# NOT RUN { set.seed(1) pneumo <- transform(pneumo, let = log(exposure.time), x3 = runif(nrow(pneumo))) fit1 <- vglm(cbind(normal, mild, severe) ~ let , propodds, data = pneumo) fit2 <- vglm(cbind(normal, mild, severe) ~ let + x3, propodds, data = pneumo) fit3 <- vglm(cbind(normal, mild, severe) ~ let , cumulative, data = pneumo) # Various equivalent specifications of the LR test for testing x3 (ans1 <- lrtest(fit2, fit1)) ans2 <- lrtest(fit2, 2) ans3 <- lrtest(fit2, "x3") ans4 <- lrtest(fit2, . ~ . - x3) c(all.equal(ans1, ans2), all.equal(ans1, ans3), all.equal(ans1, ans4)) # Doing it manually (testStatistic <- 2 * (logLik(fit2) - logLik(fit1))) (mypval <- pchisq(testStatistic, df = length(coef(fit2)) - length(coef(fit1)), lower.tail = FALSE)) (ans4 <- lrtest(fit3, fit1)) # Test proportional odds (parallelism) assumption # }
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