From 3110e50f7194677fd2c553538223f0645ae284e0 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Mon, 15 Sep 2025 17:50:00 +0000 Subject: [PATCH 01/14] Initial plan From ccbe8d007de96125af59897348fab802d7c481bd Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Mon, 15 Sep 2025 18:46:04 +0000 Subject: [PATCH 02/14] Fix sort parameter logic for parameters_model plots Co-authored-by: IndrajeetPatil <11330453+IndrajeetPatil@users.noreply.github.com> --- R/plot.parameters_model.R | 8 +++--- tests/testthat/test-plot.parameters_model.R | 32 +++++++++++++++++++++ 2 files changed, 36 insertions(+), 4 deletions(-) diff --git a/R/plot.parameters_model.R b/R/plot.parameters_model.R index 49076abe6..57b9eb85b 100644 --- a/R/plot.parameters_model.R +++ b/R/plot.parameters_model.R @@ -410,12 +410,12 @@ plot.see_parameters_model <- function( if (isTRUE(sort) || (!is.null(sort) && sort == "ascending")) { x$Parameter <- factor( x$Parameter, - levels = rev(unique(x$Parameter)[order(x$Coefficient)]) + levels = unique(x$Parameter)[order(x$Coefficient)] ) } else if (!is.null(sort) && sort == "descending") { x$Parameter <- factor( x$Parameter, - levels = unique(x$Parameter)[order(x$Coefficient)] + levels = rev(unique(x$Parameter)[order(x$Coefficient)]) ) } else { # sort coefficients as they appear in the classical summary output by default @@ -807,10 +807,10 @@ plot.see_parameters_model <- function( if (isTRUE(sort) || (!is.null(sort) && sort == "ascending")) { x$Level <- factor( x$Level, - levels = rev(unique(x$Level)[order(x$Coefficient)]) + levels = unique(x$Level)[order(x$Coefficient)] ) } else if (!is.null(sort) && sort == "descending") { - x$Level <- factor(x$Level, levels = unique(x$Level)[order(x$Coefficient)]) + x$Level <- factor(x$Level, levels = rev(unique(x$Level)[order(x$Coefficient)])) } else { # sort coefficients as they appear in the classical summary output by default x$Level <- factor(x$Level, levels = rev(unique(x$Level))) diff --git a/tests/testthat/test-plot.parameters_model.R b/tests/testthat/test-plot.parameters_model.R index abbe59ec9..f2e25adcf 100644 --- a/tests/testthat/test-plot.parameters_model.R +++ b/tests/testthat/test-plot.parameters_model.R @@ -14,6 +14,38 @@ test_that("`plot.see_parameters_model()` works", { }) +test_that("`plot.see_parameters_model()` sort parameter works for fixed effects", { + m <- lm(mpg ~ wt + cyl + gear + disp, data = mtcars) + result <- parameters::model_parameters(m) + + # Test sort = TRUE (should be same as ascending) + p1 <- plot(result, sort = TRUE) + expect_s3_class(p1, "gg") + + # Test sort = "ascending" + p2 <- plot(result, sort = "ascending") + expect_s3_class(p2, "gg") + + # Test sort = "descending" + p3 <- plot(result, sort = "descending") + expect_s3_class(p3, "gg") + + # Test with labels + p4 <- plot(result, sort = "ascending", show_labels = TRUE) + expect_s3_class(p4, "gg") + + vdiffr::expect_doppelganger( + title = "plot.model_parameters_sort_ascending", + fig = plot(result, sort = "ascending", show_labels = TRUE) + ) + + vdiffr::expect_doppelganger( + title = "plot.model_parameters_sort_descending", + fig = plot(result, sort = "descending", show_labels = TRUE) + ) +}) + + test_that("`plot.see_parameters_model()` errors for anova tables", { skip_if_not_installed("parameters") data(iris) From 847507e387fc2aa917e167d8d62764e32054bc81 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Mon, 15 Sep 2025 19:01:12 +0000 Subject: [PATCH 03/14] Add script to generate missing vdiffr snapshots for sort parameter tests Co-authored-by: IndrajeetPatil <11330453+IndrajeetPatil@users.noreply.github.com> --- DESCRIPTION.bak | 129 +++++++++++++++++++++++++++++++++++ generate_missing_snapshots.R | 51 ++++++++++++++ 2 files changed, 180 insertions(+) create mode 100644 DESCRIPTION.bak create mode 100644 generate_missing_snapshots.R diff --git a/DESCRIPTION.bak b/DESCRIPTION.bak new file mode 100644 index 000000000..28ca678bb --- /dev/null +++ b/DESCRIPTION.bak @@ -0,0 +1,129 @@ +Type: Package +Package: