serosvy_known_sample_posterior: Tidy output for the Bayesian serological sampling functions...

In avallecam/serosurvey: Serological Survey Analysis For Prevalence Estimation Under Misclassification

Tidy output for the Bayesian serological sampling functions for one or more sub-population and known test performance

Description

one or sub population - known test performance - posterior distribution of prevalence. source here

Usage

serosvy_known_sample_posterior(
  positive_number_test,
  total_number_test,
  sensitivity,
  specificity
)

Arguments

positive_number_test	number of positive tests population
total_number_test	number of total tests in population
sensitivity	known sensitivity of test
specificity	known specificity of test

Value

tibble of prevalence posterior distribution

Functions

• serosvy_known_sample_posterior: sub population - known test performance - posterior distribution of prevalence. source here

References

Larremore, D. B., Fosdick, B. K., Bubar, K. M., Zhang, S., Kissler, S. M., Metcalf, C. J. E., ... & Grad, Y. (2020). Estimating SARS-CoV-2 seroprevalence and epidemiological parameters with uncertainty from serological surveys. medRxiv. doi: https://doi.org/10.1101/2020.04.15.20067066

Examples

## Not run: 

library(tidyverse)
library(skimr)

sensitivity = 0.93
specificity = 0.975
positive_pop <- c(321, 123, 100, 10)
negative_pop <- c(1234, 500, 375, 30)

# reproducible example 01 -------------------------------------


tidy_result <- serosvy_known_sample_posterior(
  positive_number_test = positive_pop[1],
  total_number_test = positive_pop[1]+negative_pop[1],
  # sensitivity = 1,specificity = 1
  sensitivity = 0.93,
  specificity = 0.975
)

tidy_result_out <-
  tidy_result %>%
  select(summary) %>%
  unnest(cols = c(summary)) %>%
  unite_dotwhiskers(variable_dot = numeric.mean,
                              variable_low = numeric.p05,
                              variable_upp = numeric.p95,
                              digits_dot = 4,
                              digits_low = 3,
                              digits_upp = 3) %>%
  print()

#posterior distribution
tidy_result %>%
 select(posterior) %>%
 unnest(cols = c(posterior)) %>%
 ggplot(aes(x = r1)) +
 geom_histogram(aes(y=..density..),binwidth = 0.005) +
 geom_density() +
 geom_vline(aes(xintercept=tidy_result_out %>%
                  pull(numeric.mean)),
            color="red",lwd=1) +
 geom_vline(aes(xintercept=tidy_result_out %>%
                  pull(numeric.p05)),
            color="red") +
 geom_vline(aes(xintercept=tidy_result_out %>%
                  pull(numeric.p95)),
            color="red") +
 scale_x_continuous(breaks = scales::pretty_breaks())


# reproducible example 02 -------------------------------------

library(purrr)
library(furrr)
library(tictoc)


# plan(sequential)
plan(multisession, workers = availableCores())
tic()
result <- tibble(
  g=1:2,
  p=seq(10L,20L,10L),
  n=seq(200L,100L,-100L),
  se=seq(0.9,0.8,-0.1),
  sp=seq(0.8,0.9,0.1)
) %>%
  # mutate(fix=pmap(.l = select(.,
  mutate(fix=future_pmap(.l = select(.,
                              positive_number_test=p,
                              total_number_test=n,
                              sensitivity=se,
                              specificity=sp),
                  .f = possibly(serosvy_known_sample_posterior,otherwise = NA_real_)))
toc()

result %>%
  unnest(fix) %>%
  unnest(summary) %>%
  mutate(raw=p/n) %>%
  unite_dotwhiskers(variable_dot = numeric.mean,
                              variable_low = numeric.p05,
                              variable_upp = numeric.p95,
                              digits_dot = 2,
                              digits_low = 2,
                              digits_upp = 3) %>%
  glimpse()


## End(Not run)

avallecam/serosurvey documentation built on Feb. 12, 2023, 4:13 p.m.