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develop: replacing mets::phreg.par with mets::phreg_weibull #27

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Merged
benesom merged 3 commits into from
Feb 16, 2026
Merged

develop: replacing mets::phreg.par with mets::phreg_weibull #27

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348ae5e
wip
benesom Feb 12, 2026
269f2bf
fix
benesom Feb 16, 2026
21e3e31
trigger workflows
benesom Feb 16, 2026
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40 changes: 26 additions & 14 deletions inst/tinytest/test_outcome_models.R
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Original file line number Diff line number Diff line change
Expand Up @@ -116,7 +116,7 @@ test_outcome_continuous()

test_outcome_phreg <- function() {
phreg <- mets::phreg
phreg.par <- mets::phreg.par
phreg_weibull <- mets::phreg_weibull
Surv <- survival::Surv #nolint

par1 <- list(scale = 1 / 100, shape = 2)
Expand Down Expand Up @@ -183,13 +183,20 @@ test_outcome_phreg <- function() {
xx0 <- covar(1e4)
dd <- outcome(xx0) |> cbind(xx0)

cox1 <- phreg.par(Surv(time, status) ~ a + x, data = dd)
expect_equivalent(coef(cox1), c(log(unlist(par1)), 0, 0),
tolerance = 0.2)
cox1 <- phreg_weibull(Surv(time, status) ~ a + x, data = dd)
# par1$scale ** par1$shape because of transformation in coxWeibull.lvm
expect_equivalent(
coef(cox1),
c(log(par1$scale ** par1$shape), 0, 0, log(par1$shape)),
tolerance = 0.2
)

cox0 <- phreg.par(Surv(time, status) ~ a + x, data = dd)
expect_equivalent(coef(cox0), c(log(unlist(par0)), 0, 0),
tolerance = 0.2)
cox0 <- phreg_weibull(Surv(time, status) ~ a + x, data = dd)
expect_equivalent(
coef(cox0),
c(log(par1$scale ** par1$shape), 0, 0, log(par1$shape)),
tolerance = 0.2
)

## Specify parameters
outcome <- setargs(outcome_phreg,
Expand All @@ -200,14 +207,19 @@ test_outcome_phreg <- function() {
)
dd <- outcome(xx0) |> cbind(xx0)

cox1 <- phreg.par(Surv(time, status) ~ a + x, data = dd)
expect_equivalent(coef(cox1), c(log(unlist(par1)), coef(fit1)),
tolerance = 0.2)

cox0 <- phreg.par(Surv(time, status) ~ a + x, data = dd)
expect_equivalent(coef(cox0), c(log(unlist(par0)), coef(fit1)),
tolerance = 0.2)
cox1 <- phreg_weibull(Surv(time, status) ~ a + x, data = dd)
expect_equivalent(
coef(cox1),
c(log(par1$scale ** par1$shape), coef(fit1), log(par1$shape)),
tolerance = 0.2
)

cox0 <- phreg_weibull(Surv(time, status) ~ a + x, data = dd)
expect_equivalent(
coef(cox0),
c(log(par0$scale ** par1$shape), coef(fit1), log(par0$shape)),
tolerance = 0.2
)

# Specify design via `lp` argument
outcome <- setallargs(
Expand Down
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