single unit-test for residuals

R/Residuals.R

@@ -27,6 +27,7 @@
 #'                  either a vector of numbers or covariateId names
 #' @param type      Character string indicating the type of residual desires. Possible
 #'                  values are "schoenfeld".
+#' @param ...		Additional parameters for compatibility with S3 parent function
 #'
 #' @importFrom stats residuals
 #'
@@ -42,7 +43,7 @@ residuals.cyclopsFit <- function(object, parm, type = "schoenfeld", ...) {
 
     .checkInterface(object$cyclopsData, testOnly = TRUE)
 
-    res <- .cyclopsGetSchoenfeldResiduals(cyclopsFitRight$interface, NULL)
+    res <- .cyclopsGetSchoenfeldResiduals(object$interface, NULL)
 
     result <- res$residuals
     names(result) <- res$times

tests/testthat/test-smallCox.R

@@ -34,6 +34,21 @@ start, length, event, x1, x2
     tolerance <- 1E-4
     expect_equal(coef(cyclopsFitRight), coef(goldRight), tolerance = tolerance)
 
+    # Test residuals
+
+    goldRes <- residuals(goldCounting, "schoenfeld")[,1]
+    cyclopsRes <- residuals(cyclopsFitRight, "schoenfeld")
+
+    expect_equal(cyclopsRes, goldRes, tolerance = tolerance)
+
+    # cox2.zph(goldCounting, transform = "identity")
+    # residuals2.coxph(goldCounting, type = "scaledsch")
+    #
+    # # rr <- rr * vv * ndead + coef
+    #
+    # hand <- rev(navg) * goldCounting$var[1,1] * sum(event)  + coef(goldCounting)
+    #
+    # expect_equivalent(res2, hand) # scaled
 
     goldStrat <- coxph(Surv(length, event) ~ x1 + strata(x2), test)
 
@@ -42,6 +57,10 @@ start, length, event, x1, x2
                                        modelType = "cox")
     cyclopsFitStrat <- fitCyclopsModel(dataPtrStrat)
     expect_equal(coef(cyclopsFitStrat), coef(goldStrat), tolerance = tolerance)
+
+    goldStratRes <- residuals(goldStrat, "schoenfeld")
+    cyclopsStratRes <- residuals(cyclopsFitStrat, "schoenfeld")
+    # TODO Not yet the same order!!!
 })