test_that("Greenwood standard error of cifcurve() yields the same outputs as separate analysis when strata is present", {
  testdata <- createTestData1(20, 1, first_zero=TRUE, last_zero=FALSE, subset_present=FALSE, logical_strata=TRUE, na_strata=FALSE)
  testdata1 <- subset(testdata, strata==FALSE)
  testdata2 <- subset(testdata, strata==TRUE)
  t <- cifcurve(Event(t, d)~strata, testdata, outcome.type="S", weight="w", error = "greenwood")
  e1 <- cifcurve(Event(t, d)~1, testdata1, outcome.type="S", weight="w", error = "greenwood")
  e2 <- cifcurve(Event(t, d)~1, testdata2, outcome.type="S", weight="w", error = "greenwood")
  expected <- c(e1$std.err, e2$std.err)
  tested <- t$std.err
  expect_equal(expected, tested)
})

test_that("cifcurve() produced the same outputs as survfit() in survival in survival data", {
  testthat::skip_if_not_installed("survival")
  testdata <- createTestData1(20, 1, first_zero=FALSE, last_zero=TRUE, subset_present=FALSE, logical_strata=TRUE, na_strata=FALSE)
  e <- survival::survfit(survival::Surv(t, d)~strata, testdata, weight=w, conf.type = "none")
  t <- cifcurve(Event(t, d) ~ strata, data = testdata, weight="w", conf.type = "none", outcome.type = "SURVIVAL", engine="calculateKM")
  #  expected <- as.numeric(c(e$time, round(e$surv,digit=5), e$n, e$n.risk, e$n.event, e$n.censor, round(e$std.err,digit=5), e$strata))
  #  tested <- as.numeric(c(t$time, round(t$surv,digit=5), t$n, t$n.risk, t$n.event, t$n.censor, round(t$std.err,digit=5), t$strata))
  expected <- as.numeric(c(e$time, round(e$surv,digit=5), e$n, e$n.risk, e$n.event, e$n.censor, e$lower, e$strata))
  tested <- as.numeric(c(t$time, round(t$surv,digit=5), t$n, t$n.risk, t$n.event, t$n.censor, t$lower, t$strata))
  expect_equal(expected, tested)
})

test_that("cifcurve() produced the same estimates as cif() in mets in competing risks data", {
  testthat::skip_if_not_installed("mets")
  library(mets)
  data(diabetes.complications)
  cif_fit <- mets::cif(Event(t,epsilon) ~ +1, data=diabetes.complications, cause=1)
  surv_fit <- cifcurve(Event(t, epsilon) ~ +1, data = diabetes.complications, conf.type = "none", outcome.type = "C", error="delta")
  index<-c(1,3,5,6,8,10,12,13,15,16,17,18)
  expected <- round(1-surv_fit$surv[index],digit=5)
  tested <- round(cif_fit$mu[1:12],digit=5)
  expect_equal(expected, tested)
})

test_that("cifcurve yields the same outputs as cif of mets", {
  skip_on_cran()
  skip_if_not_installed("mets")
  skip_if_not_installed("Rcpp")
  testdata <- createTestData1(20, 1, first_zero=TRUE, last_zero=TRUE, subset_present=FALSE, logical_strata=TRUE, na_strata=FALSE)
  library(mets)
  library(Rcpp)
  e <- cif(Event(t,epsilon)~1, data=testdata, cause=1)
  e_surv <- 1-e$mu
  e_time <- e$times
  expected <- as.numeric(c(e_surv[c(1,2,4,6,8,10,12,14)], e_time[c(1,2,4,6,8,10,12,14)]))
  t <- cifcurve(Event(t, epsilon)~1, data=testdata, conf.type = "none", outcome.type = "COMPETING-RISK")
  tested <- as.numeric(c(t$surv[c(2:9)], t$time[c(2:9)]))
  expect_equal(tested, expected)
})

