Find all vectors of recurrence states compatible with relationship graph

Finds all possible recurrence states for each recurrence compatible with the relationship graph, then takes the Cartesian product to get all vectors of recurrence states. For a recurrence to be a recrudescence, all edges between the recurrent infection and the immediately preceding infection must be clonal edges. For a recurrence to be a reinfection, all edges between the recurrent infection and any preceding infection must be stranger edges. All recurrences may possibly be relapses.

Usage

compatible_rstrs(RG, gs_per_ts)

Arguments

RG

Relationship graph; see enumerate_RGs.

gs_per_ts

List of vectors of genotypes for each infection.

Value

Vector of strings (consisting of "C", "L", "I" for recrudescence, relapse, reinfection respectively) compatible with relationship graph.

Examples

MOIs <- c(2, 2, 1)
RG <- enumerate_RGs(MOIs, igraph = TRUE)[[175]]
#> Number of valid relationship graphs (RGs) is 250
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gs_per_ts <- split(paste0("g", 1:sum(MOIs)), rep(1:length(MOIs), MOIs))
# 1st recurrence can't be recrudescence, 2nd recurrence can't be reinfection
plot_RG(RG, edge.curved = 0.2)

compatible_rstrs(RG, gs_per_ts) # "LL" "IL" "LC" "IC"
#> [1] "LL" "IL" "LC" "IC"