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tidy coefficents for linear smoothers #411

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Feb 25, 2025
Merged

tidy coefficents for linear smoothers #411

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11 changes: 11 additions & 0 deletions R/tidy.R
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Original file line number Diff line number Diff line change
Expand Up @@ -155,6 +155,17 @@ tidy.sdmTMB <- function(x, effects = c("fixed", "ran_pars", "ran_vals"), model =
)
}

if (x$tmb_data$has_smooths) {
p <- print_smooth_effects(x)
mm <- p$smooth_effects
out <- rbind(out,
data.frame(term = rownames(mm),
estimate = mm[,"bs"],
std.error = mm[,"bs_se"],
stringsAsFactors = FALSE))
}


if (conf.int) {
out$conf.low <- as.numeric(trans(out$estimate - crit * out$std.error))
out$conf.high <- as.numeric(trans(out$estimate + crit * out$std.error))
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1 change: 0 additions & 1 deletion sdmTMB.Rproj
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@@ -1,5 +1,4 @@
Version: 1.0
ProjectId: 1e54a969-ff39-402d-83f4-c260f1f06bda

RestoreWorkspace: No
SaveWorkspace: No
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10 changes: 10 additions & 0 deletions tests/testthat/test-tidy.R
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Expand Up @@ -45,4 +45,14 @@ test_that("tidy works", {
x <- tidy(fit, "ran_pars", conf.int = TRUE)
x
expect_true(sum(is.na(x$std.error)) == 0L)

# test smooth handling
fit <- sdmTMB(
density ~ s(depth),
data = pcod_2011, mesh = mesh,
family = tweedie(link = "log")
)
x <- tidy(fit)
expect_equal(x$term, c("(Intercept)", "sdepth"))

})
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