Linking to {epireview} and {cfr}

[pratikunterwegs]

A small example showing how to get onset to death delay distribution parameters for Ebola from {epireview}, convert them to <epidist>, and use them to estimate a delay corrected static CFR using {cfr}. cc @adamkucharski

library(epireview)
#> Loading required package: epitrix
#> Loading required package: ggplot2
#> Loading required package: ggforce
library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union

data = load_epidata("ebola")
#> Warning: One or more parsing issues, call `problems()` on your data frame for details,
#> e.g.:
#>   dat <- vroom(...)
#>   problems(dat)
#> Warning in load_epidata_raw(pathogen, "outbreak"): No data found for ebola
#> Warning: One or more parsing issues, call `problems()` on your data frame for details,
#> e.g.:
#>   dat <- vroom(...)
#>   problems(dat)
#> Warning in load_epidata("ebola"): No outbreaks information found for ebola
#> Data loaded for ebola

names(data)
#> [1] "articles"  "params"    "models"    "outbreaks"
param_data = data$params

# get all onset to death distribution data
# select high quality with Gamma dist
param_data = filter(
  param_data,
  parameter_type == "Human delay - Symptom Onset/Fever to Death",
  distribution_type == "Gamma",
  article_qa_score > 50
) %>%
  head(1)

# transform to epidist
# NOTE which parameters are used for uncertainty
# this differs between studies/entries
onset_to_death_mean = pull(param_data, parameter_value)
onset_to_death_sd = pull(param_data, distribution_par2_value)

# assume a Gamma distribution?
dist_params = epiparameter::convert_summary_stats_to_params(
  x = "gamma",
  mean = onset_to_death_mean,
  sd = onset_to_death_sd
)

# select one with shape and scale
epidist_ebola_otd = epiparameter::epidist(
  "Ebola virus disease",
  "Ebolavirus",
  epi_dist = "onset_to_death",
  prob_distribution = "gamma",
  prob_distribution_params = unlist(dist_params)
)
#> Citation cannot be created as author, year, journal or title is missing

# Calculate CFR using {cfr}
cfr::cfr_static(
  data = cfr::ebola1976,
  delay_density = function(x) { density(epidist_ebola_otd, x)}
)
#>   severity_mean severity_low severity_high
#> 1         0.959        0.842             1

^{Created on 2024-03-27 with reprex v2.0.2}