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Fix bug in issue #179 #189

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Fix bug in issue #179 #189

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533ffc4
Update cfr_rolling.R
adamkucharski Apr 24, 2025
db188dc
Fix conditional bug
adamkucharski Apr 24, 2025
aaa835e
Fix linting
adamkucharski Apr 24, 2025
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3 changes: 3 additions & 0 deletions R/cfr_rolling.R
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Original file line number Diff line number Diff line change
Expand Up @@ -121,6 +121,9 @@ cfr_rolling <- function(data,
# guaranteed in the early stages of an outbreak due to poor data
p_mid_values <- cumulative_deaths / round(cumulative_outcomes)

# Handle edge cases where p_mid might be NA or Inf
p_mid_values[is.na(p_mid_values) | is.infinite(p_mid_values)] <- 0

if (any(is.infinite(p_mid_values) | p_mid_values < 1e-4)) {
message(
"Some daily ratios of total deaths to total cases with known outcome",
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17 changes: 8 additions & 9 deletions R/estimate_severity.R
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Expand Up @@ -133,17 +133,16 @@
.select_func_likelihood <- function(total_cases, poisson_threshold, p_mid) {
# NOTE: internal function is not input checked
# switch likelihood function based on total cases and p_mid
# Binomial approx
if (total_cases < poisson_threshold || (p_mid >= 0.05)) {
func_likelihood <- function(total_outcomes, total_deaths, pp) {
lchoose(round(total_outcomes), total_deaths) +
(total_deaths * log(pp)) +
(((total_outcomes) - total_deaths) * log(1.0 - pp))
}

# Default to binomial likelihood
func_likelihood <- function(total_outcomes, total_deaths, pp) {
lchoose(round(total_outcomes), total_deaths) +
(total_deaths * log(pp)) +
(((total_outcomes) - total_deaths) * log(1.0 - pp))
}

# Poisson approx
if ((total_cases >= poisson_threshold) && (p_mid < 0.05)) {
# Poisson approx - only switch to Poisson if conditions are met
if ((total_cases >= poisson_threshold) && (!is.na(p_mid)) && (p_mid < 0.05)) {
func_likelihood <- function(total_outcomes, total_deaths, pp) {
stats::dpois(
total_deaths, pp * round(total_outcomes),
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