see +Title: Model Visualisation Toolbox for 'easystats' and 'ggplot2' +Version: 0.12.0 +Authors@R: + c(person(given = "Daniel", + family = "Lüdecke", + role = c("aut", "ctb"), + email = "d.luedecke@uke.de", + comment = c(ORCID = "0000-0002-8895-3206")), + person(given = "Dominique", + family = "Makowski", + role = c("aut", "inv"), + email = "dom.makowski@gmail.com", + comment = c(ORCID = "0000-0001-5375-9967")), + person(given = "Indrajeet", + family = "Patil", + role = c("aut", "cre"), + email = "patilindrajeet.science@gmail.com", + comment = c(ORCID = "0000-0003-1995-6531")), + person(given = "Mattan S.", + family = "Ben-Shachar", + role = c("aut", "ctb"), + email = "matanshm@post.bgu.ac.il", + comment = c(ORCID = "0000-0002-4287-4801")), + person(given = "Brenton M.", + family = "Wiernik", + role = c("aut", "ctb"), + email = "brenton@wiernik.org", + comment = c(ORCID = "0000-0001-9560-6336")), + person(given = "Rémi", + family = "Thériault", + role = c("aut", "ctb"), + email = "remi.theriault@mail.mcgill.ca", + comment = c(ORCID = "0000-0003-4315-6788")), + person(given = "Philip", + family = "Waggoner", + role = c("aut", "ctb"), + email = "philip.waggoner@gmail.com", + comment = c(ORCID = "0000-0002-7825-7573")), + person(given = "Jeffrey R.", + family = "Stevens", + role = "ctb", + email = "jeffrey.r.stevens@gmail.com", + comment = c(ORCID = "0000-0003-2375-1360")), + person(given = "Matthew", + family = "Smith", + role = "rev", + email = "M.Smith3@napier.ac.uk"), + person(given = "Jakob", + family = "Bossek", + role = "rev", + email = "bossek@wi.uni-muenster.de")) +Maintainer: Indrajeet Patil +Description: Provides plotting utilities supporting packages in the 'easystats' + ecosystem () and some extra themes, + geoms, and scales for 'ggplot2'. Color scales are based on + . + References: Lüdecke et al. (2021) . +License: MIT + file LICENSE +URL: https://easystats.github.io/see/ +BugReports: https://github.com/easystats/see/issues +Depends: + graphics, + grDevices, + R (>= 4.1), + stats +Imports: + bayestestR (>= 0.17.0), + correlation (>= 0.8.8), + datawizard (>= 1.2.0), + effectsize (>= 1.0.1), + ggplot2 (>= 4.0.0), + insight (>= 1.4.1), + modelbased (>= 0.13.0), + patchwork (>= 1.3.2), + parameters (>= 0.28.1), + performance (>= 0.15.1) +Suggests: + BH, + brms, + collapse, + curl, + DHARMa, + discovr, + emmeans, + factoextra, + Formula, + ggdag, + ggdist, + ggraph, + ggrepel, + ggridges, + ggside, + glmmTMB, + grid, + httr2, + lavaan, + lme4, + logspline, + marginaleffects, + MASS, + mclogit, + mclust, + merDeriv, + mgcv, + metafor, + NbClust, + nFactors, + psych, + qqplotr (>= 0.0.6), + randomForest, + RcppEigen, + rlang, + rmarkdown, + rstanarm, + scales (>= 1.4.0), + splines, + testthat (>= 3.2.1), + tidygraph, + vdiffr (>= 1.0.8) +Encoding: UTF-8 +Language: en-US +Roxygen: list(markdown = TRUE) +RoxygenNote: 7.3.3 +Config/testthat/edition: 3 +Config/testthat/parallel: true +Config/Needs/website: easystats/easystatstemplate +Config/rcmdcheck/ignore-inconsequential-notes: true diff --git a/generate_missing_snapshots.R b/generate_missing_snapshots.R new file mode 100644 index 000000000..45c81c058 --- /dev/null +++ b/generate_missing_snapshots.R @@ -0,0 +1,51 @@ +# Script to generate missing vdiffr snapshots for sort parameter tests +# Run this in an R environment with proper dependencies installed + +# Install required packages if not already installed +if (!requireNamespace("testthat", quietly = TRUE)) install.packages("testthat") +if (!requireNamespace("vdiffr", quietly = TRUE)) install.packages("vdiffr") +if (!requireNamespace("parameters", quietly = TRUE)) install.packages("parameters") +if (!requireNamespace("see", quietly = TRUE)) install.packages("see") + +# Load libraries +library(testthat) +library(vdiffr) +library(parameters) +library(see) + +# Ensure we're in the correct directory (package root) +if (!file.exists("DESCRIPTION") || !file.exists("tests/testthat/test-plot.parameters_model.R")) { + stop("Please run this