specified elements will be included in network. |
elements_by_redox |
A logical. If FALSE (default), element nodes will be constructed regardless of redox state. If TRUE, creates separate node for each element's redox state, e.g. Fe2+ and Fe3+ would be separate nodes. |
restrict_to_elements |
A logical. If FALSE (default), constructed network will _only_ contain the specified focal element(s) |
ignore_na_redox |
A logical. If TRUE and elements_by_redox is TRUE, element nodes without redox states will be removed from the network. |
age_range |
A array of two numbers giving inclusive range of mineral ages in Ga to include in network. |
max_age_type |
A string indicating how mineral ages should be assessed. If "Maximum" (default), filters minerals using maximum known ages at localities. If "Minimum", filters minerals using minimum known ages at localities. |
cluster_algorithm |
A string giving community clustering algorithm, one of "Louvain" (default) or "Leading eigenvector". |
cluster_seed |
An integer giving a random seed for reproducible clustering. Default is NULL. "Louvain" (default) or "Leading eigenvector". |
use_data_cache |
A logical. If TRUE (default) cached Mineral Evolution Database will be used to build the network. If FALSE, data will be fetched from MED here. CAUTION: Requires internet connection and will take several minutes to update. |
Named list containing an igraph-formatted network (‘network’), an igraph::communities object giving node cluster memberships (‘clustering’), a tibble of nodes associated metadata (‘nodes’), and a tibble of edges and associated metadata (‘edges’), and a tibble of mineral locality information ('locality_info')
## Not run: # Include all Iron minerals whose maximum known age is between 1-2 Gya, and apply # Louvain community clustering initialize_network("Fe", age_range = c(1,2)) # Include all minerals containing either Iron and Oxygen whose maximum known age # is between 1-2 Gya initialize_network(c("Fe", "O"), age_range = c(1,2)) # Include all minerals containing both Iron and Oxygen whose maximum known age is # between 1-2 Gya initialize_network(c("Fe", "O"), force_all_elements = TRUE, age_range = c(1,2)) # Build the full mineral network initialize_network("all") ## End(Not run)
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