test_that("cifcurve by strata yields the same outputs as subsetting", {
  skip_on_cran()
  skip_if_not_installed("mets")
  skip_if_not_installed("Rcpp")
  testdata <- createTestData1(20, 1, first_zero=TRUE, last_zero=TRUE, subset_present=FALSE, logical_strata=TRUE, na_strata=FALSE)
  testdata_f <- testdata[testdata$strata==FALSE,]
  library(Rcpp)
  e <- cif(Event(t,epsilon)~1, data=testdata, cause=1)
  e <- cifcurve(Event(t, epsilon)~1, data=testdata_f, conf.type = "none", outcome.type = "COMPETING-RISK")
  expected <- c(e$surv, e$time)
  t <- cifcurve(Event(t, epsilon)~strata, data=testdata, conf.type = "none", outcome.type = "COMPETING-RISK")
  tested <- c(t$surv[c(1:5)], t$time[c(1:5)])
  expect_equal(tested, expected)
})

test_that("cifcurve() yields the same outputs as survfit() with log-log transformation", {
  skip_on_cran()
  skip_if_not_installed("survival")

  df_test <- createTestData1(200, 2, first_zero=TRUE, last_zero=TRUE, subset_present=FALSE, logical_strata=FALSE, na_strata=FALSE)
  e <- survival::survfit(Surv(t, d)~strata, df_test, weight=w, conf.type = "log-log")
  t <- cifcurve(Surv(t, d)~strata, df_test, weight="w", conf.type = "log-log", report.survfit.std.err = TRUE, outcome.type = "SURVIVAL", engine="calculateKM")
  #t <- cifcurve(Surv(t, d)~strata, df_test, weight="w", conf.type = "log-log", report.survfit.std.err = TRUE, outcome.type = "SURVIVAL")
  e$std.err <- sapply(e$std.err, function(x) ifelse(is.nan(x), NA, x))
  e$lower <- sapply(e$lower, function(x) ifelse(is.nan(x), NA, x))
  e$upper <- sapply(e$upper, function(x) ifelse(is.nan(x), NA, x))
  e$std.err <- sapply(e$std.err, function(x) ifelse(is.infinite(x), NA, x))
  e$lower <- sapply(e$lower, function(x) ifelse(is.infinite(x), NA, x))
  e$upper <- sapply(e$upper, function(x) ifelse(is.infinite(x), NA, x))
  e$std.err <- sapply(e$std.err, function(x) ifelse(x>=1, NA, x))
  e$lower <- sapply(e$lower, function(x) ifelse(x>=1, NA, x))
  e$upper <- sapply(e$upper, function(x) ifelse(x>=1, NA, x))
  e$std.err <- sapply(e$std.err, function(x) ifelse(x<=0, NA, x))
  e$lower <- sapply(e$lower, function(x) ifelse(x<=0, NA, x))
  e$upper <- sapply(e$upper, function(x) ifelse(x<=0, NA, x))
  t$std.err <- sapply(t$std.err, function(x) ifelse(is.nan(x), NA, x))
  t$lower <- sapply(t$lower, function(x) ifelse(is.nan(x), NA, x))
  t$upper <- sapply(t$upper, function(x) ifelse(is.nan(x), NA, x))
  t$std.err <- sapply(t$std.err, function(x) ifelse(is.infinite(x), NA, x))
  t$lower <- sapply(t$lower, function(x) ifelse(is.infinite(x), NA, x))
  t$upper <- sapply(t$upper, function(x) ifelse(is.infinite(x), NA, x))
  t$std.err <- sapply(t$std.err, function(x) ifelse(x>=1, NA, x))
  t$lower <- sapply(t$lower, function(x) ifelse(x>=1, NA, x))
  t$upper <- sapply(t$upper, function(x) ifelse(x>=1, NA, x))
  t$std.err <- sapply(t$std.err, function(x) ifelse(x<=0, NA, x))
  t$lower <- sapply(t$lower, function(x) ifelse(x<=0, NA, x))
  t$upper <- sapply(t$upper, function(x) ifelse(x<=0, NA, x))
  expected <- as.numeric(c(e$time, round(e$surv,digit=5), e$n, e$n.risk, e$n.event, e$n.censor, round(e$std.err,digit=5), round(e$lower,digit=5), round(e$upper,digit=5), e$strata))
  tested <- as.numeric(c(t$time, round(t$surv,digit=5), t$n, t$n.risk, t$n.event, t$n.censor, round(t$std.err,digit=5), round(t$lower,digit=5), round(t$upper,digit=5), t$strata))
  expect_equal(expected, tested)
})

