### Regression tests for the transformation functions set.seed(290875) library("coin") isequal <- coin:::isequal options(useFancyQuotes = FALSE) ### NA handling: continuous x <- c(1L, 2L, NA, 3L, 3L, NA, 4L, 5L, NA) cc <- complete.cases(x) id_trafo(x) id_trafo(x[cc]) rank_trafo(x) rank_trafo(x[cc]) rank_trafo(x, ties.method = "random") rank_trafo(x[cc], ties.method = "random") normal_trafo(x) normal_trafo(x[cc]) normal_trafo(x, ties.method = "average-scores") normal_trafo(x[cc], ties.method = "average-scores") median_trafo(x) median_trafo(x[cc]) median_trafo(x, mid.score = "0.5") median_trafo(x[cc], mid.score = "0.5") median_trafo(x, mid.score = "1") median_trafo(x[cc], mid.score = "1") savage_trafo(x) savage_trafo(x[cc]) savage_trafo(x, ties.method = "average-scores") savage_trafo(x[cc], ties.method = "average-scores") consal_trafo(x) consal_trafo(x[cc]) consal_trafo(x, a = c(2, 5)) consal_trafo(x[cc], a = c(2, 5)) consal_trafo(x, ties.method = "average-scores") consal_trafo(x[cc], ties.method = "average-scores") consal_trafo(x, ties.method = "average-scores", a = c(2, 5)) consal_trafo(x[cc], ties.method = "average-scores", a = c(2, 5)) koziol_trafo(x) koziol_trafo(x[cc]) koziol_trafo(x, j = 2) koziol_trafo(x[cc], j = 2) koziol_trafo(x, ties.method = "average-scores") koziol_trafo(x[cc], ties.method = "average-scores") koziol_trafo(x, ties.method = "average-scores", j = 2) koziol_trafo(x[cc], ties.method = "average-scores", j = 2) klotz_trafo(x) klotz_trafo(x[cc]) klotz_trafo(x, ties.method = "average-scores") klotz_trafo(x[cc], ties.method = "average-scores") mood_trafo(x) mood_trafo(x[cc]) mood_trafo(x, ties.method = "average-scores") mood_trafo(x[cc], ties.method = "average-scores") ansari_trafo(x) ansari_trafo(x[cc]) ansari_trafo(x, ties.method = "average-scores") ansari_trafo(x[cc], ties.method = "average-scores") fligner_trafo(x) fligner_trafo(x[cc]) fligner_trafo(x, ties.method = "average-scores") fligner_trafo(x[cc], ties.method = "average-scores") maxstat_trafo(x) maxstat_trafo(x[cc]) maxstat_trafo(x, minprob = 0.3, maxprob = 0.51) maxstat_trafo(x[cc], minprob = 0.3, maxprob = 0.51) ### NA handling: survival x <- c(1, 2, NA, 3, 3, NA, 4, 5, NA) cc <- complete.cases(x) logrank_trafo(Surv(x)) logrank_trafo(Surv(x)[cc]) logrank_trafo(Surv(x), ties.method = "Hothorn-Lausen") logrank_trafo(Surv(x)[cc], ties.method = "Hothorn-Lausen") logrank_trafo(Surv(x), ties.method = "average-scores") logrank_trafo(Surv(x)[cc], ties.method = "average-scores") x <- c(1, 2, 3, 3, 3, 4, 4, 5, 5) e <- rep(c(0, NA, 1, 1), length.out = 9) cc <- complete.cases(x, e) logrank_trafo(Surv(x, e)) logrank_trafo(Surv(x, e)[cc]) logrank_trafo(Surv(x, e), ties.method = "Hothorn-Lausen") logrank_trafo(Surv(x, e)[cc], ties.method = "Hothorn-Lausen") logrank_trafo(Surv(x, e), ties.method = "average-scores") logrank_trafo(Surv(x, e)[cc], ties.method = "average-scores") x <- c(1, 2, NA, 3, 3, NA, 4, 5, NA) e <- rep(c(0, NA, 1, 1), length.out = 9) cc <- complete.cases(x, e) logrank_trafo(Surv(x, e)) logrank_trafo(Surv(x, e)[cc]) logrank_trafo(Surv(x, e), ties.method = "Hothorn-Lausen") logrank_trafo(Surv(x, e)[cc], ties.method = "Hothorn-Lausen") logrank_trafo(Surv(x, e), ties.method = "average-scores") logrank_trafo(Surv(x, e)[cc], ties.method = "average-scores") ### NA handling: factor x <- factor(c(1, 1, NA, 2, NA, 3, 3, NA, 4), labels = as.roman(1:4)) ox <- ordered(x) cc <- complete.cases(x) f_trafo(x) f_trafo(x[cc]) of_trafo(x) of_trafo(x[cc]) of_trafo(x, scores = 5:8) of_trafo(x[cc], scores = 5:8) of_trafo(x, scores = list(s1 = 5:8, s2 = 9:12)) of_trafo(x[cc], scores = list(s1 = 5:8, s2 = 