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stan_clogit: allow y to be a factor #520

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May 11, 2021
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stan_clogit: allow y to be a factor #520

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stan_clogit: allow y to be a factor
jgabry May 11, 2021
37271c1
Update NEWS.md
jgabry May 11, 2021
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2 changes: 2 additions & 0 deletions NEWS.md
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Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,8 @@ intercept only models by allowing data frames with 0 columns and multiple rows.

* Effective number of parameters are computed for K-fold CV not just LOO CV. (#462)

* `stan_clogit()` now allows outcome variable to be a factor. (#520)

# rstanarm 2.21.1

* Compatible with rstan v2.21.1
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6 changes: 4 additions & 2 deletions R/stan_clogit.R
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Expand Up @@ -125,8 +125,7 @@ stan_clogit <- function(formula, data, subset, na.action = NULL, contrasts = NUL
group <- glmod$reTrms
group$strata <- glmod$strata <- as.factor(mf[,"(weights)"])
group$decov <- prior_covariance
}
else {
} else {
validate_glm_formula(formula)
mf[[1L]] <- as.name("model.frame")
mf$drop.unused.levels <- TRUE
Expand All @@ -137,6 +136,9 @@ stan_clogit <- function(formula, data, subset, na.action = NULL, contrasts = NUL
Y <- array1D_check(model.response(mf, type = "any"))
}
contrasts <- attr(X, "contrasts")
if (is.factor(Y)) {
Y <- fac2bin(Y)
}

ord <- order(group$strata)
if (any(diff(ord) <= 0)) {
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10 changes: 10 additions & 0 deletions tests/testthat/test_stan_clogit.R
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Expand Up @@ -42,6 +42,16 @@ test_that("stan_clogit runs for infert example", {
expect_stanreg(fit)
})

test_that("stan_clogit works when y is a factor", {
d <- infert[order(infert$stratum), ]
d$case <- factor(d$case, labels = c("A", "B"))
SW(fit_factor <- stan_clogit(case ~ spontaneous + induced, strata = stratum, prior = NULL,
data = infert[order(infert$stratum), ],
QR = TRUE, init_r = 0.5,
chains = CHAINS, iter = ITER, seed = SEED, refresh = 0))
expect_equal(coef(fit_factor), coef(fit))
})

test_that("stan_clogit throws error if data are not sorted", {
expect_error(update(fit, data = infert),
regexp = "Data must be sorted")
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