From 4464143e509b7eedfb1511ee0aeed56df7e1d843 Mon Sep 17 00:00:00 2001
From: Sean Anderson <sean@seananderson.ca>
Date: Wed, 19 Jun 2024 10:10:56 -0700
Subject: [PATCH] Fix exponentiate in tidy() #353

And make conf.int = TRUE default
---
 R/tidy.R           | 5 +++--
 man/tidy.sdmTMB.Rd | 2 +-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/R/tidy.R b/R/tidy.R
index e1dff0112..0d42765a0 100644
--- a/R/tidy.R
+++ b/R/tidy.R
@@ -45,7 +45,7 @@
 #' tidy(fit, "ran_vals")
 
 tidy.sdmTMB <- function(x, effects = c("fixed", "ran_pars", "ran_vals"), model = 1,
-                 conf.int = FALSE, conf.level = 0.95, exponentiate = FALSE,
+                 conf.int = TRUE, conf.level = 0.95, exponentiate = FALSE,
                  silent = FALSE, ...) {
   effects <- match.arg(effects)
   assert_that(is.logical(exponentiate))
@@ -131,7 +131,6 @@ tidy.sdmTMB <- function(x, effects = c("fixed", "ran_pars", "ran_vals"), model =
   b_j_se <- se$b_j[!fe_names == "offset", drop = TRUE]
   fe_names <- fe_names[!fe_names == "offset"]
   out <- data.frame(term = fe_names, estimate = b_j, std.error = b_j_se, stringsAsFactors = FALSE)
-  if (exponentiate) out$estimate <- trans(out$estimate)
 
   if (x$tmb_data$threshold_func > 0) {
     if (x$threshold_function == 1L) {
@@ -152,6 +151,8 @@ tidy.sdmTMB <- function(x, effects = c("fixed", "ran_pars", "ran_vals"), model =
     out$conf.low <- as.numeric(trans(out$estimate - crit * out$std.error))
     out$conf.high <- as.numeric(trans(out$estimate + crit * out$std.error))
   }
+  out$estimate <- trans(out$estimate)
+  if (exponentiate) out$std.error <- NULL
 
   out_re <- list()
   log_name <- c("log_range")
diff --git a/man/tidy.sdmTMB.Rd b/man/tidy.sdmTMB.Rd
index a9ae62a67..d7d03ce3e 100644
--- a/man/tidy.sdmTMB.Rd
+++ b/man/tidy.sdmTMB.Rd
@@ -8,7 +8,7 @@
   x,
   effects = c("fixed", "ran_pars", "ran_vals"),
   model = 1,
-  conf.int = FALSE,
+  conf.int = TRUE,
   conf.level = 0.95,
   exponentiate = FALSE,
   silent = FALSE,