tests/testthat/test_valmeta_0.R

In metamisc: Meta-Analysis of Diagnosis and Prognosis Research Studies

context("valmeta 0. calculation of c-statistic")
skip_on_cran()

data(EuroSCORE)

test_that("Transformation of the c-statistic", {
  
  # Logit transformation
  logitc1 <- log(EuroSCORE$c.index/(1-EuroSCORE$c.index))
  logitc2 <- logit(EuroSCORE$c.index) #built-in function
  logitc3 <- (ccalc(cstat=c.index, cstat.se=se.c.index, data=EuroSCORE, g="log(cstat/(1-cstat))"))$theta
  expect_equal(logitc1, logitc2, logitc3)
  
  # Back-transformation
  ilogitc1 <- 1/(1+exp(-logitc1))
  ilogitc2 <- inv.logit(logitc2)
  expect_equal(ilogitc1, ilogitc2)

  # Arcsine square root transformed proportion
  ft1 <- asin(sqrt(EuroSCORE$c.index))
  ft2 <- (ccalc(cstat=c.index, cstat.se=se.c.index, data=EuroSCORE, g="asin(sqrt(cstat))"))$theta
  expect_equal(ft1, ft2)
  
})

test_that("Standard error of transformed c-statistic", {
  
  # Logit transformation
  logitcse1 <- EuroSCORE$se.c.index/(EuroSCORE$c.index*(1-EuroSCORE$c.index))
  logitcse2 <- (ccalc(cstat=c.index, cstat.se=se.c.index, data=EuroSCORE, g="log(cstat/(1-cstat))"))$theta.se
  expect_equal(logitcse1, logitcse2)
  
})


test_that("Preparation of untransformed aggregate data", {
  
  # Create test dataset provided by Anneke Damen
  testdat <- data.frame(Authoryear = c("Andersson 2015", "Chia 2014", "Goff 2014", "Goff 2014", "Jung 2015", 
                                       "Kavousi 2014", "Khalili 2015", "Lee 2015", "Muntner 2014",
                                       "De Filippis 2017", "De Las Heras Gala 2016", "De Las Heras Gala 2016"),
                   Samplesize = c(3396, 307, 5041, 735, 114622, 1513, 2353, 679, NA, 3053, 2584, 2005),
                   N_events = c(284, 22, 539, 107, 7669, 192, 200, 80, 376, 220, 257, 186),
                   Cstat = c(0.72, 0.55, 0.6843, 0.7109, 0.727, 0.67, 0.74, 0.714, 0.65, 0.71, 0.736, 0.67),
                   Cstat95LB = c(NA, NA, NA, NA, 0.721, 0.630, 0.710, 0.567, 0.620, NA, NA, NA),
                   Cstat95UB = c(NA, NA, NA, NA, 0.734, 0.710, 0.780, 0.770, 0.680, NA, NA, NA),
                   CstatSE = c(0.014, 0.050, NA, NA, NA, NA, NA, NA, NA, NA, 0.015, 0.020))
  
  ad <- ccalc(cstat = Cstat, cstat.cilb = Cstat95LB, cstat.ciub = Cstat95UB, 
              cstat.se = CstatSE, N = Samplesize, O = N_events, data = testdat, 
              slab = Authoryear)
  
  # Check whether the prepared aggregate data for Andersson 2015 is identical to the supplied one
  expect_equal(as.character(ad["Andersson 2015","theta.se.source"]), "Standard Error")
  expect_equal(ad["Andersson 2015","theta.se"], subset(testdat, Authoryear == "Andersson 2015")$CstatSE)
  
  # Check whether the prepared aggregate data for Chia 2014 is identical to the supplied one
  expect_equal(as.character(ad["Chia 2014","theta.se.source"]), "Standard Error")
  expect_equal(ad["Chia 2014","theta.se"], subset(testdat, Authoryear == "Chia 2014")$CstatSE)
  
  # Check whether the prepared aggregate data for Jung 2015 is identical to the supplied one
  expect_equal(as.character(ad["Jung 2015","theta.se.source"]), "Confidence Interval")
  expect_equal(ad["Jung 2015","theta.cilb"], subset(testdat, Authoryear == "Jung 2015")$Cstat95LB)
  expect_equal(ad["Jung 2015","theta.ciub"], subset(testdat, Authoryear == "Jung 2015")$Cstat95UB)
  
  # Check whether the prepared aggregate data for Kavousi 2014 is identical to the supplied one
  expect_equal(as.character(ad["Kavousi 2014","theta.se.source"]), "Confidence Interval")
  expect_equal(ad["Kavousi 2014","theta.cilb"], subset(testdat, Authoryear == "Kavousi 2014")$Cstat95LB)
  expect_equal(ad["Kavousi 2014","theta.ciub"], subset(testdat, Authoryear == "Kavousi 2014")$Cstat95UB)
  
  # Check whether the prepared aggregate data for Muntner 2014 is identical to the supplied one
  expect_equal(as.character(ad["Muntner 2014","theta.se.source"]), "Confidence Interval")
  expect_equal(ad["Muntner 2014","theta.cilb"], subset(testdat, Authoryear == "Muntner 2014")$Cstat95LB)
  expect_equal(ad["Muntner 2014","theta.ciub"], subset(testdat, Authoryear == "Muntner 2014")$Cstat95UB)
  
  # Check whether the NewCombe method is used for DeFilippis
  expect_equal(as.character(ad["De Filippis 2017","theta.se.source"]), "Newcombe (Method 4)")

})