script from the package root directory") +} + +# Set up the test environment +withr::local_dir(here::here()) + +# Create test data (matching the test file) +m <- lm(mpg ~ wt + cyl + gear + disp, data = mtcars) +result <- parameters::model_parameters(m) + +# Generate the missing snapshots +message("Generating vdiffr snapshots for sort parameter tests...") + +# Test context setup +testthat::test_that("Generate missing sort parameter snapshots", { + + # Generate ascending sort snapshot + vdiffr::expect_doppelganger( + title = "plot.model_parameters_sort_ascending", + fig = plot(result, sort = "ascending", show_labels = TRUE) + ) + + # Generate descending sort snapshot + vdiffr::expect_doppelganger( + title = "plot.model_parameters_sort_descending", + fig = plot(result, sort = "descending", show_labels = TRUE) + ) + +}) + +message("Snapshots should now be generated in tests/testthat/_snaps/plot.parameters_model/") +message("Expected files:") +message("- plot-model-parameters-sort-ascending.svg") +message("- plot-model-parameters-sort-descending.svg") \ No newline at end of file From 771b723d6f0f3b3ada1e7529f9a74c30a680f1c2 Mon Sep 17 00:00:00 2001 From: Indrajeet Patil Date: Mon, 15 Sep 2025 21:49:48 +0200 Subject: [PATCH 04/14] generate snapshots --- .../plot-model-parameters-random-4.svg | 432 +++++++++--------- .../plot-model-parameters-random-5.svg | 396 ++++++++-------- .../plot-model-parameters-random-6.svg | 216 ++++----- .../plot-model-parameters-sort-ascending.svg | 64 +++ .../plot-model-parameters-sort-descending.svg | 64 +++ 5 files changed, 650 insertions(+), 522 deletions(-) create mode 100644 tests/testthat/_snaps/plot.parameters_model/plot-model-parameters-sort-ascending.svg create mode 100644 tests/testthat/_snaps/plot.parameters_model/plot-model-parameters-sort-descending.svg diff --git a/tests/testthat/_snaps/plot.parameters_model/plot-model-parameters-random-4.svg b/tests/testthat/_snaps/plot.parameters_model/plot-model-parameters-random-4.svg index 48c3f396e..db0b2b123 100644 --- a/tests/testthat/_snaps/plot.parameters_model/plot-model-parameters-random-4.svg +++ b/tests/testthat/_snaps/plot.parameters_model/plot-model-parameters-random-4.svg @@ -28,96 +28,96 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -2.26 [-21.40, 25.92] --40.40 [-64.06, -16.74] --38.96 [-62.62, -15.30] -23.69 [0.03, 47.35] -22.26 [-1.40, 45.92] -9.04 [-14.62, 32.70] -16.84 [-6.82, 40.50] --7.23 [-30.89, 16.43] --0.33 [-23.99, 23.32] -34.89 [11.23, 58.55] --25.21 [-48.87, -1.55] --13.07 [-36.73, 10.59] -4.58 [-19.08, 28.24] -20.86 [-2.79, 44.52] -3.28 [-20.38, 26.93] --25.61 [-49.27, -1.95] -0.81 [-22.85, 24.47] -12.31 [-11.34, 35.97] + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +2.26 [-21.40, 25.92] +-40.40 [-64.06, -16.74] +-38.96 [-62.62, -15.30] +23.69 [0.03, 47.35] +22.26 [-1.40, 45.92] +9.04 [-14.62, 32.70] +16.84 [-6.82, 40.50] +-7.23 [-30.89, 16.43] +-0.33 [-23.99, 23.32] +34.89 [11.23, 58.55] +-25.21 [-48.87, -1.55] +-13.07 [-36.73, 10.59] +4.58 [-19.08, 28.24] +20.86 [-2.79, 44.52] +3.28 [-20.38, 26.93] +-25.61 [-49.27, -1.95] +0.81 [-22.85, 24.47] +12.31 [-11.34, 35.97] @@ -129,96 +129,96 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -9.20 [4.68, 13.72] --8.62 [-13.14, -4.10] --5.45 [-9.97, -0.93] --4.81 [-9.33, -0.30] --3.07 [-7.59, 1.45] --0.27 [-4.79, 4.25] --0.22 [-4.74, 4.29] -1.07 [-3.44, 5.59] --10.75 [-15.27, -6.23] -8.63 [4.11, 13.15] -1.17 [-3.34, 5.69] -6.61 [2.10, 11.13] --3.02 [-7.53, 1.50] -3.54 [-0.98, 8.05] -0.87 [-3.65, 5.39] -4.82 [0.31, 9.34] --0.99 [-5.51, 3.53] -1.28 [-3.23, 5.80] + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +9.20 [4.68, 13.72] +-8.62 [-13.14, -4.10] +-5.45 [-9.97, -0.93] +-4.81 [-9.33, -0.30] +-3.07 [-7.59, 1.45] +-0.27 [-4.79, 4.25] +-0.22 [-4.74, 4.29] +1.07 [-3.44, 5.59] +-10.75 [-15.27, -6.23] +8.63 [4.11, 13.15] +1.17 [-3.34, 5.69] +6.61 [2.10, 11.13] +-3.02 [-7.53, 1.50] +3.54 [-0.98, 8.05] +0.87 [-3.65, 5.39] +4.82 [0.31, 9.34] +-0.99 [-5.51, 3.53] +1.28 [-3.23, 