library(dplyr, warn.conflicts = FALSE)
library(survival)

testthat::test_that(
  "residuals_phregr: null model for right-censored data", {
    pbc <- pbc %>% mutate(event = 1 * (status == 2))

    for (type in c("martingale", "deviance")) {
      fit1 <- phregr(pbc, time = "time", event = "event", covariates = "")
      rr1 <- residuals_phregr(fit1, type = type)

      fit2 <- coxph(Surv(time, event) ~ 1, data = pbc)
      rr2 <- resid(fit2, type = type)

      names(rr2) <- NULL
      testthat::expect_equal(rr1, rr2)
    }
  })


testthat::test_that(
  "residuals_phregr: right-censored data with covariates", {
    pbc <- pbc %>% mutate(event = 1 * (status == 2))

    for (type in c("martingale", "deviance", "score", "schoenfeld",
                   "dfbeta", "dfbetas", "scaledsch")) {
      fit1 <- phregr(pbc, time = "time", event = "event",
                     covariates = c("age", "edema", "log(bili)",
                                    "log(protime)", "log(albumin)"))

      rr1 <- residuals_phregr(fit1, type = type)

      fit2 <- coxph(Surv(time, event) ~ age + edema + log(bili) +
                      log(protime) + log(albumin), data = pbc)

      rr2 <- resid(fit2, type = type)

      if (type == "martingale" || type == "deviance") {
        names(rr2) <- NULL
      } else {
        rownames(rr2) <- NULL
        if (type == "schoenfeld" || type == "scaledsch") {
          attr(rr1, "time") <- NULL
        } else if (type == "dfbeta" || type == "dfbetas") {
          colnames(rr1) <- NULL
        }
      }

      testthat::expect_equal(rr1, rr2)
    }
  })


testthat::test_that(
  "residuals_phregr: null model for counting process data", {
    pbcseq <- pbcseq %>%
      group_by(id) %>%
      arrange(id, day) %>%
      mutate(tstart = day,
             tstop = ifelse(row_number() != n(), lead(day), futime),
             event = ifelse(row_number() != n(), 0, 1 * (status == 2)))

    for (type in c("martingale", "deviance")) {
      fit1 <- phregr(pbcseq, time = "tstart", time2 = "tstop", event = "event",
                     covariates = "", id = "id", robust = TRUE)

      rr1 <- residuals_phregr(fit1, type = type)

      fit2 <- coxph(Surv(tstart, tstop, event) ~ 1, data = pbcseq,
                    cluster = id, robust = TRUE)

      rr2 <- resid(fit2, type = type)

      names(rr2) <- NULL
      testthat::expect_equal(rr1, rr2)
    }
  })


testthat::test_that(
  "residuals_phregr: counting process data with covariates", {
    pbcseq <- pbcseq %>%
      group_by(id) %>%
      arrange(id, day) %>%
      mutate(tstart = day,
             tstop = ifelse(row_number() != n(), lead(day), futime),
             event = ifelse(row_number() != n(), 0, 1 * (status == 2)))

    for (type in c("martingale", "deviance", "score", "schoenfeld",
                   "dfbeta", "dfbetas", "scaledsch")) {
      fit1 <- phregr(pbcseq, time = "tstart", time2 = "tstop", event = "event",
                     covariates = c("age", "edema", "log(bili)",
                                    "log(protime)", "log(albumin)"),
                     id = "id", robust = TRUE)

      rr1 <- residuals_phregr(fit1, type = type)

      fit2 <- coxph(Surv(tstart, tstop, event) ~ age + edema + log(bili) +
                      log(protime) + log(albumin), data = pbcseq,
                    cluster = id, robust = TRUE)

      rr2 <- resid(fit2, type = type)

      if (type == "martingale" || type == "deviance") {
        names(rr2) <- NULL
      } else {
        rownames(rr2) <- NULL
        if (type == "schoenfeld" || type == "scaledsch") {
          attr(rr1, "time") <- NULL
        } else if (type == "dfbeta" || type == "dfbetas") {
          colnames(rr1) <- NULL
        }
      }

      testthat::expect_equal(rr1, rr2)
    }
  })