update tests

R/1_model_parameters.R

@@ -605,7 +605,7 @@ model_parameters.default <- function(model,
       standardize = standardize,
       exponentiate = exponentiate,
       p_adjust = p_adjust,
-      summary = summary,
+      include_info = include_info,
       keep_parameters = keep,
       drop_parameters = drop,
       vcov = vcov,

tests/testthat/_snaps/model_parameters.fixest.new.md

@@ -0,0 +1,17 @@
+# model_parameters.fixest
+
+    Code
+      model_parameters(m1, include_info = TRUE, verbose = FALSE)
+    Output
+      # Fixed Effects
+      
+      Parameter | Coefficient |   SE |         95% CI | t(187) |      p
+      -----------------------------------------------------------------
+      time      |        1.09 | 0.67 | [-0.23,  2.41] |   1.63 | 0.106 
+      phq4      |       -3.66 | 0.67 | [-4.98, -2.34] |  -5.45 | < .001
+      
+      Model: QoL ~ time + phq4 (564 Observations)
+      Sigma: 12.365 (df = 561)
+      r2: 0.743; ar2: 0.613; wr2: 0.180; war2: 0.175
+      RMSE : 10.069
+

tests/testthat/_snaps/model_parameters.glm.new.md

@@ -0,0 +1,39 @@
+# print digits model_parameters.lm
+
+    Code
+      params
+    Output
+      Parameter   | Coefficient |   SE |         95% CI | t(30) |      p
+      ------------------------------------------------------------------
+      (Intercept) |       37.29 | 1.88 | [33.45, 41.12] | 19.86 | < .001
+      wt          |       -5.34 | 0.56 | [-6.49, -4.20] | -9.56 | < .001
+      
+      Model: mpg ~ wt (32 Observations)
+      Sigma: 3.046 (df = 30)
+      R2: 0.753; adjusted R2: 0.745
+      RMSE : 2.949
+
+---
+
+    Code
+      params
+    Output
+      Parameter   | Coefficient |   SE |         95% CI | t(30) |      p
+      ------------------------------------------------------------------
+      (Intercept) |       37.29 | 1.88 | [33.45, 41.12] | 19.86 | < .001
+      wt          |       -5.34 | 0.56 | [-6.49, -4.20] | -9.56 | < .001
+
+# model_parameters.glm - Gamma - print
+
+    Code
+      mp
+    Output
+      Parameter   | Prevalence Ratio |    SE |           95% CI |   t(7) |      p
+      ---------------------------------------------------------------------------
+      (Intercept) |           245.48 | 46.72 | [173.66, 351.67] |  28.92 | < .001
+      u [log]     |             0.55 |  0.03 | [  0.49,   0.61] | -10.88 | < .001
+    Message
+      
+      Uncertainty intervals (profile-likelihood) and p-values (two-tailed)
+        computed using a Wald t-distribution approximation.
+