5.80] @@ -246,43 +246,43 @@ 0 50 -337 -330 -331 -352 -333 -372 -332 -351 -369 -308 -371 -335 -334 -350 -349 -370 -310 -309 +309 +310 +370 +349 +350 +334 +335 +371 +308 +369 +351 +332 +372 +333 +352 +331 +330 +337 -337 -330 -331 -352 -333 -372 -332 -351 -369 -308 -371 -335 -334 -350 -349 -370 -310 -309 +309 +310 +370 +349 +350 +334 +335 +371 +308 +369 +351 +332 +372 +333 +352 +331 +330 +337 Coefficient Level plot.model_parameters_random_4 diff --git a/tests/testthat/_snaps/plot.parameters_model/plot-model-parameters-random-5.svg b/tests/testthat/_snaps/plot.parameters_model/plot-model-parameters-random-5.svg index 90a3a03f0..1018365b9 100644 --- a/tests/testthat/_snaps/plot.parameters_model/plot-model-parameters-random-5.svg +++ b/tests/testthat/_snaps/plot.parameters_model/plot-model-parameters-random-5.svg @@ -28,96 +28,96 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -2.26 [-21.40, 25.92] --40.40 [-64.06, -16.74] --38.96 [-62.62, -15.30] -23.69 [0.03, 47.35] -22.26 [-1.40, 45.92] -9.04 [-14.62, 32.70] -16.84 [-6.82, 40.50] --7.23 [-30.89, 16.43] --0.33 [-23.99, 23.32] -34.89 [11.23, 58.55] --25.21 [-48.87, -1.55] --13.07 [-36.73, 10.59] -4.58 [-19.08, 28.24] -20.86 [-2.79, 44.52] -3.28 [-20.38, 26.93] --25.61 [-49.27, -1.95] -0.81 [-22.85, 24.47] -12.31 [-11.34, 35.97] + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +2.26 [-21.40, 25.92] +-40.40 [-64.06, -16.74] +-38.96 [-62.62, -15.30] +23.69 [0.03, 47.35] +22.26 [-1.40, 45.92] +9.04 [-14.62, 32.70] +16.84 [-6.82, 40.50] +-7.23 [-30.89, 16.43] +-0.33 [-23.99, 23.32] +34.89 [11.23, 58.55] +-25.21 [-48.87, -1.55] +-13.07 [-36.73, 10.59] +4.58 [-19.08, 28.24] +20.86 [-2.79, 44.52] +3.28 [-20.38, 26.93] +-25.61 [-49.27, -1.95] +0.81 [-22.85, 24.47] +12.31 [-11.34, 35.97] @@ -129,96 +129,96 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -9.20 [4.68, 13.72] --8.62 [-13.14, -4.10] --5.45 [-9.97, -0.93] --4.81 [-9.33, -0.30] --3.07 [-7.59, 1.45] --0.27 [-4.79, 4.25] --0.22 [-4.74, 4.29] -1.07 [-3.44, 5.59] --10.75 [-15.27, -6.23] -8.63 [4.11, 13.15] -1.17 [-3.34, 5.69] -6.61 [2.10, 11.13] --3.02 [-7.53, 1.50] -3.54 [-0.98, 8.05] -0.87 [-3.65, 5.39] -4.82 [0.31, 9.34] --0.99 [-5.51, 3.53] -1.28 [-3.23, 5.80] + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +9.20 [4.68, 13.72] +-8.62 [-13.14, -4.10] +-5.45 [-9.97, -0.93] +-4.81 [-9.33, -0.30] +-3.07 [-7.59, 1.45] +-0.27 [-4.79, 4.25] +-0.22 [-4.74, 4.29] +1.07 [-3.44, 5.59] +-10.75 [-15.27, -6.23] +8.63 [4.11, 13.15] +1.17 [-3.34, 5.69] +6.61 [2.10, 11.13] +-3.02 [-7.53, 1.50] +3.54 [-0.98, 8.05] +0.87 [-3.65, 5.39] +4.82 [0.31, 9.34] +-0.99 [-5.51, 3.53] +1.28 [-3.23, 5.80] @@ -256,24 +256,24 @@ 100 150 -337 -330 -331 -352 -333 -372 -332 -351 -369 -308 -371 -335 -334 -350 -349 -370 -310 -309 +309 +310 +370 +349 +350 +334 +335 +371 +308 +369 +351 +332 +372 +333 +352 +331 +330 +337 Coefficient Level plot.model_parameters_random_5 diff --git a/tests/testthat/_snaps/plot.parameters_model/plot-model-parameters-random-6.svg b/tests/testthat/_snaps/plot.parameters_model/plot-model-parameters-random-6.svg index f277c1d03..c50c03686 100644 --- a/tests/testthat/_snaps/plot.parameters_model/plot-model-parameters-random-6.svg +++ b/tests/testthat/_snaps/plot.parameters_model/plot-model-parameters-random-6.svg @@ -28,96 +28,96 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -9.20 [4.68, 13.72] --8.62 [-13.14, -4.10] --5.45 [-9.97, -0.93] --4.81 [-9.33, -0.30] --3.07 [-7.59, 1.45] --0.27 [-4.79, 4.25] --0.22 [-4.74, 4.29] -1.07 [-3.44, 5.59] --10.75 [-15.27, -6.23] -8.63 [4.11, 13.15] -1.17 [-3.34, 5.69] -6.61 [2.10, 11.13] --3.02 [-7.53, 1.50] -3.54 [-0.98, 8.05] -0.87 [-3.65, 5.39] -4.82 [0.31, 9.34] --0.99 [-5.51, 3.53] -1.28 [-3.23, 5.80] + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +9.20 [4.68, 13.72] +-8.62 [-13.14, -4.10] +-5.45 [-9.97, -0.93] +-4.81 [-9.33, -0.30] +-3.07 [-7.59, 1.45] +-0.27 [-4.79, 4.25] +-0.22 [-4.74, 4.29] +1.07 [-3.44, 5.59] +-10.75 [-15.27, -6.23] +8.63 [4.11, 13.15] +1.17 [-3.34, 5.69] +6.61 [2.10, 11.13] +-3.02 [-7.53, 1.50] +3.54 [-0.98, 8.05] +0.87 [-3.65, 5.39] +4.82 [0.31, 9.34] +-0.99 [-5.51, 3.53] +1.28 [-3.23, 5.80] @@ -137,24 +137,24 @@ 10 20 -308 -337 -350 -370 -352 -372 -349 -334 -369 -333 -332 -371 -351 -331 -330 -310 -309 -335 +335 +309 +310 +330 +331 +351 +371 +332 +333 +369 +334 +349 +372 +352 +370 +350 +337 +308 Coefficient Level plot.model_parameters_random_6 diff --git a/tests/testthat/_snaps/plot.parameters_model/plot-model-parameters-sort-ascending.svg b/tests/testthat/_snaps/plot.parameters_model/plot-model-parameters-sort-ascending.svg new file mode 100644 index 000000000..ff95933cc --- /dev/null +++ b/tests/testthat/_snaps/plot.parameters_model/plot-model-parameters-sort-ascending.svg @@ -0,0 +1,64 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +-3.79 [-6.01, -1.57] +-1.78 [-3.04, -0.52] +-0.49 [-2.11, 1.13] +0.01 [-0.02, 0.03] + + + +wt +cyl +gear +disp + +-5 +0 +Coefficient +plot.model_parameters_sort_ascending + + diff --git a/tests/testthat/_snaps/plot.parameters_model/plot-model-parameters-sort-descending.svg b/tests/testthat/_snaps/plot.parameters_model/plot-model-parameters-sort-descending.svg new file mode 100644 index 000000000..14c2307d8 --- /dev/null +++ b/tests/testthat/_snaps/plot.parameters_model/plot-model-parameters-sort-descending.svg @@ -0,0 +1,64 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +-3.79 [-6.01, -1.57] +-1.78 [-3.04, -0.52] +-0.49 [-2.11, 1.13] +0.01 [-0.02, 0.03] + + + +disp +gear +cyl +wt + +-5 +0 +Coefficient +plot.model_parameters_sort_descending + + From b32581cbf5f3d6ac5fc59bc5b26075120597d480 Mon Sep 17 00:00:00 2001 From: Indrajeet Patil Date: Mon, 15 Sep 2025 21:51:32 +0200 Subject: [PATCH 05/14] Update generate_missing_snapshots.R [skip ci] Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- generate_missing_snapshots.R | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/generate_missing_snapshots.R b/generate_missing_snapshots.R index 45c81c058..53e5824f6 100644 --- a/generate_missing_snapshots.R +++ b/generate_missing_snapshots.R @@ -2,10 +2,18 @@ # Run this in an R environment with proper dependencies installed # Install required packages if not already installed -if (!requireNamespace("testthat", quietly = TRUE)) install.packages("testthat") -if (!requireNamespace("vdiffr", quietly = TRUE)) install.packages("vdiffr") -if (!requireNamespace("parameters", quietly = TRUE)) install.packages("parameters") -if (!requireNamespace("see", quietly = TRUE)) install.packages("see") +if (!requireNamespace("testthat", quietly = TRUE)) { + install.packages("testthat") +} +if (!requireNamespace("vdiffr", quietly = TRUE)) { + install.packages("vdiffr") +} +if (!requireNamespace("parameters", quietly = TRUE)) { + install.packages("parameters") +} +if (!requireNamespace("see", quietly = TRUE)) { + install.packages("see") +} # Load libraries library(testthat) From ac7af53faf9019d9eca6ab554c6c4e89eec3cbca Mon Sep 17 00:00:00 2001 From: Indrajeet Patil Date: Mon, 15 Sep 2025 21:51:42 +0200 Subject: [PATCH 06/14] Update generate_missing_snapshots.R [skip ci] Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- generate_missing_snapshots.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/generate_missing_snapshots.R b/generate_missing_snapshots.R index 53e5824f6..ad927d7b2 100644 --- a/generate_missing_snapshots.R +++ b/generate_missing_snapshots.R @@ -44,8 +44,8 @@ testthat::test_that("Generate missing sort parameter snapshots", { title = "plot.model_parameters_sort_ascending", fig = plot(result, sort = "ascending", show_labels = TRUE) ) - - # Generate descending sort snapshot + + # Generate descending sort snapshot vdiffr::expect_doppelganger( title = "plot.model_parameters_sort_descending", fig = plot(result, sort = "descending", show_labels = TRUE) From 91280033a68c059070899f6a184dd8d478b576ca Mon Sep 17 00:00:00 2001 From: Indrajeet Patil Date: Mon, 15 Sep 2025 21:51:50 +0200 Subject: [PATCH 07/14] Update tests/testthat/test-plot.parameters_model.R [skip