test_that("cifcurve() yields the same outputs as survfit() with log transformation", {
  skip_on_cran()
  skip_if_not_installed("survival")

  df_test <- createTestData1(200, 2, first_zero=TRUE, last_zero=TRUE, subset_present=FALSE, logical_strata=FALSE, na_strata=FALSE)
  e <- survival::survfit(Surv(t, d)~strata, df_test, weight=w, conf.type = "log")
  #t <- cifcurve(Surv(t, d)~strata, df_test, weight="w", conf.type = "log", report.survfit.std.err = TRUE, outcome.type = "SURVIVAL")
  t <- cifcurve(Surv(t, d)~strata, df_test, weight="w", conf.type = "log", report.survfit.std.err = TRUE, outcome.type = "SURVIVAL", engine="calculateKM")
  e$std.err <- sapply(e$std.err, function(x) ifelse(is.nan(x), NA, x))
  e$lower <- sapply(e$lower, function(x) ifelse(is.nan(x), NA, x))
  e$upper <- sapply(e$upper, function(x) ifelse(is.nan(x), NA, x))
  e$std.err <- sapply(e$std.err, function(x) ifelse(is.infinite(x), NA, x))
  e$lower <- sapply(e$lower, function(x) ifelse(is.infinite(x), NA, x))
  e$upper <- sapply(e$upper, function(x) ifelse(is.infinite(x), NA, x))
  e$std.err <- sapply(e$std.err, function(x) ifelse(x>=1, NA, x))
  e$lower <- sapply(e$lower, function(x) ifelse(x>=1, NA, x))
  e$upper <- sapply(e$upper, function(x) ifelse(x>=1, NA, x))
  e$std.err <- sapply(e$std.err, function(x) ifelse(x<=0, NA, x))
  e$lower <- sapply(e$lower, function(x) ifelse(x<=0, NA, x))
  e$upper <- sapply(e$upper, function(x) ifelse(x<=0, NA, x))
  t$std.err <- sapply(t$std.err, function(x) ifelse(is.nan(x), NA, x))
  t$lower <- sapply(t$lower, function(x) ifelse(is.nan(x), NA, x))
  t$upper <- sapply(t$upper, function(x) ifelse(is.nan(x), NA, x))
  t$std.err <- sapply(t$std.err, function(x) ifelse(is.infinite(x), NA, x))
  t$lower <- sapply(t$lower, function(x) ifelse(is.infinite(x), NA, x))
  t$upper <- sapply(t$upper, function(x) ifelse(is.infinite(x), NA, x))
  t$std.err <- sapply(t$std.err, function(x) ifelse(x>=1, NA, x))
  t$lower <- sapply(t$lower, function(x) ifelse(x>=1, NA, x))
  t$upper <- sapply(t$upper, function(x) ifelse(x>=1, NA, x))
  t$std.err <- sapply(t$std.err, function(x) ifelse(x<=0, NA, x))
  t$lower <- sapply(t$lower, function(x) ifelse(x<=0, NA, x))
  t$upper <- sapply(t$upper, function(x) ifelse(x<=0, NA, x))
  expected <- as.numeric(c(e$time, round(e$surv,digit=5), e$n, e$n.risk, e$n.event, e$n.censor, round(e$std.err,digit=5), round(e$lower,digit=5), round(e$upper,digit=5), e$strata))
  tested <- as.numeric(c(t$time, round(t$surv,digit=5), t$n, t$n.risk, t$n.event, t$n.censor, round(t$std.err,digit=5), round(t$lower,digit=5), round(t$upper,digit=5), t$strata))
  expect_equal(expected, tested)
})

test_that("cifcurve() yields the same outputs as survfit() with arcsine transformation", {
  skip_on_cran()
  skip_if_not_installed("survival")

