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Ignore class when comparing with msm qmatrix #127

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merged 2 commits into from
Sep 6, 2024
Merged

Ignore class when comparing with msm qmatrix #127

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54ea2a4
Ignore class when comparing with msm qmatrix
chjackson Aug 19, 2024
544b456
Update tests/testthat/test-tpmatrix.R
chjackson Sep 6, 2024
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17 changes: 11 additions & 6 deletions tests/testthat/test-tpmatrix.R
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Original file line number Diff line number Diff line change
Expand Up @@ -229,8 +229,9 @@ fit <- msm(state_id ~ time, subject = patient_id,

test_that("qmatrix.msm() works with factor covariates and 'newdata' is one row" , {
newdata <- data.frame(strategy_name = "New 1", age = 50)
msmq <- msm::qmatrix.msm(fit, newdata[1, , drop = FALSE], ci = "none")
expect_equal(
msm::qmatrix.msm(fit, newdata[1, , drop = FALSE], ci = "none"),
unclass(msmq),
qmatrix(fit, newdata, uncertainty = "none")[, , 1],
check.attributes = FALSE
)
Expand All @@ -239,8 +240,9 @@ test_that("qmatrix.msm() works with factor covariates and 'newdata' is one row"
test_that("qmatrix.msm() works with factor covariates and 'newdata' is multiple rows" , {
newdata <- data.frame(strategy_name = c("New 1", "New 2"),
age = c(50, 55))
msmq <- msm::qmatrix.msm(fit, newdata[2, , drop = FALSE], ci = "none")
expect_equal(
msm::qmatrix.msm(fit, newdata[2, , drop = FALSE], ci = "none"),
unclass(msmq),
qmatrix(fit, newdata, uncertainty = "none")[, , 2],
check.attributes = FALSE
)
Expand All @@ -250,8 +252,9 @@ test_that("qmatrix.msm() works with covariates that vary by transition" , {
fit <- update(fit, covariates = list("1-2" = ~ strategy_name + age))
newdata <- data.frame(strategy_name = c("New 1", "New 2"),
age = c(50, 55))
msmq <- msm::qmatrix.msm(fit, newdata[2, , drop = FALSE], ci = "none")
expect_equal(
msm::qmatrix.msm(fit, newdata[2, , drop = FALSE], ci = "none"),
unclass(msmq),
qmatrix(fit, newdata, uncertainty = "none")[, , 2],
check.attributes = FALSE
)
Expand All @@ -277,8 +280,9 @@ test_that("qmatrix.msm() works with a hidden Markov model" , {
hconstraint = list(acute = c(1, 1)),
death = 3,
method = "BFGS")
msmq <- msm::qmatrix.msm(fith, covariates = list(acute = 0), ci = "none")
expect_equal(
msm::qmatrix.msm(fith, covariates = list(acute = 0), ci = "none"),
unclass(msmq),
qmatrix(fith, data.frame(acute = 0), uncertainty = "none")[,,1],
check.attributes = FALSE
)
Expand All @@ -299,8 +303,9 @@ test_that("qmatrix.msm() requires 'newdata' if covariates are included in the mo

test_that("qmatrix.msm() does not require 'newdata' if no covariates are included in the model." , {
fit <- update(fit, covariates =~ 1)
msmq <- msm::qmatrix.msm(fit, ci = "none")
expect_equal(
msm::qmatrix.msm(fit, ci = "none"),
unclass(msmq),
qmatrix(fit, uncertainty = "none")[,,1],
check.attributes = FALSE
)
Expand Down Expand Up @@ -408,4 +413,4 @@ test_that("apply_rr() can only have one complementary column for each row in mat
complement = list(c(1, 1), c(1,2))),
"There can only be one complementary column in each row."
)
})
})
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