From dc1c9067448fb3c170023e8ccfc190daa9b3f4a0 Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Tue, 21 Nov 2023 11:20:04 +0100
Subject: [PATCH] add tests

---
 DESCRIPTION                                   |  1 +
 R/methods_logistf.R                           |  2 +-
 .../windows/model_parameters.logistf.md       | 63 +++++++++++++++++++
 .../testthat/test-model_parameters.logistf.R  | 27 ++++++++
 4 files changed, 92 insertions(+), 1 deletion(-)
 create mode 100644 tests/testthat/_snaps/windows/model_parameters.logistf.md
 create mode 100644 tests/testthat/test-model_parameters.logistf.R

diff --git a/DESCRIPTION b/DESCRIPTION
index 9d2abefc3..b16d757e7 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -146,6 +146,7 @@ Suggests:
     lme4,
     lmerTest,
     lmtest,
+    logistf,
     logspline,
     lqmm,
     M3C,
diff --git a/R/methods_logistf.R b/R/methods_logistf.R
index 2912c488b..27f47562e 100644
--- a/R/methods_logistf.R
+++ b/R/methods_logistf.R
@@ -49,7 +49,7 @@ p_value.logistf <- function(model, ...) {
   utils::capture.output(s <- summary(model)) # nolint
 
   .data_frame(
-    Parameter = .remove_backticks_from_string(names(s$prob)),
+    Parameter = .remove_backticks_from_string(names(s$coefficients)),
     p = as.vector(s$prob)
   )
 }
diff --git a/tests/testthat/_snaps/windows/model_parameters.logistf.md b/tests/testthat/_snaps/windows/model_parameters.logistf.md
new file mode 100644
index 000000000..d15d7ac16
--- /dev/null
+++ b/tests/testthat/_snaps/windows/model_parameters.logistf.md
@@ -0,0 +1,63 @@
+# model_parameters.logistf
+
+    Code
+      params
+    Output
+      # Fixed Effects
+      
+      Parameter   | Log-Odds |   SE |         95% CI | Chi2(1) |      p
+      -----------------------------------------------------------------
+      (Intercept) |     0.12 | 0.48 | [-0.82,  1.07] |    0.06 | 0.802 
+      age         |    -1.11 | 0.41 | [-1.97, -0.31] |    7.51 | 0.006 
+      oc          |    -0.07 | 0.43 | [-0.94,  0.79] |    0.02 | 0.875 
+      vic         |     2.27 | 0.54 | [ 1.27,  3.44] |   22.93 | < .001
+      vicl        |    -2.11 | 0.53 | [-3.26, -1.12] |   19.10 | < .001
+      vis         |    -0.79 | 0.41 | [-1.61,  0.02] |    3.70 | 0.054 
+      dia         |     3.10 | 1.51 | [ 0.77,  8.03] |    7.90 | 0.005 
+    Message
+      
+      Uncertainty intervals (profile-likelihood) and p-values (two-tailed)
+        computed using a Wald z-distribution approximation.
+
+# model_parameters.flic
+
+    Code
+      params
+    Output
+      # Fixed Effects
+      
+      Parameter   | Log-Odds |   SE |         95% CI | Chi2(1) |      p
+      -----------------------------------------------------------------
+      (Intercept) |     0.13 | 0.28 | [-0.82,  1.08] |    0.85 | 0.358 
+      age         |    -1.11 | 0.29 | [-1.97, -0.31] |    7.51 | 0.006 
+      oc          |    -0.07 | 0.24 | [-0.94,  0.79] |    0.02 | 0.875 
+      vic         |     2.27 | 0.24 | [ 1.27,  3.44] |   22.93 | < .001
+      vicl        |    -2.11 | 0.25 | [-3.26, -1.12] |   19.10 | < .001
+      vis         |    -0.79 | 0.26 | [-1.61,  0.02] |    3.70 | 0.054 
+      dia         |     3.10 | 0.41 | [ 0.77,  8.03] |    7.90 | 0.005 
+    Message
+      
+      Uncertainty intervals (profile-likelihood) and p-values (two-tailed)
+        computed using a Wald z-distribution approximation.
+
+# model_parameters.flac
+
+    Code
+      params
+    Output
+      # Fixed Effects
+      
+      Parameter   | Log-Odds |   SE |         95% CI | Chi2(1) |      p
+      -----------------------------------------------------------------
+      (Intercept) |     0.12 | 0.48 | [-0.81,  1.07] |    0.07 | 0.797 
+      age         |    -1.10 | 0.42 | [-1.95, -0.31] |    7.55 | 0.006 
+      oc          |    -0.07 | 0.43 | [-0.93,  0.79] |    0.02 | 0.879 
+      vic         |     2.28 | 0.54 | [ 1.29,  3.43] |   23.37 | < .001
+      vicl        |    -2.11 | 0.53 | [-3.24, -1.13] |   19.45 | < .001
+      vis         |    -0.79 | 0.41 | [-1.60,  0.01] |    3.74 | 0.053 
+      dia         |     3.18 | 1.53 | [ 0.87,  7.99] |    8.54 | 0.003 
+    Message
+      
+      Uncertainty intervals (profile-likelihood) and p-values (two-tailed)
+        computed using a Wald z-distribution approximation.
+
diff --git a/tests/testthat/test-model_parameters.logistf.R b/tests/testthat/test-model_parameters.logistf.R
new file mode 100644
index 000000000..824b74226
--- /dev/null
+++ b/tests/testthat/test-model_parameters.logistf.R
@@ -0,0 +1,27 @@
+skip_if_not_installed("logistf")
+skip_if_not_installed("withr")
+
+# skip_on_cran()
+
+withr::with_options(
+  list(parameters_exponentiate = FALSE),
+  {
+    data(sex2, package = "logistf")
+    m1 <- logistf::logistf(case ~ age + oc + vic + vicl + vis + dia, data = sex2)
+    m2 <- logistf::flic(m1)
+    m3 <- logistf::flac(m1, data = sex2)
+
+    test_that("model_parameters.logistf", {
+      params <- model_parameters(m1)
+      expect_snapshot(params, variant = "windows")
+    })
+    test_that("model_parameters.flic", {
+      params <- model_parameters(m2)
+      expect_snapshot(params, variant = "windows")
+    })
+    test_that("model_parameters.flac", {
+      params <- model_parameters(m3)
+      expect_snapshot(params, variant = "windows")
+    })
+  }
+)