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Fix test superinfection #179

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Fix test superinfection #179

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9bee4d6
Hard-code seeds for test_superinfection.R
WongDWai Jul 3, 2026
16fef1d
Hard-code seeds for test_superinfection.R
WongDWai Jul 3, 2026
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72 changes: 21 additions & 51 deletions tests/testthat/test_superinfection.R
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Original file line number Diff line number Diff line change
Expand Up @@ -23,31 +23,16 @@ try_model <- function(path) {
)
}

# find an outer tree that has at least one SI event and a single active root
.get_outer_with_superinfection <- function(mod, seeds = 1:500) {
for (s in seeds) {
set.seed(s)
dyn <- tryCatch(sim.dynamics(mod, max.attempts = 10),
warning = function(w) NULL, error = function(e) NULL)
if (is.null(dyn)) next

outer <- tryCatch(
withCallingHandlers(sim.outer.tree(dyn),
warning = function(w) invokeRestart("muffleWarning")),
error = function(e) NULL)
if (is.null(outer)) next

log <- outer$get.log()
si <- log[log$event == "transmission" &
!is.na(log$from.comp) & log$from.comp == "I" &
!is.na(log$to.comp) & log$to.comp == "I", ]
if (outer$get.active()$count.type() != 1) next
if (nrow(si) == 0) next
if (outer$get.sampled()$count.type() < 1) next

return(list(outer = outer, dyn = dyn, seed = s, si_log = si))
}
NULL
# seed 10 verified to produce an outer tree with SI events and sampled hosts
.get_outer_with_superinfection <- function(mod) {
set.seed(10)
dyn <- sim.dynamics(mod, max.attempts=10)
outer <- suppressWarnings(sim.outer.tree(dyn))
log <- outer$get.log()
si <- log[log$event == "transmission" &
!is.na(log$from.comp) & log$from.comp == "I" &
!is.na(log$to.comp) & log$to.comp == "I", ]
list(outer=outer, dyn=dyn, seed=10, si_log=si)
}

.try_inner <- function(outer) {
Expand All @@ -59,35 +44,20 @@ try_model <- function(path) {
})
}

# seed 10 verified to produce a valid single-root outer tree with phylo
.get_valid_phylo <- function(mod) {
for (s in c(21, 77, 99, 200, 300, 400, 500)) {
set.seed(s)
dyn <- tryCatch(sim.dynamics(mod, max.attempts = 10), warning = function(w) NULL)
if (is.null(dyn)) next
outer <- tryCatch(
withCallingHandlers(sim.outer.tree(dyn),
warning = function(w) invokeRestart("muffleWarning")),
error = function(e) NULL)
if (is.null(outer)) next
if (outer$get.active()$count.type() != 1) next
phy <- tryCatch(as.phylo(outer), error = function(e) NULL)
if (!is.null(phy)) return(list(phy = phy, outer = outer))
}
NULL
set.seed(10)
dyn <- sim.dynamics(mod, max.attempts=10)
outer <- suppressWarnings(sim.outer.tree(dyn))
phy <- as.phylo(outer)
list(phy=phy, outer=outer)
}

.get_valid_outer <- function(mod, seeds = c(99, 21, 77, 42, 55, 100, 200)) {
for (s in seeds) {
set.seed(s)
dyn <- tryCatch(sim.dynamics(mod, max.attempts = 15), warning = function(w) NULL)
if (is.null(dyn)) next
outer <- tryCatch(
withCallingHandlers(sim.outer.tree(dyn),
warning = function(w) invokeRestart("muffleWarning")),
error = function(e) NULL)
if (!is.null(outer)) return(outer)
}
NULL
# seed 1 verified to produce a valid outer tree
.get_valid_outer <- function(mod) {
set.seed(1)
dyn <- sim.dynamics(mod, max.attempts=15)
suppressWarnings(sim.outer.tree(dyn))
}


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