Nothing
context("Test formula special.")
test_that("Formula special 'func' works as expected", {
## time + latency + covar (DLNM approach)
cumu1 <- eval_special(~ cumulative(t, latency(te), x, tz_var = "te"))[[1]]
expect_list(cumu1, any.missing = TRUE, len = 5)
expect_identical(cumu1$latency_var, "te")
expect_identical(cumu1$tz_var, "te")
expect_identical(cumu1$col_vars, c("t", "te", "x"))
expect_function(cumu1$ll_fun, args = c("t", "tz"))
expect_identical(cumu1$suffix, NULL)
})
test_that("Formula special 'concurrent' works as expected", {
## time + latency + covar (DLNM approach)
ccr1 <- eval_special(~ concurrent(x1, x2, tz_var = "te"),
special = "concurrent")[[1]]
expect_list(ccr1, any.missing = TRUE, len = 5)
expect_identical(ccr1$tz_var, "te")
expect_identical(ccr1$col_vars, c("x1", "x2"))
expect_function(ccr1$ll_fun, args = c("t"))
expect_identical(ccr1$lag, 0)
expect_identical(ccr1$suffix, NULL)
data("pbc", package = "survival")
event_df <- pbc %>%
filter(id <= 5) %>%
mutate(event = 1L*(status == 2)) %>%
select(id, time, event, sex, bili, protime, albumin)
tdc_df <- pbcseq %>%
filter(id <= 5) %>%
select(id, day, bili, protime, albumin)
formula <- Surv(time, event)~ concurrent(bili, protime, tz_var = "day") +
concurrent(albumin, tz_var = "day")
nested_fdf <- nest_tdc(list(event_df, tdc_df), formula, id = "id")
ped_ccr <- as_ped(list(event_df, tdc_df), formula, id = "id")
})
context("Transformation of longitudinal covariates to functional covariates")
test_that("Covariate to matrix Transformation works", {
event_df <- filter(patient, CombinedID == 1116)
tdc_df <- filter(daily, CombinedID == 1116)
## check nesting
nested_df <- nest_tdc(
data = list(event_df, tdc_df),
formula = Surv(survhosp, status)~ . +
cumulative(Study_Day, caloriesPercentage, tz_var="Study_Day") +
cumulative(proteinGproKG, tz_var="Study_Day"),
cut = 0:30,
id = "CombinedID")
expect_tibble(nested_df, any.missing=FALSE, nrows=1, ncols=15)
expect_identical(colnames(nested_df), c("Year", "CombinedicuID", "CombinedID", "Survdays",
"PatientDied", "survhosp", "Gender", "Age", "AdmCatID", "ApacheIIScore",
"BMI", "DiagID2", "Study_Day", "caloriesPercentage", "proteinGproKG"))
expect_identical(names(attributes(nested_df))[-c(1:3)],
c("id_var", "time_var", "status_var", "tdc_vars",
"breaks", "func_list", "id_n", "id_tseq", "id_tz_seq"))
## check data trafo
expect_error(get_cumulative(nested_df, ~cumulative(t)))
f1 <- get_cumulative(nested_df, ~ . +
cumulative(survhosp, latency(Study_Day), caloriesPercentage, tz_var = "Study_Day"))
expect_list(f1$func_mats, types=c("numeric", "numeric", "numeric", "integer"),
any.missing=FALSE, len=4, names="named")
f2 <- get_cumulative(nested_df,
~. + cumulative(survhosp, latency(Study_Day), caloriesPercentage, tz_var = "Study_Day") +
cumulative(proteinGproKG, tz_var = "Study_Day"))
expect_list(f2$func_mats, types=c(rep("numeric", 3), "integer", "numeric"),
any.missing = FALSE, len=5, names="named")
})
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