  df_test <- createTestData1(200, 2, first_zero=TRUE, last_zero=TRUE, subset_present=FALSE, logical_strata=FALSE, na_strata=FALSE)
  e <- survival::survfit(Surv(t, d)~strata, df_test, weight=w, conf.type = "a")
  #t <- cifcurve(Surv(t, d)~strata, df_test, weight="w", conf.type = "a", report.survfit.std.err = TRUE, outcome.type = "SURVIVAL")
  t <- cifcurve(Surv(t, d)~strata, df_test, weight="w", conf.type = "a", report.survfit.std.err = TRUE, outcome.type = "SURVIVAL", engine="calculateKM")
  e$std.err <- sapply(e$std.err, function(x) ifelse(is.nan(x), NA, x))
  e$lower <- sapply(e$lower, function(x) ifelse(is.nan(x), NA, x))
  e$upper <- sapply(e$upper, function(x) ifelse(is.nan(x), NA, x))
  e$std.err <- sapply(e$std.err, function(x) ifelse(is.infinite(x), NA, x))
  e$lower <- sapply(e$lower, function(x) ifelse(is.infinite(x), NA, x))
  e$upper <- sapply(e$upper, function(x) ifelse(is.infinite(x), NA, x))
  e$std.err <- sapply(e$std.err, function(x) ifelse(x>=1, NA, x))
  e$lower <- sapply(e$lower, function(x) ifelse(x>=1, NA, x))
  e$upper <- sapply(e$upper, function(x) ifelse(x>=1, NA, x))
  e$std.err <- sapply(e$std.err, function(x) ifelse(x<=0, NA, x))
  e$lower <- sapply(e$lower, function(x) ifelse(x<=0, NA, x))
  e$upper <- sapply(e$upper, function(x) ifelse(x<=0, NA, x))
  t$std.err <- sapply(t$std.err, function(x) ifelse(is.nan(x), NA, x))
  t$lower <- sapply(t$lower, function(x) ifelse(is.nan(x), NA, x))
  t$upper <- sapply(t$upper, function(x) ifelse(is.nan(x), NA, x))
  t$std.err <- sapply(t$std.err, function(x) ifelse(is.infinite(x), NA, x))
  t$lower <- sapply(t$lower, function(x) ifelse(is.infinite(x), NA, x))
  t$upper <- sapply(t$upper, function(x) ifelse(is.infinite(x), NA, x))
  t$std.err <- sapply(t$std.err, function(x) ifelse(x>=1, NA, x))
  t$lower <- sapply(t$lower, function(x) ifelse(x>=1, NA, x))
  t$upper <- sapply(t$upper, function(x) ifelse(x>=1, NA, x))
  t$std.err <- sapply(t$std.err, function(x) ifelse(x<=0, NA, x))
  t$lower <- sapply(t$lower, function(x) ifelse(x<=0, NA, x))
  t$upper <- sapply(t$upper, function(x) ifelse(x<=0, NA, x))
  expected <- as.numeric(c(e$time, round(e$surv,digit=5), e$n, e$n.risk, e$n.event, e$n.censor, round(e$std.err,digit=5), round(e$lower,digit=5), round(e$upper,digit=5), e$strata))
  tested <- as.numeric(c(t$time, round(t$surv,digit=5), t$n, t$n.risk, t$n.event, t$n.censor, round(t$std.err,digit=5), round(t$lower,digit=5), round(t$upper,digit=5), t$strata))
  expect_equal(expected, tested)
})

test_that("cifcurve() yields the same outputs as survfit()", {
  skip_on_cran()
  skip_if_not_installed("survival")

