convert_to_cophy: Converts an object into an object of type cophy
In treeducken: Nested Phylogenetic Tree Simulator

Description Usage Arguments Details Value See Also Examples

Functions for converting either a list of three components (host_tree, symb_tree, and association_mat) into an object of class cophy Otherwise turns arguments into the cophy object if inputting a hostTree of type 'phylo', a symbiont tree of type 'phylo', and a matrix of type eventHistory.

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convert_to_cophy(hostTree, symbTree, assocMat, eventHistory = NULL)

to_cophy(hostTree, symbTree, assocMat, eventHistory = NULL)

`hostTree`	An object of type 'phylo'
`symbTree`	An object of type 'phylo'
`assocMat`	A matrix with rows being extant symbionts and columns being extant hosts
`eventHistory`	An optional data frame of four columns: Symbiont Index, Host Index, Event Type (see details), and Event Time

The association matrix must be with rows equal to the number of extant symbionts and columns equal to the number of extant hosts. Non-zero values in this matrix indicate associations (typically this will be a matrix of just zeros and ones).

The eventHistory parameter has four columns: Symbiont Index, Host Index, Event Type (see details), and Event Time. The indexing of the first two columns should follow the indexing of the 'phylo' objects 'hostTree' and 'symbTree'. The types of events are as follows: * HG - a host speciation event * HL - a host extinction event * C - a cospeciation event * SG - a symbiont speciation event * SL - a symbiont extinction event * AG - an association gain between symbiont x and host y * AL - an association loss between symbiont x and host y

An object of type cophy

is.cophy

gopher_lice_map_path <- system.file("extdata",
                                  "gopher_lice_mapping.txt",
                                   package = "treeducken")
gopher_lice_map <- read.table(gopher_lice_map_path,
                              stringsAsFactors = FALSE,
                              header = TRUE)
gopher_tree_path <- system.file("extdata",
                                "gophers_bd.tre",
                                 package = "treeducken")
gopher_lice_assoc_matrix <- convert_assoc_table_to_matrix(gopher_lice_map)
gopher_tree <- ape::read.nexus(gopher_tree_path)
lice_tree_path <- system.file("extdata",
                              "lice_bd.tre",
                               package = "treeducken")
lice_tree <- ape::read.nexus(lice_tree_path)
gopher_lice_cophy <- to_cophy(hostTree = gopher_tree,
                                         symbTree = lice_tree,
                                         assocMat = gopher_lice_assoc_matrix)