Convert host-symbiont associations to binary presence-absence matrix

Transforms a long-format data frame of host-symbiont associations into a wide-format binary matrix suitable for co-phylogenetic analysis methods like PACo and ParaFit.

Usage

host_symbiont_links(Host_to_Symbiont_df)

Arguments

Host_to_Symbiont_df

A data frame with columns "Host" and "Symbiont" where each row represents one association. Symbionts must be unique (one symbiont per host per row).

Value

A binary matrix with hosts as rows and symbionts as columns, filled with 0s and 1s where 1 indicates the symbiont was isolated from that host.

Examples

hs_df <- data.frame(
  Host = c("H1", "H1", "H2", "H2", "H3"),
  Symbiont = c("S1", "S2", "S3", "S4", "S5")
)
mat <- host_symbiont_links(hs_df)