  df_test <- createTestData1(200, 2, first_zero=TRUE, last_zero=TRUE, subset_present=FALSE, logical_strata=FALSE, na_strata=FALSE)
  e <- survival::survfit(Surv(t, d)~strata, df_test, weight=w, conf.type = "plain")
  t <- cifcurve(Surv(t, d)~strata, df_test, weight="w", conf.type = "plain", report.survfit.std.err = TRUE, outcome.type = "SURVIVAL", engine="calculateAJ_Rcpp")
  #t <- cifcurve(Surv(t, d)~strata, df_test, weight="w", conf.type = "plain", report.survfit.std.err = TRUE, outcome.type = "SURVIVAL", engine="calculateKM")
  e$std.err <- sapply(e$std.err, function(x) ifelse(is.nan(x), NA, x))
  e$lower <- sapply(e$lower, function(x) ifelse(is.nan(x), NA, x))
  e$upper <- sapply(e$upper, function(x) ifelse(is.nan(x), NA, x))
  e$std.err <- sapply(e$std.err, function(x) ifelse(is.infinite(x), NA, x))
  e$lower <- sapply(e$lower, function(x) ifelse(is.infinite(x), NA, x))
  e$upper <- sapply(e$upper, function(x) ifelse(is.infinite(x), NA, x))
  e$std.err <- sapply(e$std.err, function(x) ifelse(x>=1, NA, x))
  e$lower <- sapply(e$lower, function(x) ifelse(x>=1, NA, x))
  e$upper <- sapply(e$upper, function(x) ifelse(x>=1, NA, x))
  e$std.err <- sapply(e$std.err, function(x) ifelse(x<=0, NA, x))
  e$lower <- sapply(e$lower, function(x) ifelse(x<=0, NA, x))
  e$upper <- sapply(e$upper, function(x) ifelse(x<=0, NA, x))
  t$std.err <- sapply(t$std.err, function(x) ifelse(is.nan(x), NA, x))
  t$lower <- sapply(t$lower, function(x) ifelse(is.nan(x), NA, x))
  t$upper <- sapply(t$upper, function(x) ifelse(is.nan(x), NA, x))
  t$std.err <- sapply(t$std.err, function(x) ifelse(is.infinite(x), NA, x))
  t$lower <- sapply(t$lower, function(x) ifelse(is.infinite(x), NA, x))
  t$upper <- sapply(t$upper, function(x) ifelse(is.infinite(x), NA, x))
  t$std.err <- sapply(t$std.err, function(x) ifelse(x>=1, NA, x))
  t$lower <- sapply(t$lower, function(x) ifelse(x>=1, NA, x))
  t$upper <- sapply(t$upper, function(x) ifelse(x>=1, NA, x))
  t$std.err <- sapply(t$std.err, function(x) ifelse(x<=0, NA, x))
  t$lower <- sapply(t$lower, function(x) ifelse(x<=0, NA, x))
  t$upper <- sapply(t$upper, function(x) ifelse(x<=0, NA, x))
  expected <- as.numeric(c(e$time, round(e$surv,digit=5), e$n, e$n.risk, e$n.event, e$n.censor, round(e$std.err,digit=5), round(e$lower,digit=5), round(e$upper,digit=5), e$strata))
  tested <- as.numeric(c(t$time, round(t$surv,digit=5), t$n, t$n.risk, t$n.event, t$n.censor, round(t$std.err,digit=5), round(t$lower,digit=5), round(t$upper,digit=5), t$strata))
  expect_equal(expected, tested)
})

test_that("Greenwood standard error of cifcurve() yields the same outputs as separate analysis when strata is present", {
  testdata <- createTestData1(20, 1, first_zero=TRUE, last_zero=FALSE, subset_present=FALSE, logical_strata=TRUE, na_strata=FALSE)
  testdata1 <- subset(testdata, strata==FALSE)
  testdata2 <- subset(testdata, strata==TRUE)
  t <- cifcurve(Surv(t, d)~strata, testdata, weight="w", error = "greenwood", outcome.type = "SURVIVAL")
  e1 <- cifcurve(Surv(t, d)~1, testdata1, weight="w", error = "greenwood", outcome.type = "SURVIVAL")
  e2 <- cifcurve(Surv(t, d)~1, testdata2, weight="w", error = "greenwood", outcome.type = "SURVIVAL")
  expected <- c(e1$std.err, e2$std.err)
  tested <- t$std.err
  expect_equal(expected, tested)
})