tests/testthat/_snaps/model_parameters.mixed.new.md

@@ -0,0 +1,72 @@
+# print-model_parameters
+
+    Code
+      model_parameters(model, effects = "fixed")
+    Output
+      Parameter   | Coefficient |   SE |         95% CI | t(558) |      p
+      -------------------------------------------------------------------
+      (Intercept) |       71.53 | 1.56 | [68.48, 74.59] |  45.98 | < .001
+      time        |        1.09 | 0.64 | [-0.17,  2.34] |   1.70 | 0.089 
+      
+      # Within-Effects
+      
+      Parameter   | Coefficient |   SE |         95% CI | t(558) |      p
+      -------------------------------------------------------------------
+      phq4 within |       -3.66 | 0.41 | [-4.46, -2.86] |  -8.95 | < .001
+      
+      # Between-Effects
+      
+      Parameter    | Coefficient |   SE |         95% CI | t(558) |      p
+      --------------------------------------------------------------------
+      phq4 between |       -6.28 | 0.50 | [-7.27, -5.30] | -12.53 | < .001
+    Message
+      
+      Uncertainty intervals (equal-tailed) and p-values (two-tailed) computed
+        using a Wald t-distribution approximation.
+
+---
+
+    Code
+      model_parameters(m1, effects = "all")
+    Output
+      # Fixed Effects
+      
+      Parameter   | Coefficient |   SE |        95% CI | t(28) |      p
+      -----------------------------------------------------------------
+      (Intercept) |        0.65 | 0.50 | [-0.38, 1.68] |  1.29 | 0.206 
+      cyl         |        0.40 | 0.08 | [ 0.25, 0.56] |  5.29 | < .001
+      
+      # Random Effects
+      
+      Parameter            | Coefficient |   SE |       95% CI
+      --------------------------------------------------------
+      SD (Intercept: gear) |        0.27 | 0.24 | [0.05, 1.54]
+      SD (Residual)        |        0.59 | 0.08 | [0.46, 0.77]
+    Message
+      
+      Uncertainty intervals (equal-tailed) and p-values (two-tailed) computed
+        using a Wald t-distribution approximation. Uncertainty intervals for
+        random effect variances computed using a Wald z-distribution
+        approximation.
+
+---
+
+    Code
+      model_parameters(m1, effects = "fixed", include_info = TRUE)
+    Output
+      # Fixed Effects
+      
+      Parameter   | Coefficient |   SE |        95% CI | t(28) |      p
+      -----------------------------------------------------------------
+      (Intercept) |        0.65 | 0.50 | [-0.38, 1.68] |  1.29 | 0.206 
+      cyl         |        0.40 | 0.08 | [ 0.25, 0.56] |  5.29 | < .001
+      
+      Model: wt ~ cyl (32 Observations)
+      Sigma: 0.594 (df = 28)
+      Conditional R2: 0.628; Marginal R2: 0.550
+      RMSE : 0.564
+    Message
+      
+      Uncertainty intervals (equal-tailed) and p-values (two-tailed) computed
+        using a Wald t-distribution approximation.
+

tests/testthat/_snaps/printing.md

@@ -92,8 +92,9 @@
       Species [virginica] * Petal Length  |        0.45 | 0.29 | [-0.12,  1.03] |   1.56 | 0.120 
       
       Model: Sepal.Length ~ Species * Petal.Length (150 Observations)
-      Residual standard deviation: 0.336 (df = 144)
+      Sigma: 0.336 (df = 144)
       R2: 0.840; adjusted R2: 0.835
+      RMSE : 0.330
     Message
       
       Uncertainty intervals (equal-tailed) and p-values (two-tailed) computed

tests/testthat/test-model_parameters.fixest.R

@@ -35,7 +35,7 @@ test_that("model_parameters.fixest", {
   # currently, a bug for fixest 10.4 on R >= 4.3
   # skip_if_not(getRversion() < "4.2.0")
   expect_snapshot(
-    model_parameters(m1, summary = TRUE, verbose = FALSE)
+    model_parameters(m1, include_info = TRUE, verbose = FALSE)
   )
 
   # Poission, df = Inf

tests/testthat/test-model_parameters.glm.R

@@ -36,10 +36,10 @@ test_that("print digits model_parameters.lm", {
   skip_if_not_installed("performance")
   model <- lm(mpg ~ wt, data = mtcars)
 
-  params <- model_parameters(model, summary = TRUE, verbose = FALSE)
+  params <- model_parameters(model, include_info = TRUE, verbose = FALSE)
   expect_snapshot(params)
 
-  params <- model_parameters(model, summary = FALSE, verbose = FALSE)
+  params <- model_parameters(model, include_info = FALSE, verbose = FALSE)
   expect_snapshot(params)
 })
 

tests/testthat/test-model_parameters.mixed.R

@@ -129,5 +129,5 @@ test_that("print-model_parameters", {
   skip_if_not_installed("merDeriv")
   expect_snapshot(model_parameters(m1, effects = "all"))
 
