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Summarize which hosts have co-diversifying symbionts

Source: R/host_codiv_summary.R
host_codiv_summary.Rd

Reports, for each host, how many co-diversifying clades it participates in. A node counts as co-diversifying when its statistic exceeds stat_threshold and its p-value is below p_threshold (the defaults, Hommola_r > 0.75 and p < 0.01, follow Sanders et al. 2023 and Sprockett et al. 2025). The hosts in each node are read from the per-node host tree stored by codiv().

Usage

host_codiv_summary(
  codiv_results,
  statistic = NULL,
  stat_threshold = 0.75,
  pvalue = NULL,
  p_threshold = 0.01
)

Arguments

codiv_results

A codiv result (or data frame) from codiv()

statistic

Name of the test-statistic column. NULL (default) uses Hommola_r, the collapsed Hommola correlation that codiv() always writes when the Hommola method runs

stat_threshold

A node is co-diversifying when its statistic exceeds this value; default 0.75

pvalue

Name of the p-value column. NULL (default) resolves alongside statistic

p_threshold

A node is co-diversifying when its p-value is below this value; default 0.01

Value

A data frame with one row per host (ordered by n_codiversifying_nodes, descending):

  • Host: host tip label

  • n_codiversifying_nodes: co-diversifying nodes that include this host

  • n_scanned_nodes: all scanned nodes that include this host

  • prop_codiversifying: n_codiversifying_nodes / n_scanned_nodes

  • max_statistic: the largest statistic value among this host's co-diversifying nodes (NA if none)

Details

Scanned nodes are nested, so a host appears in several overlapping nodes; the counts are a descriptive ranking of which hosts carry the most co-diversifying symbiont lineages, not independent tallies.

Examples

# \donttest{
sim <- simulate_codiv_data(n_hosts = 10, clades = list(
  list(codiversifying = TRUE,  congruence = 1, n_per_host = 2),
  list(codiversifying = FALSE, n_per_host = 2)), seed = 3)
results <- codiv(sim$host_tree, sim$symbiont_tree, sim$links,
                 methods = "hommola", permutations = 99, verbose = FALSE)
host_codiv_summary(results)
#>   Host n_codiversifying_nodes n_scanned_nodes prop_codiversifying max_statistic
#> 1   H3                      0               1                   0            NA
#> 2   H4                      0               1                   0            NA
#> 3   H5                      0               2                   0            NA
#> 4   H6                      0               3                   0            NA
#> 5   H7                      0               3                   0            NA
#> 6   H8                      0               3                   0            NA
#> 7   H9                      0               2                   0            NA
# }