A few more tests

R/msmbayes_internal.R

@@ -25,20 +25,6 @@ form_qmodel <- function(Q,Qfix=NULL){
   )
 }
 
-tidy_Q <- function(Q, full=FALSE){
-  nst <- nrow(Q)
-  fromnames <- rownames(Q)
-  tonames <- colnames(Q)
-  if (is.null(fromnames)) fromnames <- as.character(1:nst)
-  if (is.null(tonames)) tonames <- as.character(1:nst)
-  dat <- data.frame(fromstate = fromnames[row(Q)],
-                    tostate = tonames[col(Q)],
-                    rate = as.vector(Q))
-  dat <- dat[dat$fromstate != dat$tostate,,drop=FALSE]
-  if (!full) dat <- dat[dat$rate >0,,drop=FALSE]
-  dat
-}
-
 #' @return List of information about the misclassification structure
 #'
 #' @noRd

tests/testthat/test_msmbayes.R

@@ -38,5 +38,16 @@ test_that("Covariates msmbayes model agrees with msm",{
                     (bayes_ests_age |> pull(`97.5%`)  >  msm_age)))
   expect_true(all((bayes_ests_sex |> pull(`2.5%`)  <  msm_sex) &
                     (bayes_ests_sex |> pull(`97.5%`)  >  msm_sex)))
+  expect_s3_class(summary(draws)$value,"rvar")
 })
 
+
+test_that("Phase-type model runs, print and summary",{
+  draws <- msmbayes(infsim2, state="state", time="months", subject="subject",
+                    Q=Q, nphase=c(1,2), fit_method="optimize")
+  expect_s3_class(draws,"msmbayes")
+  print(draws)
+  expect_s3_class(summary(draws)$value,"rvar")
+  expect_true(nrow(mean_sojourn(draws, by_phase=FALSE)) == 2)
+  expect_true(nrow(mean_sojourn(draws, by_phase=TRUE)) == 3)
+})

tests/testthat/test_msmhist.R

@@ -0,0 +1,8 @@
+test_that("msmhist runs",{
+  p <- msmhist(infsim, "state","months", "subject", nbins=10)
+  expect_s3_class(p, "ggplot")
+  p <- msmhist(infsim, "state","months", "subject", absorbing=2, nbins=10)
+  expect_s3_class(p, "ggplot")
+  bdat <- msmhist_bardata(infsim, "state","months", "subject", nbins=10)
+  expect_s3_class(bdat, "data.frame")
+})