9:12)) zheng_trafo(x, increment = 0.5) zheng_trafo(x[cc], increment = 0.5) of_trafo(ox) of_trafo(ox[cc]) of_trafo(ox, scores = 5:8) of_trafo(ox[cc], scores = 5:8) of_trafo(ox, scores = list(s1 = 5:8, s2 = 9:12)) of_trafo(ox[cc], scores = list(s1 = 5:8, s2 = 9:12)) zheng_trafo(ox, increment = 0.5) zheng_trafo(ox[cc], increment = 0.5) fmaxstat_trafo(x) fmaxstat_trafo(x[cc]) fmaxstat_trafo(x, minprob = 0.49) fmaxstat_trafo(x[cc], minprob = 0.49) ofmaxstat_trafo(ox) ofmaxstat_trafo(ox[cc]) ofmaxstat_trafo(ox, minprob = 0.49) ofmaxstat_trafo(ox[cc], minprob = 0.49) mcp_trafo(x = "Tukey")(data.frame(x)) mcp_trafo(x = "Tukey")(data.frame(x = x[cc])) x[9] <- NA ox[9] <- NA cc <- complete.cases(x) f_trafo(x) f_trafo(x[cc]) of_trafo(x) of_trafo(x[cc]) of_trafo(x, scores = 5:8) of_trafo(x[cc], scores = 5:8) of_trafo(x, scores = list(s1 = 5:8, s2 = 9:12)) of_trafo(x[cc], scores = list(s1 = 5:8, s2 = 9:12)) zheng_trafo(x, increment = 0.5) zheng_trafo(x[cc], increment = 0.5) of_trafo(ox) of_trafo(ox[cc]) of_trafo(ox, scores = 5:8) of_trafo(ox[cc], scores = 5:8) of_trafo(ox, scores = list(s1 = 5:8, s2 = 9:12)) of_trafo(ox[cc], scores = list(s1 = 5:8, s2 = 9:12)) zheng_trafo(ox, increment = 0.5) zheng_trafo(ox[cc], increment = 0.5) fmaxstat_trafo(x) fmaxstat_trafo(x[cc]) fmaxstat_trafo(x, minprob = 0.4, maxprob = 0.51) fmaxstat_trafo(x[cc], minprob = 0.4, maxprob = 0.51) ofmaxstat_trafo(ox) ofmaxstat_trafo(ox[cc]) ofmaxstat_trafo(ox, minprob = 0.4, maxprob = 0.51) ofmaxstat_trafo(ox[cc], minprob = 0.4, maxprob = 0.51) mcp_trafo(x = "Tukey")(data.frame(x)) mcp_trafo(x = "Tukey")(data.frame(x = x[cc])) ### Weighted logrank scores x <- c(1, 2, 3, 3, 3, 6, 6, 6, 9, 10) e <- c(1, 0, 1, 0, 1, 1, 0, 1, 0, 1) logrank_trafo(Surv(x, e)) logrank_trafo(Surv(x, e), ties.method = "Hothorn-Lausen") logrank_trafo(Surv(x, e), ties.method = "average-scores") logrank_trafo(Surv(x, e), type = "Gehan-Breslow") logrank_trafo(Surv(x, e), ties.method = "Hothorn-Lausen", type = "Gehan-Breslow") logrank_trafo(Surv(x, e), ties.method = "average-scores", type = "Gehan-Breslow") logrank_trafo(Surv(x, e), type = "Tarone-Ware") logrank_trafo(Surv(x, e), ties.method = "Hothorn-Lausen", type = "Tarone-Ware") logrank_trafo(Surv(x, e), ties.method = "average-scores", type = "Tarone-Ware") logrank_trafo(Surv(x, e), type = "Prentice") logrank_trafo(Surv(x, e), ties.method = "Hothorn-Lausen", type = "Prentice") logrank_trafo(Surv(x, e), ties.method = "average-scores", type = "Prentice") logrank_trafo(Surv(x, e), type = "Prentice-Marek") logrank_trafo(Surv(x, e), ties.method = "Hothorn-Lausen", type = "Prentice-Marek") logrank_trafo(Surv(x, e), ties.method = "average-scores", type = "Prentice-Marek") logrank_trafo(Surv(x, e), type = "Andersen-Borgan-Gill-Keiding") logrank_trafo(Surv(x, e), ties.method = "Hothorn-Lausen", type = "Andersen-Borgan-Gill-Keiding") logrank_trafo(Surv(x, e), ties.method = "average-scores", type = "Andersen-Borgan-Gill-Keiding") logrank_trafo(Surv(x, e), type = "Fleming-Harrington") logrank_trafo(Surv(x, e), ties.method = "Hothorn-Lausen", type = "Fleming-Harrington") logrank_trafo(Surv(x, e), ties.method = "average-scores", type = "Fleming-Harrington") logrank_trafo(Surv(x, e), type = "Gaugler-Kim-Liao") logrank_trafo(Surv(x, e), ties.method = "Hothorn-Lausen", type = "Gaugler-Kim-Liao") logrank_trafo(Surv(x, e), ties.method = "average-scores", type = "Gaugler-Kim-Liao") logrank_trafo(Surv(x, e), type = "Self") logrank_trafo(Surv(x, e), ties.method = "Hothorn-Lausen", type = "Self") logrank_trafo(Surv(x, e), ties.method = "average-scores", type = "Self")
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