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generate_initial_disease_states() errors when number_initial_E = 0, and can miscount when number_initial_S = 0

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Evaluación

Dificultad
2/5
Tiempo estimado
1-3 horas
Aptitud para principiantes
92/100
Tipo de issue
Error
Claridad
Bien especificado
Estado de actividad
Activo
Stack tecnológico
r
Área
backend

Línea de trabajo

Comienza con generate_initial_disease_states() y reproduce ambos fallos usando los ejemplos de parámetros del issue. Añade casos de regresión a test-variables.R para cero personas expuestas y cero personas susceptibles; después, ejecuta las pruebas relevantes de R. Se termina cuando cada combinación válida de recuentos iniciales produce los recuentos S, E, I y R solicitados, incluidos los pools que contienen solo una persona.

Escrito por el modelo de indexación a partir del texto del issue.

Descripción

bug

Summary

generate_initial_disease_states() breaks on two kinds of valid initial conditions:

  1. number_initial_E = 0 with any initial I or R people errors with invalid first argument. For example, you can't start an epidemic from infectious people alone.
  2. number_initial_S = 0 can silently give the wrong counts. When only one person is left for the last draw, that draw can pick someone already assigned to an earlier state.

Both bugs are on main. They have been there since 6b5daf8 (2024-07-23), which added explicit initial I and R counts.

Reproducer

p <- list(human_population = 100, number_initial_S = 95, number_initial_E = 0,
          number_initial_I = 5, number_initial_R = 0, seed = 1)
generate_initial_disease_states(p)
#> Error in sample.int(length(x), size, replace, prob) : invalid first argument

The same error comes through get_parameters() and create_variables(), so run_simulation() can't start either.

p <- list(human_population = 10, number_initial_S = 0, number_initial_E = 9,
          number_initial_I = 1, number_initial_R = 0, seed = 1)
table(generate_initial_disease_states(p))
#>      E I_mild      S
#>      8      1      1

Seeds 1, 4 and 5 give E = 8 and S = 1 instead of E = 9 and S = 0. Seeds 2 and 3 happen to be correct.

Which inputs are affected

Tested with human_population = 100, with each count set to 0 or 5:

E I R Result
0 0 0 ok
0 > 0 any error
0 0 > 0 error
> 0 any any ok, unless S = 0 (below)

With S = 0, the counts are wrong for some seeds whenever exactly one person is left for the I draw or the R draw. For example, with N = 10: E = 9, I = 1, R = 0, or E = 5, I = 4, R = 1.

Cause

Two R gotchas in how the remaining pool is built and sampled:

  1. x[-integer(0)] returns an empty vector, not x. When E = 0, exposed_index is integer(0). So population_index[-exposed_index] is empty, and the I and R draws sample from nobody.
  2. sample(x, size) treats a single number x as 1:x. When one person is left in the pool, sample() draws from everyone up to that person's index, which can include people already made E or I. The draw overwrites them, and the person who should have been drawn stays S.

Proposed fix

Build each remaining pool with setdiff(), and draw with sample.int() so a pool of one person is handled correctly:

draw <- function(pool, size) pool[sample.int(length(pool), size)]

pool <- seq_along(initial_disease_states)
exposed_index <- draw(pool, parameters_list$number_initial_E)
initial_disease_states[exposed_index] <- "E"
pool <- setdiff(pool, exposed_index)

infectious_index <- draw(pool, parameters_list$number_initial_I)
initial_disease_states[infectious_index] <- "I_mild"
pool <- setdiff(pool, infectious_index)

recovered_index <- draw(pool, parameters_list$number_initial_R)
initial_disease_states[recovered_index] <- "R"

I checked this against the current function for every case above, with seeds 1 to 20:

  • It gives the right counts in every case.
  • It gives identical output in every case where the current function is already correct, so existing seeded runs don't change.

A single shuffle, sample(rep(c("S", "E", "I_mild", "R"), counts)), would be simpler. But it changes the initial state of every seeded run.

test-variables.R should get cases for E = 0 with I > 0, and for S = 0.

Lenguaje dominante
R
Estrellas
8
Forks
4
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