update confint

NAMESPACE

@@ -7,6 +7,7 @@ S3method(as.cov_struct,cov_struct)
 S3method(as.cov_struct,formula)
 S3method(augment,mmrm)
 S3method(coef,mmrm_tmb)
+S3method(confint,mmrm)
 S3method(deviance,mmrm_tmb)
 S3method(fitted,mmrm_tmb)
 S3method(format,cov_struct)

NEWS.md

@@ -5,6 +5,7 @@
 - `Anova` is implemented for `mmrm` models and available upon loading the `car` package. It supports type II and III hypothesis testing.
 - The argument `start` for `mmrm_control()` is updated to allow function/numeric input for better
 choices of initial values.
+- `confint` on `mmrm` models will give t-based confidence interval now, instead of the normal approximation.
 
 ### Miscellaneous
 

R/mmrm-methods.R

@@ -20,6 +20,10 @@
 #'    2. If the covariance structure is spatial, the covariance matrix of two time points with unit distance
 #'       will be displayed.
 #'
+#' `confint` is used to obtain the confidence intervals for the coefficients.
+#' Please note that this is different from the confidence interval of difference
+#' of least square means from `emmeans`.
+#'
 #' @name mmrm_methods
 #'
 #' @seealso [`mmrm_tmb_methods`], [`mmrm_tidiers`] for additional methods.
@@ -227,3 +231,31 @@ print.summary.mmrm <- function(x,
   cat("\n")
   invisible(x)
 }
+
+
+#' @describeIn mmrm_methods obtain the confidence interval for the MMRM fit results.
+#' @exportS3Method
+#' @examples
+#' # Confidence Interval:
+#' confint(object)
+confint.mmrm <- function(object, parm, level = 0.95, ...) {
+  cf <- coef(object)
+  pnames <- names(cf)
+  if (missing(parm))
+    parm <- pnames
+  assert(
+    check_subset(parm, pnames),
+    check_integerish(parm, lower = 1L, upper = length(cf))
+  )
+  if (is.numeric(parm)) parm <- pnames[parm]
+  assert_number(level, lower = 0, upper = 1)
+  a <- (1 - level) / 2
+  pct <- paste(format(100 * c(a, 1 - a), trim = TRUE, scientific = FALSE, digits = 3), "%")
+  coef_table <- h_coef_table(object)
+  df <- coef_table[parm, "df"]
+  ses <- coef_table[parm, "Std. Error"]
+  fac <- stats::qt(a, df = df)
+  ci <- array(NA, dim = c(length(parm), 2L), dimnames = list(parm, pct))
+  ci[] <- cf[parm] + (ses * fac) %o% c(1, -1)
+  ci
+}

tests/testthat/test-mmrm-methods.R

@@ -103,3 +103,40 @@ test_that("print.summary.mmrm works as expected for spatial fits", {
   result <- summary(object)
   expect_snapshot_output(print(result, digits = 1), cran = FALSE)
 })
+
+# confint ----
+
+test_that("confint works for different significance levels", {
+  object <- get_mmrm()
+  expect_silent(confint(object, level = 1))
+  expect_silent(confint(object, level = 0))
+  expect_silent(confint(object, level = 0.5))
+})
+
+test_that("confint works for different `parm` input", {
+  object <- get_mmrm()
+  res <- expect_silent(confint(object, parm = c(1, 2, 3)))
+  expect_identical(row.names(res), names(coef(object))[c(1, 2, 3)])
+
+  res <- expect_silent(confint(object, parm = c("ARMCDTRT", "AVISITVIS4")))
+  expect_identical(row.names(res), c("ARMCDTRT", "AVISITVIS4"))
+
+  expect_error(
+    confint(object, parm = 100),
+    "Element 1 is not <= 11"
+  )
+  expect_error(
+    confint(object, parm = c("a", "b")),
+    "Must be a subset of"
+  )
+})
+
+test_that("confint give same result as emmeans if no ", {
+  object <- mmrm(FEV1 ~ ARMCD + us(AVISIT |USUBJID), data = fev_data)
+  emm <- emmeans(object, ~ ARMCD)
+  emm_pair <- pairs(emm, reverse = TRUE)
+  conf <- confint(emm_pair)
+  conf_coef <- confint(object, 2)
+  expect_equal(conf$lower.CL, conf_coef[, 1])
+  expect_equal(conf$upper.CL, conf_coef[, 2])
+})

vignettes/subsections/_intro-hypothesis_testing.Rmd

@@ -94,6 +94,15 @@ pairs(lsmeans_by_visit, reverse = TRUE)
 Note that we use here the `reverse` argument to obtain treatment minus
 placebo results, instead of placebo minus treatment results.
 
+To further obtain the confidence interval of the least square mean differences, we can apply
+`confint()` on the result returned by `pairs()` .
+
+This is similar to the `LSMEANS` in SAS, with `CL` and `DIFF` options.
+
+```{r pdiffci}
+confint(pairs(lsmeans_by_visit, reverse = TRUE))
+```
+
 ## Support for car
 
 This package includes methods that allow `mmrm` objects to be used with the