update proportion transmission argument name

Author: avallecam

episodes/superspreading-estimate.Rmd

@@ -589,12 +589,12 @@ across_offspring <- epidist_string %>%
  # unnest parameters
  unnest_wider(col = epidist_params) %>%
  # to each disease, add sequence from 0.01 to 1 (proportion of transmission)
- expand_grid(percent_transmission = seq(from = 0.01, to = 1, by = 0.01)) %>%
+ expand_grid(prop_transmission = seq(from = 0.01, to = 1, by = 0.01)) %>%
  # estimate proportion of cases responsible of proportion of transmission (row)
  mutate(
  transmission_output =
  pmap(
- .l = dplyr::select(., R = mean, k = dispersion, percent_transmission),
+ .l = dplyr::select(., R = mean, k = dispersion, prop_transmission),
  .f = superspreading::proportion_transmission,
  format_prop = FALSE,
  simulate = TRUE # use a numerical simulation
@@ -617,8 +617,8 @@ across_offspring <- epidist_string %>%
 # get a position to the ggplot text annotation
 across_offspring_tip <- across_offspring %>%
  group_by(disease) %>%
- filter(percent_transmission < 0.98, percent_transmission > 0.85) %>%
- slice_max(percent_transmission) %>%
+ filter(prop_transmission < 0.98, prop_transmission > 0.85) %>%
+ slice_max(prop_transmission) %>%
  ungroup() %>%
  mutate(disease = case_when(
  str_detect(disease, stringr::fixed("Hantavirus")) ~ "Hantavirus",
@@ -632,7 +632,7 @@ across_offspring %>%
  geom_line(
  aes(
  x = percent_cases,
- y = percent_transmission,
+ y = prop_transmission,
  color = dispersion,
  group = disease
  )
@@ -641,7 +641,7 @@ across_offspring %>%
  data = across_offspring_tip,
  aes(
  x = percent_cases,
- y = percent_transmission,
+ y = prop_transmission,
  label = disease
  ),
  hjust = 0.0,
@@ -859,7 +859,7 @@ ebola_params
 superspreading::proportion_transmission(
  R = ebola_params[["mean"]],
  k = ebola_params[["dispersion"]],
- percent_transmission = 0.8
+ prop_transmission = 0.8
 )
 
 #' estimate for sars --------------
@@ -870,7 +870,7 @@ superspreading::proportion_transmission(
 superspreading::proportion_transmission(
  R = sars_params[["mean"]],
  k = sars_params[["dispersion"]],
- percent_transmission = 0.8
+ prop_transmission = 0.8
 )
 
 
@@ -882,7 +882,7 @@ superspreading::proportion_transmission(
 superspreading::proportion_transmission(
  R = offspring_fit$estimate["mu"],
  k = offspring_fit$estimate["size"],
- percent_transmission = 0.8
+ prop_transmission = 0.8
 )
 ```