tests/testthat/test-dataConversionUnstratified.R

library("testthat")
library("survival")
library("Andromeda")
library("gnm")

context("test-dataConversionUnstratified.R")

test_that("Test data.frame to data for lr", {
  skip_on_cran()
  gold <- glm(case ~ spontaneous + induced, data=infert, family="binomial")

  #Convert infert dataset to Cyclops format:
  covariates <- data.frame(rowId = rep(1:nrow(infert),2),
                           covariateId = rep(1:2,each=nrow(infert)),
                           covariateValue = c(infert$spontaneous,infert$induced))
  outcomes <- data.frame(rowId = 1:nrow(infert),
                         y = infert$case)
  #Make sparse:
  covariates <- covariates[covariates$covariateValue != 0,]

  andr <- andromeda(outcomes = outcomes, covariates = covariates)
  cyclopsDataAndr <- convertToCyclopsData(andr$outcomes,andr$covariates,modelType = "lr",addIntercept = TRUE)
  fitAndr <- fitCyclopsModel(cyclopsDataAndr,prior = createPrior("none"))

  cyclopsData <- convertToCyclopsData(outcomes,covariates,modelType = "lr",addIntercept = TRUE)
  fit <- fitCyclopsModel(cyclopsData,prior = createPrior("none"))


  tolerance <- 1E-4
  expect_equal(as.vector(coef(fit)), as.vector(coef(gold)), tolerance = tolerance)
  expect_equal(as.vector(coef(fitAndr)), as.vector(coef(gold)), tolerance = tolerance)
})

test_that("Test unstratified cox using lung dataset ", {
  skip_on_cran()
  test <- lung
  test[is.na(test)] <- 0 # Don't want to bother with missing values

  gold <- coxph(Surv(time, status) ~ age + ph.ecog + ph.karno + pat.karno + meal.cal + wt.loss, test, method="breslow")

  cyclopsDataFormula <- createCyclopsData(Surv(time, status) ~ age + ph.ecog + ph.karno + pat.karno + meal.cal + wt.loss, data=test,modelType="cox")
  fitFormula <- fitCyclopsModel(cyclopsDataFormula)

  #Convert to data.frames for Cyclops:
  nCovars = 6
  covariates <- data.frame(stratumId = 0,
                           rowId = rep(1:nrow(test),nCovars),
                           covariateId = rep(1:nCovars,each = nrow(test)),
                           covariateValue = c(test$age,test$ph.ecog,test$ph.karno,test$pat.karno,test$meal.cal,test$wt.loss))
  outcomes <- data.frame(stratumId = 0,
                         rowId = 1:nrow(test),
                         y = test$status-1,
                         time = test$time)

  #Make sparse:
  covariates <- covariates[covariates$covariateValue != 0,]

  andr <- andromeda(outcomes = outcomes, covariates = covariates)
  cyclopsDataAndr <- convertToCyclopsData(andr$outcomes,andr$covariates,modelType = "cox")
  fitAndr <- fitCyclopsModel(cyclopsDataAndr,prior = createPrior("none"))

  cyclopsData <- convertToCyclopsData(outcomes,covariates,modelType = "cox")
  fit <- fitCyclopsModel(cyclopsData,prior = createPrior("none"))

  tolerance <- 1E-4
  expect_equal(as.vector(coef(fit)), as.vector(coef(fitFormula)), tolerance = tolerance)
  expect_equal(as.vector(coef(fit)), as.vector(coef(gold)), tolerance = tolerance)
  expect_equal(as.vector(coef(fitAndr)), as.vector(coef(gold)), tolerance = tolerance)
})


test_that("Test poisson regression", {
  skip_on_cran()
  sim <- simulateCyclopsData(nstrata = 1, nrows = 10000, ncovars = 2, eCovarsPerRow = 0.5, effectSizeSd = 1,model = "poisson")
  covariates <- sim$covariates
  outcomes <- sim$outcomes

  #Convert to data format for gnm:
  ncovars <- max(covariates$covariateId)
  nrows <- nrow(outcomes)
  m <- matrix(0,nrows,ncovars)
  for (i in 1:nrow(covariates)){
    m[covariates$rowId[i],covariates$covariateId[i]] <- 1
  }
  data <- as.data.frame(m)

  data$rowId <- 1:nrow(data)
  data <- merge(data,outcomes)
  data <- data[order(data$stratumId,data$rowId),]
  formula <- as.formula(paste(c("y ~ V1",paste("V",2:ncovars,sep="")),collapse=" + "))

  gold <- gnm(formula, family=poisson, offset=log(time), data = data)

  cyclopsDataFormula <- createCyclopsData(formula, offset=log(time), data=data,modelType="pr")
  fitFormula <- fitCyclopsModel(cyclopsDataFormula)

  andr <- andromeda(outcomes = outcomes, covariates = covariates)
  cyclopsDataAndr <- convertToCyclopsData(andr$outcomes,andr$covariates,modelType = "pr",addIntercept = TRUE)
  fitAndr <- fitCyclopsModel(cyclopsDataAndr,prior = createPrior("none"))

  cyclopsData <- convertToCyclopsData(outcomes,covariates,modelType = "pr",addIntercept = TRUE)
  fit <- fitCyclopsModel(cyclopsData,prior = createPrior("none"))

  tolerance <- 1E-4
  expect_equal(as.vector(sort(coef(fit))), as.vector(sort(coef(fitFormula))), tolerance = tolerance)
  expect_equal(as.vector(sort(coef(fit))), as.vector(sort(coef(gold))), tolerance = tolerance)
  expect_equal(as.vector(sort(coef(fitAndr))), as.vector(sort(coef(gold))), tolerance = tolerance)
})

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Cyclops documentation built on Aug. 10, 2022, 5:08 p.m.