test_that("COPD incidence is set so that prevalence is independent of calendar year within GOLD and gender stratas", {
settings <- default_settings
settings$record_mode <- record_mode["record_mode_event"]
init_session(settings = settings)
run()
data <- as.data.frame(Cget_all_events_matrix())
terminate_session()
dataF <- data[which(data[, "event"] == 1), ] #1 is event_fixed
dataF[, "age"] <- dataF[, "local_time"] + dataF[, "age_at_creation"]
dataF[, "copd"] <- (dataF[, "gold"] > 0) * 1
dataF[, "gold2p"] <- (dataF[, "gold"] > 1) * 1
dataF[, "gold3p"] <- (dataF[, "gold"] > 2) * 1
dataF[, "year"] <- dataF[, "local_time"] + dataF[, "time_at_creation"]
res <- glm(data = dataF[which(dataF[, "female"] == 0), ], formula = copd ~ age + pack_years + smoking_status + year, family = binomial(link = logit))
expect_lt (coefficients(res)[5], 0.02)
res <- glm(data = dataF[which(dataF[ "female"] == 1), ], formula = copd ~ age + pack_years + smoking_status + year, family = binomial(link = logit))
expect_lt (coefficients(res)[5], 0.02)
res <- glm(data = dataF[which(dataF[, "female"] == 0), ], formula = gold2p ~ age + pack_years + smoking_status + year, family = binomial(link = logit))
expect_lt (coefficients(res)[5], 0.02)
res <- glm(data = dataF[which(dataF[, "female"] == 1), ], formula = gold2p ~ age + pack_years + smoking_status + year, family = binomial(link = logit))
expect_lt (coefficients(res)[5], 0.02)
# For GOLD stage III and IV, the sample size is small and higher error is expected.
res <- glm(data = dataF[which(dataF[, "female"] == 0), ], formula = gold3p ~ age + pack_years + smoking_status + year, family = binomial(link = logit))
expect_lt (coefficients(res)[5], 0.07)
res <- glm(data = dataF[which(dataF[, "female"] == 1), ], formula = gold3p ~ age + pack_years + smoking_status + year, family = binomial(link = logit))
expect_lt (coefficients(res)[5], 0.07)
})
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