Nothing
context("reg")
test_that("reg_x for lm, glm and coxph model", {
# basic models
fit<-reg_x(data = diabetes, x = c(1:4, 6), y ="diabetes" , factors = c(1, 3, 4), model = 'lm')
plot(fit)
fit<-reg_x(data = diabetes, x = c(1:4, 6), y ="diabetes" , factors = c(1, 3, 4), model = 'glm')
plot(fit)
fit<-reg_x(data = diabetes, x = c(3:4, 6), y ="diabetes",time=2,factors = c(1, 3, 4), model = 'coxph')
plot(fit)
#cov_show
fit<-reg_x(data = diabetes, x = c(1:4, 6), y ="diabetes" ,cov=13:14, factors = c(1, 3, 4), model = 'lm',cov_show = TRUE)
expect_message(plot(fit))
fit<-reg_x(data = diabetes, x = c(1:4, 6), y ="diabetes" ,cov=13:14, factors = c(1, 3, 4), model = 'glm',cov_show = TRUE)
expect_message(plot(fit))
fit<-reg_x(data = diabetes, x = c(3:4, 6), y ="diabetes",cov=13:14,time=2,factors = c(1, 3, 4), model = 'coxph',cov_show = TRUE)
expect_message(plot(fit))
#detail_show
fit<-reg_x(data = diabetes, x = c(1:4, 6), y ="diabetes" , factors = c(1, 3, 4), model = 'lm',detail_show = TRUE)
expect_error(plot(fit))
fit<-reg_x(data = diabetes, x = c(1:4, 6), y ="diabetes" , factors = c(1, 3, 4), model = 'glm',detail_show = TRUE)
expect_error(plot(fit))
fit<-reg_x(data = diabetes, x = c(3:4, 6), y ="diabetes",time=2,factors = c(1, 3, 4), model = 'coxph',detail_show = TRUE)
expect_error(plot(fit))
# y is also in x
expect_warning(fit<-reg_x(data = diabetes, x = c(1:4, 5), y ="diabetes" , factors = c(1, 3, 4), model = 'lm'))
})
test_that("reg_y for lm, glm and coxph model", {
# basic models
fit<-reg_y(data = diabetes, x = c(1:4, 6), y =c("diabetes","C2rs9332739","CFBrs641153") , factors = c(1, 3, 4), model = 'lm')
expect_message(plot(fit))
fit<-reg_y(data = diabetes, x = c(1:4, 6), y =c("diabetes","C2rs9332739","CFBrs641153") , factors = c(1, 3, 4), model = 'glm')
expect_message(plot(fit))
fit<-reg_y(data = diabetes, x = c(3:4, 6), y =c("diabetes","C2rs9332739","CFBrs641153"),time=2,factors = c(1, 3, 4), model = 'coxph')
expect_message(plot(fit))
#cov_show
fit<-reg_y(data = diabetes, x = c(1:3, 6), y =c("diabetes","C2rs9332739","CFBrs641153") ,cov=c(11,14), factors = c(1, 3, 4), model = 'lm',cov_show = TRUE)
expect_message(plot(fit))
fit<-reg_y(data = diabetes, x = c(1:3, 6), y =c("diabetes","C2rs9332739","CFBrs641153") ,cov=c(11,14), factors = c(1, 3, 4), model = 'glm',cov_show = TRUE)
expect_message(plot(fit))
fit<-reg_y(data = diabetes, x = c(1,3, 6), y =c("diabetes","C2rs9332739","CFBrs641153"),time=2,cov=c(11,14),factors = c(1, 3, 4), model = 'coxph',cov_show = TRUE)
expect_message(plot(fit))
# y is also in x
expect_warning(fit<-reg_y(data = diabetes, x = c(1:4, 5), y =c("diabetes","C2rs9332739","CFBrs641153") , factors = c(1, 3, 4), model = 'lm'))
})
test_that("reg for lm, glm and coxph model", {
## subgroup analysis for reg
fit<-reg(data = diabetes, x = c(2:4),group=c(1,13,14), y ="diabetes" , factors = c(1, 3, 4), model = 'glm')
expect_message(plot(fit))
fit<-reg(data = diabetes, x = c(2:4),group=c(1,13,14), y ="diabetes" , factors = c(1, 3, 4), model = 'glm',group_combine = TRUE)
expect_message(plot(fit))
fit<-reg(data = diabetes, x = c(2:4),group=c(1,13,14),cov=c(11,12), y ="diabetes" , factors = c(1, 3, 4), model = 'glm',cov_show = TRUE)
expect_message(plot(fit))
fit<-reg(data = diabetes, x = c(2:4),group=c(1,14),cov=c(11,12),y ="diabetes" , factors = c(1, 3, 4), model = 'glm',group_combine = TRUE)
expect_message(plot(fit))
fit<-reg(data = diabetes, x = c(2:4),group=c(1,14),cov=c(11,12), y =c("diabetes","CFBrs641153"), factors = c(1, 3, 4), model = 'glm',group_combine = TRUE,cov_show = TRUE)
expect_message(plot(fit))
})
test_that("display_table", {
dd<-display_table(data=diabetes,variables =c(1:4,6:10),group="diabetes")
expect_warning(dd<-display_table(data=diabetes,group="diabetes"))
dd<-display_table(data=diabetes,variables =c(1:4,6:10),group="diabetes",mean_or_median="median")
dd<-display_table(data=diabetes,variables =c(1:4,6:10),group="diabetes",mean_or_median="median",addNA = FALSE)
dd<-display_table(data=diabetes,variables =c(1:4,6:10),group="diabetes",mean_or_median="median",addNA = FALSE,discrete_limit = 3)
dd<-display_table(data=diabetes,variables =c(1:4,6:10),group="diabetes",mean_or_median="mean",addNA = TRUE,discrete_limit = 3)
expect_warning({
data<-diabetes
data$CFHrs2230199<-as.factor(data$CFHrs2230199)
dd<-display_table(data=data,variables =c(1:4,6:14),group="diabetes",mean_or_median="mean",addNA = TRUE,discrete_limit = 2,exclude_discrete = TRUE)
dd<-display_table(data=data,variables =c(1:4,6:14),group="diabetes",mean_or_median="mean",addNA = TRUE,discrete_limit = 2,exclude_discrete = FALSE)
})
dd<-display_table(data=diabetes,variables =c(1:4,6:10),group="diabetes",normtest = "shapiro.test")
dd<-display_table(data=diabetes,variables =c(1:4,6:10),group="diabetes",normtest = "lillie.test")
})
test_that("display_table_group", {
result_1<-display_table_group(data=diabetes,variables=c("age","smoking","education"),group="CFHrs2230199",super_group = "sex")
result_2<-display_table_group(data=diabetes,variables=c("age","education"),group=c("smoking"),super_group = c("CFHrs2230199","sex"))
result_3<-display_table_group(data=diabetes,variables=c("age","education"),group=c("smoking"),super_group = c("CFHrs2230199","sex"),group_combine=TRUE)
})
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