add tests

DESCRIPTION

@@ -146,6 +146,7 @@ Suggests:
     lme4,
     lmerTest,
     lmtest,
+    logistf,
     logspline,
     lqmm,
     M3C,

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)
   )
 }

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.
+

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")
+    })
+  }
+)