ci] Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- tests/testthat/test-plot.parameters_model.R | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/testthat/test-plot.parameters_model.R b/tests/testthat/test-plot.parameters_model.R index f2e25adcf..cd95e9d21 100644 --- a/tests/testthat/test-plot.parameters_model.R +++ b/tests/testthat/test-plot.parameters_model.R @@ -29,7 +29,6 @@ test_that("`plot.see_parameters_model()` sort parameter works for fixed effects" # Test sort = "descending" p3 <- plot(result, sort = "descending") expect_s3_class(p3, "gg") - # Test with labels p4 <- plot(result, sort = "ascending", show_labels = TRUE) expect_s3_class(p4, "gg") From b6b1eceb2d1752650b42e9be0c2736ee3bdf130f Mon Sep 17 00:00:00 2001 From: Indrajeet Patil Date: Mon, 15 Sep 2025 21:51:58 +0200 Subject: [PATCH 08/14] Update tests/testthat/test-plot.parameters_model.R [skip ci] Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- tests/testthat/test-plot.parameters_model.R | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/testthat/test-plot.parameters_model.R b/tests/testthat/test-plot.parameters_model.R index cd95e9d21..629928e57 100644 --- a/tests/testthat/test-plot.parameters_model.R +++ b/tests/testthat/test-plot.parameters_model.R @@ -32,7 +32,6 @@ test_that("`plot.see_parameters_model()` sort parameter works for fixed effects" # Test with labels p4 <- plot(result, sort = "ascending", show_labels = TRUE) expect_s3_class(p4, "gg") - vdiffr::expect_doppelganger( title = "plot.model_parameters_sort_ascending", fig = plot(result, sort = "ascending", show_labels = TRUE) From 1175773b464c4ea0905a0304808b017e5aaa6c53 Mon Sep 17 00:00:00 2001 From: Indrajeet Patil Date: Mon, 15 Sep 2025 21:52:08 +0200 Subject: [PATCH 09/14] Update tests/testthat/test-plot.parameters_model.R [skip ci] Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- tests/testthat/test-plot.parameters_model.R | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/testthat/test-plot.parameters_model.R b/tests/testthat/test-plot.parameters_model.R index 629928e57..90718c4d7 100644 --- a/tests/testthat/test-plot.parameters_model.R +++ b/tests/testthat/test-plot.parameters_model.R @@ -36,7 +36,6 @@ test_that("`plot.see_parameters_model()` sort parameter works for fixed effects" title = "plot.model_parameters_sort_ascending", fig = plot(result, sort = "ascending", show_labels = TRUE) ) - vdiffr::expect_doppelganger( title = "plot.model_parameters_sort_descending", fig = plot(result, sort = "descending", show_labels = TRUE) From 27b75ac6685113d19e9e7f59b04f90b41db3ba44 Mon Sep 17 00:00:00 2001 From: Indrajeet Patil Date: Mon, 15 Sep 2025 21:52:16 +0200 Subject: [PATCH 10/14] Update tests/testthat/test-plot.parameters_model.R [skip ci] Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- tests/testthat/test-plot.parameters_model.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/testthat/test-plot.parameters_model.R b/tests/testthat/test-plot.parameters_model.R index 90718c4d7..4db3b2e32 100644 --- a/tests/testthat/test-plot.parameters_model.R +++ b/tests/testthat/test-plot.parameters_model.R @@ -37,7 +37,7 @@ test_that("`plot.see_parameters_model()` sort parameter works for fixed effects" fig = plot(result, sort = "ascending", show_labels = TRUE) ) vdiffr::expect_doppelganger( - title = "plot.model_parameters_sort_descending", + title = "plot.model_parameters_sort_descending", fig = plot(result, sort = "descending", show_labels = TRUE) ) }) From 42b274e9fa7c2d1d3d358e027473e957737d32b2 Mon Sep 17 00:00:00 2001 From: Indrajeet Patil Date: Mon, 15 Sep 2025 21:52:41 +0200 Subject: [PATCH 11/14] Update generate_missing_snapshots.R [skip ci] Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- generate_missing_snapshots.R | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/generate_missing_snapshots.R b/generate_missing_snapshots.R index ad927d7b2..b9353ccaa 100644 --- a/generate_missing_snapshots.R +++ b/generate_missing_snapshots.R @@ -22,7 +22,10 @@ library(parameters) library(see) # Ensure we're in the correct directory (package root) -if (!file.exists("DESCRIPTION") || !file.exists("tests/testthat/test-plot.parameters_model.R")) { +if ( + !file.exists("DESCRIPTION") || + !file.exists("tests/testthat/test-plot.parameters_model.R") +) { stop("Please run this script from the package root directory") } From e1daeb4ff9df00629123737c30170e074ba70276 Mon Sep 17 00:00:00 2001 From: Indrajeet Patil Date: Mon, 15 Sep 2025 21:52:50 +0200 Subject: [PATCH 12/14] Update generate_missing_snapshots.R [skip ci] Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- generate_missing_snapshots.R | 1 - 1 file changed, 1 deletion(-) diff --git a/generate_missing_snapshots.R b/generate_missing_snapshots.R index b9353ccaa..cf67926a8 100644 --- a/generate_missing_snapshots.R +++ b/generate_missing_snapshots.R @@ -41,7 +41,6 @@ message("Generating vdiffr snapshots for sort parameter tests...") # Test context setup testthat::test_that("Generate missing sort parameter snapshots", { - # Generate ascending sort snapshot vdiffr::expect_doppelganger( title = "plot.model_parameters_sort_ascending", From 4d0bf1f0eb8044f5381dd1122c1702939fdd9559 Mon Sep 17 00:00:00 2001 From: Indrajeet Patil Date: Mon, 15 Sep 2025 21:53:45 +0200 Subject: [PATCH 13/14] Apply suggestion from @github-actions[bot] Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- tests/testthat/test-plot.parameters_model.R | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/testthat/test-plot.parameters_model.R b/tests/testthat/test-plot.parameters_model.R index 4db3b2e32..a3784f628 100644 --- a/tests/testthat/test-plot.parameters_model.R +++ b/tests/testthat/test-plot.parameters_model.R @@ -17,7 +17,6 @@ test_that("`plot.see_parameters_model()` works", { test_that("`plot.see_parameters_model()` sort parameter works for fixed effects", { m <- lm(mpg ~ wt + cyl + gear + disp, data = mtcars) result <- parameters::model_parameters(m) - # Test sort = TRUE (should be same as ascending) p1 <- plot(result, sort = TRUE) expect_s3_class(p1, "gg") From 1bacb0de8b9d822b607898079289a9b585687353 Mon Sep 17 00:00:00 2001 From: Indrajeet Patil Date: Mon, 15 Sep 2025 21:55:07 +0200 Subject: [PATCH 14/14] remove unneeded files --- .gitignore | 2 + DESCRIPTION.bak | 129 ----------------------------------- generate_missing_snapshots.R | 61 ----------------- 3 files changed, 2 insertions(+), 190 deletions(-) delete mode 100644 DESCRIPTION.bak delete mode 100644 generate_missing_snapshots.R diff --git a/.gitignore b/.gitignore index 7ab91810d..0bc25ec54 100644 --- a/.gitignore +++ b/.gitignore @@ -67,3 +67,5 @@ revdep/checks.noindex revdep/library.noindex revdep/data.sqlite CRAN-SUBMISSION + +*.bak diff --git a/DESCRIPTION.bak b/DESCRIPTION.bak deleted file mode 100644 index 28ca678bb..000000000 --- a/DESCRIPTION.bak +++ /dev/null @@ -1,129 +0,0 @@ -Type: Package -Package: see -Title: Model Visualisation Toolbox for 'easystats' and 'ggplot2' -Version: 0.12.0 -Authors@R: - c(person(given = "Daniel", - family = "Lüdecke", - role = c("aut", "ctb"), - email = "d.luedecke@uke.de", - comment = c(ORCID = "0000-0002-8895-3206")), - person(given = "Dominique", - family = "Makowski", - role = c("aut", "inv"), - email = "dom.makowski@gmail.com", - comment = c(ORCID = "0000-0001-5375-9967")), - person(given = "Indrajeet", - family = "Patil", - role = c("aut", "cre"), - email = "patilindrajeet.science@gmail.com", - comment = c(ORCID = "0000-0003-1995-6531")), - person(given = "Mattan S.", - family = "Ben-Shachar", - role = c("aut", "ctb"), - email = "matanshm@post.bgu.ac.il", - comment = c(ORCID = "0000-0002-4287-4801")), - person(given = "Brenton M.", - family = "Wiernik", - role = c("aut", "ctb"), - email = "brenton@wiernik.org", - comment = c(ORCID = "0000-0001-9560-6336")), - person(given = "Rémi", - family = "Thériault", - role = c("aut", "ctb"), - email = "remi.theriault@mail.mcgill.ca", - comment = c(ORCID = "0000-0003-4315-6788")), - person(given = "Philip", - family = "Waggoner", - role = c("aut", "ctb"), - email = "philip.waggoner@gmail.com", - comment = c(ORCID = "0000-0002-7825-7573")), - person(given = "Jeffrey R.", - family = "Stevens", - role = "ctb", - email = "jeffrey.r.stevens@gmail.com", - comment = c(ORCID = "0000-0003-2375-1360")), - person(given = "Matthew", - family = "Smith", - role = "rev", - email = "M.Smith3@napier.ac.uk"), - person(given = "Jakob", - family = "Bossek", - role = "rev", - email = "bossek@wi.uni-muenster.de")) -Maintainer: Indrajeet Patil -Description: Provides plotting utilities supporting packages in the 'easystats' - ecosystem () and some extra themes, - geoms, and scales for 'ggplot2'. Color scales are based on - . - References: Lüdecke et al. (2021) . -License: MIT + file LICENSE -URL: https://easystats.github.io/see/ -BugReports: https://github.com/easystats/see/issues -Depends: - graphics, - grDevices, - R (>= 4.1), - stats -Imports: - bayestestR (>= 0.17.0), - correlation (>= 0.8.8), - datawizard (>= 1.2.0), - effectsize (>= 1.0.1), - ggplot2 (>= 4.0.0), - insight (>= 1.4.1), - modelbased (>= 0.13.0), - patchwork (>= 1.3.2), - parameters (>= 0.28.1), - performance (>= 0.15.1) -Suggests: - BH, - brms, - collapse, - curl, - DHARMa, - discovr, - emmeans, - factoextra, - Formula, - ggdag, - ggdist, - ggraph, - ggrepel, - ggridges, - ggside, - glmmTMB, - grid, - httr2, - lavaan, - lme4, - logspline, - marginaleffects, - MASS, - mclogit, - mclust, - merDeriv, - mgcv, - metafor, - NbClust, - nFactors, - psych, - qqplotr (>= 0.0.6), - randomForest, - RcppEigen, - rlang, - rmarkdown, - rstanarm, - scales (>= 1.4.0), - splines, - testthat (>= 3.2.1), - tidygraph, - vdiffr (>= 1.0.8) -Encoding: UTF-8 -Language: en-US -Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.3 -Config/testthat/edition: 3 -Config/testthat/parallel: true -Config/Needs/website: easystats/easystatstemplate -Config/rcmdcheck/ignore-inconsequential-notes: true diff --git a/generate_missing_snapshots.R b/generate_missing_snapshots.R deleted file mode 100644 index cf67926a8..000000000 --- a/generate_missing_snapshots.R +++ /dev/null @@ -1,61 +0,0 @@ -# Script to generate missing vdiffr snapshots for sort parameter tests -# Run this in an R environment with proper dependencies installed - -# Install required packages if not already installed -if (!requireNamespace("testthat", quietly = TRUE)) { - install.packages("testthat") -} -if (!requireNamespace("vdiffr", quietly = TRUE)) { - install.packages("vdiffr") -} -if (!requireNamespace("parameters", quietly = TRUE)) { - install.packages("parameters") -} -if (!requireNamespace("see", quietly = TRUE)) { - install.packages("see") -} - -# Load libraries -library(testthat) -library(vdiffr) -library(parameters) -library(see) - -# Ensure we're in the correct directory (package root) -if ( - !file.exists("DESCRIPTION") || - !file.exists("tests/testthat/test-plot.parameters_model.R") -) { - stop("Please run this script from the package root directory") -} - -# Set up the test environment -withr::local_dir(here::here()) - -# Create test data (matching the test file) -m <- lm(mpg ~ wt + cyl + gear + disp, data = mtcars) -result <- parameters::model_parameters(m) - -# Generate the missing snapshots -message("Generating vdiffr snapshots for sort parameter tests...") - -# Test context setup -testthat::test_that("Generate missing sort parameter snapshots", { - # Generate ascending sort snapshot - vdiffr::expect_doppelganger( - title = "plot.model_parameters_sort_ascending", - fig = plot(result, sort = "ascending", show_labels = TRUE) - ) - - # Generate descending sort snapshot - vdiffr::expect_doppelganger( - title = "plot.model_parameters_sort_descending", - fig = plot(result, sort = "descending", show_labels = TRUE) - ) - -}) - -message("Snapshots should now be generated in tests/testthat/_snaps/plot.parameters_model/") -message("Expected files:") -message("- plot-model-parameters-sort-ascending.svg") -message("- plot-model-parameters-sort-descending.svg") \ No newline at end of file