tests/testthat/_snaps/proportion_transmission.md

In superspreading: Understand Individual-Level Variation in Infectious Disease Transmission

proportion_transmission works as expected for single R and k

Code
  proportion_transmission(R = 2, k = 0.5, percent_transmission = 0.8)
Output
    R   k prop_80
  1 2 0.5   26.4%

proportion_transmission works as expected for multiple R

Code
  proportion_transmission(R = c(1, 2, 3), k = 0.5, percent_transmission = 0.8)
Output
    R   k prop_80
  1 1 0.5   22.6%
  2 2 0.5   26.4%
  3 3 0.5     28%

proportion_transmission works as expected for multiple R & k

Code
  proportion_transmission(R = c(1, 2, 3), k = c(0.1, 0.2, 0.3),
  percent_transmission = 0.8)
Output
    R   k prop_80
  1 1 0.1   8.69%
  2 2 0.1   9.21%
  3 3 0.1   9.39%
  4 1 0.2   14.3%
  5 2 0.2   15.6%
  6 3 0.2     16%
  7 1 0.3   18.2%
  8 2 0.3   20.3%
  9 3 0.3     21%

proportion_transmission works as expected for format_prop = FALSE

Code
  proportion_transmission(R = c(1, 2, 3), k = c(0.1, 0.2, 0.3),
  percent_transmission = 0.8, format_prop = FALSE)
Output
    R   k    prop_80
  1 1 0.1 0.08693433
  2 2 0.1 0.09208820
  3 3 0.1 0.09389299
  4 1 0.2 0.14293729
  5 2 0.2 0.15561248
  6 3 0.2 0.16024765
  7 1 0.3 0.18158065
  8 2 0.3 0.20282175
  9 3 0.3 0.21039108

proportion_transmission works as expected for Inf k

Code
  proportion_transmission(R = 2, k = Inf, percent_transmission = 0.8)
Message
  Infinite values of k are being approximated by 1e+05 for calculations.
Output
    R     k prop_80
  1 2 1e+05   52.9%

proportion_transmission works for k > 1e7 for method = t_20

Code
  proportion_transmission(R = 2, k = 1e+10, percent_transmission = 0.8, method = "t_20")
Message
  Values of `k` > 1e+07 are set to 1e+07 due to numerical integration issues at higher values.
Output
    R     k prop_80
  1 2 1e+10   80.4%

proportion_transmission works for percent_transmission > 0.99

Code
  proportion_transmission(R = 2, k = 0.5, percent_transmission = 0.9999, method = "p_80")
Output
    R   k prop_99.99
  1 2 0.5      55.3%

Code
  proportion_transmission(R = 2, k = 0.5, percent_transmission = 0.9999, method = "t_20")
Message
  Values of `percent_transmission` > 0.99 are set to 0.99 due to numerical integration issues at higher values.
Output
    R   k prop_99.99
  1 2 0.5       100%

.prop_transmission_numerical works as expected

{
  "type": "double",
  "attributes": {},
  "value": [0.26347]
}

.prop_transmission_analytical works as expected

Code
  .prop_transmission_analytical(R = 2, k = 0.5, percent_transmission = 0.8)
Output
  [1] 0.264419

proportion_transmission works with

Code
  proportion_transmission(percent_transmission = 0.8, offspring_dist = od)
Output
       R    k prop_80
  1 1.63 0.16     13%

superspreading documentation built on April 4, 2025, 3:18 a.m.