-  expect_snapshot(model_parameters(m1, effects = "fixed", summary = TRUE))
+  expect_snapshot(model_parameters(m1, effects = "fixed", include_info = TRUE))
 })

tests/testthat/test-p_adjust.R

@@ -23,7 +23,7 @@ test_that("model_parameters, p-adjust after keep/drop", {
   )
 
   expect_message(
-    mp <- model_parameters(model, summary = TRUE, keep = c("wt", "hp"), p_adjust = "bonferroni"),
+    mp <- model_parameters(model, include_info = TRUE, keep = c("wt", "hp"), p_adjust = "bonferroni"),
     "more than 1 element"
   )
   expect_equal(
@@ -34,7 +34,7 @@ test_that("model_parameters, p-adjust after keep/drop", {
   )
 
   expect_message(
-    mp <- model_parameters(model, summary = TRUE, keep = c("cyl", "gear"), p_adjust = "bonferroni"),
+    mp <- model_parameters(model, include_info = TRUE, keep = c("cyl", "gear"), p_adjust = "bonferroni"),
     "more than 1 element"
   )
   expect_equal(

tests/testthat/test-printing.R

@@ -25,7 +25,7 @@ withr::with_options(
       # snapshot breaks between R CMD check "classic" and "strict"
       skip_if_not_installed("performance")
       model <- lm(Sepal.Length ~ Species * Petal.Length, data = iris)
-      out <- model_parameters(model, summary = TRUE)
+      out <- model_parameters(model, include_info = TRUE)
       expect_snapshot(print(out))
     })
 

vignettes/model_parameters.Rmd

@@ -1,6 +1,6 @@
 ---
 title: "Summary of Model Parameters"
-output: 
+output:
   rmarkdown::html_vignette:
     toc: true
     fig_width: 10.08
@@ -10,7 +10,7 @@ vignette: >
   %\VignetteIndexEntry{Summary of Model Parameters}
   \usepackage[utf8]{inputenc}
   %\VignetteEngine{knitr::rmarkdown}
-editor_options: 
+editor_options:
   chunk_output_type: console
 bibliography: bibliography.bib
 ---
@@ -150,9 +150,9 @@ glm(vs ~ poly(mpg, 2) + cyl, data = mtcars, family = binomial()) |>
 ```
 
 ```{r}
-# show Odds Ratios and include model summary
+# show Odds Ratios and include model info
 glm(vs ~ poly(mpg, 2) + cyl, data = mtcars, family = binomial()) |>
-  parameters(exponentiate = TRUE, summary = TRUE)
+  parameters(exponentiate = TRUE, include_info = TRUE)
 ```
 
 ### Mixed Models
@@ -269,7 +269,7 @@ parameters(
 
 The **parameters** package extends the support to structural models.
 
-### Principal Component Analysis (PCA) and Exploratory Factor Analysis (EFA) 
+### Principal Component Analysis (PCA) and Exploratory Factor Analysis (EFA)
 
 ```{r eval=all(successfully_loaded[c("psych", "nFactors")])}
 psych::pca(mtcars, nfactors = 3) |>

vignettes/model_parameters_print.Rmd

@@ -1,6 +1,6 @@
 ---
 title: "Printing Model Parameters"
-output: 
+output:
   rmarkdown::html_vignette:
     toc: true
     fig_width: 10.08
@@ -10,7 +10,7 @@ vignette: >
   %\VignetteIndexEntry{Printing Model Parameters}
   \usepackage[utf8]{inputenc}
   %\VignetteEngine{knitr::rmarkdown}
-editor_options: 
+editor_options:
   chunk_output_type: console
 bibliography: bibliography.bib
 ---
@@ -122,13 +122,13 @@ mp <- model_parameters(model)
 print(mp, split_component = FALSE)
 ```
 
-## Adding model summaries
+## Adding model information
 
-A model summary can be added to the table when `summary = TRUE` in the call to `model_parameters()`:
+A model summary can be added to the table when `include_info = TRUE` in the call to `model_parameters()`:
 
 ```{r}
 model <- lm(Sepal.Length ~ Species * Petal.Length, data = iris)
-model_parameters(model, summary = TRUE)
+model_parameters(model, include_info = TRUE)
 ```
 
 ## Including the reference level of categorical variables
@@ -380,6 +380,6 @@ print(tab, table_width = 80)
 
 # More advances tables and markdown / HTML formatting
 
-The `print_md()` as well as `print_html()` functions can be used to create markdown (for knitting to PDF or Word) and HTML tables. 
+The `print_md()` as well as `print_html()` functions can be used to create markdown (for knitting to PDF or Word) and HTML tables.
 
 Meanwhile, there are a lot of additional packages that allow users to have even more flexibility regarding table layouts. One package we can recommend is the [*modelsummary* package](https://vincentarelbundock.github.io/modelsummary/).