In Enpeterson/outputsim: Output Simulation Results

For testing purposes in the summarize_simulations2.R function. Stops the process if different parameters are specified from the ones the script is built to analyze.

For the purposes of testing the error inside summarize_simulations2, this markdown script provides function "summarize_simulation_error", a truncated version of summarize_simulations which takes in a single dataset instead of all the parameters.

The expected output from this "error" function is a table with 6 parameters (15 ct estimates for 4 parameters, and 2 estimates for 2 global parameters) and their point estimates and uncertainty intervals if given "workingtib" (drawn from mcmctib_n) and a stop error if given "errortib" (generated with 4 variables.)

#Load the data & source the function
library(tidyverse)
library(testthat)



errortib <- readRDS(paste(getwd(), '/test', 'errortib.RDS'))
workingtib <- readRDS(paste(getwd(), '/test', 'workingtib.RDS'))

summarize_simulation_error <-
  function(data) {
    # tib <-
    #   readRDS(paste(output.dir, '/mcmctib_', simnum, '.RDS', sep = ""))

    tidydat <- data %>%
      select(
        contains("sens"),
        contains("spec"),
        contains("vradj.ct"),
        contains("gamma.truematvr.ct")
      )

    if (ncol(tidydat) < 62) { #for testing purposes
      #only and all selected parameter should be in this set
      stop(
        paste0(
          "At least oneparameter of interest is missing. .\n",
          "Check to make sure mcmctib_ is correct"
        )
      )
      call. = FALSE
    } 
    # else {
    #   tidydat <- tidydat %>%
    #     gather(key = "parameter", value = "value") %>%
    #     group_by(parameter) %>%
    #     summarize(
    #       lower = quantile(value, .025),
    #       median = quantile(value, .5),
    #       upper = quantile(value, .975)
    #     ) %>% 
    #     #print()
    # }
  }

expect_error(summarize_simulation_error(errortib))

expect_silent(summarize_simulation_error(workingtib))


test_that("function gives error when the data is missing parameters", {
  expect_error(summarize_simulation_error(errortib))
  expect_silent(summarize_simulation_error(workingtib))
})

Enpeterson/outputsim documentation built on May 24, 2019, 9:53 a.m.