R Under development (unstable) (2026-02-10 r89394 ucrt) -- "Unsuffered Consequences" Copyright (C) 2026 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # nolint start: undesirable_function_linter. > library(testthat) > library(artma) > # nolint end: undesirable_function_linter. > > testthat::test_check("artma", reporter = "summary") Starting 2 test processes. autonomy: ..............................SS.................................. bma-auto-select: ........S............S.... > test-bma.R: PIP Post Mean Post SD Cond.Pos.Sign Idx > test-bma.R: moderator2 0.186 0.004039039 0.01661145 1 3 > test-bma.R: moderator1 0.170 -0.001841867 0.00764427 0 2 > test-bma.R: se 0.168 0.075379550 0.29503776 1 1 > test-bma.R: > test-bma.R: Mean no. regressors Draws Burnins Time > test-bma.R: "0.5240" "500" "100" "0.02591395 secs" > test-bma.R: No. models visited Modelspace 2^K % visited % Topmodels > test-bma.R: "181" "8" "2262" "100" > test-bma.R: Corr PMP No. Obs. Model Prior g-Prior > test-bma.R: "0.9983" "50" "uniform / 1.5" "UIP" > test-bma.R: Shrinkage-Stats > test-bma.R: "Av=0.9804" > test-bma.R: > test-bma.R: Time difference of 0.02591395 secs bma: ............................ box-plot-study-label: .. > test-data-auto-detection-confirmation.R: What would you like to do? > test-data-auto-detection-confirmation.R: What would you like to do? data-auto-detection-confirmation: ..................W.W. bma-collinearity: ................................................. data-column-resolution: ................................................ data-compute: ...... data-column-recognition: ....................................................................................... data-config-defaults: ............................................... > test-data-config-resolve.R: i Reading data from 'D:\temp\2026_02_11_13_55_16_2330\Rtmpcfam3U\filef9c846788b.csv' > test-data-config-resolve.R: v Data read successfully: 1000 rows, 5 columns data-index: . data-config-resolve: ..................S......... > test-data-interactive-mapping.R: > test-data-interactive-mapping.R: -- Column Mapping Summary -- > test-data-interactive-mapping.R: > test-data-interactive-mapping.R: study_id (required) -> "study_name" > test-data-interactive-mapping.R: effect (required) -> "effect" > test-data-interactive-mapping.R: ! Missing required columns: se, n_obs > test-data-interactive-mapping.R: Saving column mapping to options > test-data-interactive-mapping.R: v Column mapping saved data-interactive-mapping: ....................... data-preview: .............. > test-data-smart-detection.R: i Removing 1 empty column: "empty" > test-data-smart-detection.R: ! Found duplicate column names: "name"Making names unique... > test-data-smart-detection.R: i Removing 2 trailing empty rows > test-data-smart-detection.R: i Removing 2 empty columns: "empty1" and "empty2" > test-data-smart-detection.R: i Removing 2 trailing empty rows data-smart-detection: ................................. data-preprocess: ....W..................... dir_create_linter: .... data-utils: ............ effect-summary-stats-integration: ................................ effect-summary-stats-interactive: .................................... effect-summary-stats: ............... > test-fma.R: PIP Post Mean Post SD Cond.Pos.Sign Idx > test-fma.R: moderator1 0.254 0.004514655 0.01095860 1 2 > test-fma.R: moderator2 0.240 0.008486675 0.02046241 1 3 > test-fma.R: se 0.172 -0.075573051 0.26399473 0 1 > test-fma.R: > test-fma.R: Mean no. regressors Draws Burnins Time > test-fma.R: "0.6660" "500" "100" "0.02985787 secs" > test-fma.R: No. models visited Modelspace 2^K % visited % Topmodels > test-fma.R: "283" "8" "3538" "100" > test-fma.R: Corr PMP No. Obs. Model Prior g-Prior > test-fma.R: "0.9958" "40" "uniform / 1.5" "UIP" > test-fma.R: Shrinkage-Stats > test-fma.R: "Av=0.9756" > test-fma.R: > test-fma.R: Time difference of 0.02985787 secs fma: ....... funnel-plot: ................... indentation_guard_clause_linter: .... libs-cache: .............................................................. elliott-simulate-cdfs: ......... libs-editor: .................... modules-path: ......... > test-linear-tests.R: > test-linear-tests.R: -- Linear model tests -- > test-linear-tests.R: > test-linear-tests.R: Metric OLS Fixed Effects Between Effects > test-linear-tests.R: Publication Bias -0.25 -0.19 -1.63 > test-linear-tests.R: (Std. Error) (0.30) (0.33) (2.24) > test-linear-tests.R: Bootstrap CI (PB) [-0.28, 0.36] [-0.55, 0.19] > test-linear-tests.R: Effect Beyond Bias 0.21*** 0.20 0.36 > test-linear-tests.R: (Std. Error) (0.03) (0.33) (0.25) > test-linear-tests.R: Bootstrap CI (Effect) [0.14, 0.21] [0.16, 0.24] > test-linear-tests.R: Total Observations 30 30 30 > test-linear-tests.R: Random Effects Study Weighted OLS Precision Weighted OLS > test-linear-tests.R: -0.23 -0.33 -0.24 > test-linear-tests.R: (0.29) (0.27) (0.24) > test-linear-tests.R: [-0.58, 0.38] [-0.71, 0.10] [-0.54, 0.01] > test-linear-tests.R: 0.21*** 0.22*** 0.21*** > test-linear-tests.R: (0.03) (0.02) (0.03) > test-linear-tests.R: [0.13, 0.24] [0.17, 0.26] [0.19, 0.24] > test-linear-tests.R: 30 30 30 nonlinear-tests: .............. > test-linear-tests.R: > test-linear-tests.R: -- Linear model tests -- > test-linear-tests.R: > test-linear-tests.R: Metric OLS Fixed Effects Between Effects Random Effects > test-linear-tests.R: Publication Bias -0.245 -0.193 -1.631 -0.233 > test-linear-tests.R: (Std. Error) (0.304) (0.325) (2.239) (0.294) > test-linear-tests.R: Bootstrap CI (PB) > test-linear-tests.R: Effect Beyond Bias 0.210 0.204 0.364 0.209 > test-linear-tests.R: (Std. Error) (0.030) (0.325) (0.250) (0.029) > test-linear-tests.R: Bootstrap CI (Effect) > test-linear-tests.R: Total Observations 30 30 30 30 > test-linear-tests.R: Study Weighted OLS > test-linear-tests.R: -0.328 > test-linear-tests.R: (0.268) > test-linear-tests.R: > test-linear-tests.R: 0.218 > test-linear-tests.R: (0.025) > test-linear-tests.R: > test-linear-tests.R: 30 linear-tests: ........... options-significance-marks: ... > test-options-column-preprocessing.R: > test-options-column-preprocessing.R: -- Auto-detecting column mappings -- > test-options-column-preprocessing.R: > test-options-column-preprocessing.R: i Reading data from 'D:\temp\2026_02_11_13_55_16_2330\Rtmpcfam3U\filef9c8292a19d1.csv' > test-options.R: v The user options file 'valid.yaml' is valid. > test-options.R: x Validation failed. > test-options.R: > test-options.R: -- Validation errors found: ---------------------------------------------------- > test-options.R: x Option data.threshold must be numeric/integer, got: four > test-options.R: > test-options.R: -- Possible Resolutions: > test-options.R: * Run `artma::options.help(c('opt.name1', 'opt.name2', ...))` to view detailed > test-options.R: descriptions of the specified options. > test-options.R: * Run `artma::options.modify()` to manually modify the options file. > test-options.R: * Run `artma::options.fix()` to automatically fix detected errors where > test-options.R: possible. > test-options.R: > test-options.R: v The user options file 'valid.yaml' has been successfully copied over to 'copied.yaml'. > test-options-column-preprocessing.R: Autonomy level is high - using auto-detected column mappings > test-options.R: v Creating a user options file 'new.yaml' was successful. > test-options.R: x Validation failed. > test-options.R: > test-options.R: -- Validation errors found: ---------------------------------------------------- > test-options.R: x Option data.threshold must be numeric/integer, got: four > test-options.R: > test-options.R: -- Possible Resolutions: > test-options.R: * Run `artma::options.help(c('opt.name1', 'opt.name2', ...))` to view detailed > test-options.R: descriptions of the specified options. > test-options.R: * Run `artma::options.modify()` to manually modify the options file. > test-options.R: * Run `artma::options.fix()` to automatically fix detected errors where > test-options.R: possible. > test-options.R: > test-options.R: > test-options.R: -- Fixing User Options File ---------------------------------------------------- > test-options.R: We have detected errors in the user options file: 'invalid.yaml'. > test-options.R: > test-options.R: -- Proposed Changes: > test-options.R: * data.threshold: four -> 10 > test-options.R: > test-options.R: i Running in non-interactive mode. The proposed changes will be applied automatically. > test-options.R: An options file 'invalid.yaml' already exists. Overwriting this file... > test-options.R: v Fixing a user options file 'invalid.yaml' was successful. > test-options.R: v The user options file 'copied.yaml' has been deleted. > test-options.R: v Creating a user options file 'to_remove.yaml' was successful. > test-options.R: v The user options file 'to_remove.yaml' has been deleted. > test-options.R: ! Options file 'stale.yaml' has 1 missing option and 2 type mismatches. Proceeding with template defaults where possible. > test-options-column-preprocessing.R: > test-options-column-preprocessing.R: -- Auto-detecting column mappings -- > test-options-column-preprocessing.R: > test-options.R: ! Options file 'stale-no-prefix.yaml' has 1 missing option and 1 type mismatch. Proceeding with template defaults where possible. > test-options-column-preprocessing.R: i Reading data from 'D:\temp\2026_02_11_13_55_16_2330\Rtmpcfam3U\filef9c8276e5532.csv' options: ..................... > test-options-column-preprocessing.R: Autonomy level is high - using auto-detected column mappings options-column-preprocessing: ......................... result-formatters: ... polyfills: ............................................ runtime-methods: . run: ...... t-stat-histogram: .................... variable-suggestion: .................................................................................................................. ══ Skipped ═════════════════════════════════════════════════════════════════════ 1. should_prompt_user respects autonomy levels ('test-autonomy.R:97:5') - Reason: Test requires interactive mode 2. should_prompt_user returns TRUE when level not set (interactive mode) ('test-autonomy.R:121:1') - Reason: empty test 3. BMA suggestions exclude reference variables correctly ('test-bma-auto-select.R:148:1') - Reason: empty test 4. reference exclusion prevents dummy variable trap ('test-bma-auto-select.R:295:1') - Reason: empty test 5. invalidate_df_cache: clears internal cache state ('test-data-config-resolve.R:130:1') - Reason: empty test ══ Warnings ════════════════════════════════════════════════════════════════════ 1. present_detected_mapping handles required columns only ('test-data-auto-detection-confirmation.R:161:9') - Not running in interactive mode. Returning first choice. 2. present_detected_mapping handles mixed required and optional ('test-data-auto-detection-confirmation.R:204:9') - Not running in interactive mode. Returning first choice. 3. remove_redundant_columns removes columns with data when strategy is 'remove' ('test-data-preprocess.R:96:3') - ! Removing 1 extra column with data: "extra_col" i This will result in data loss. Consider using `options(artma.data.extra_columns_strategy = "keep")` ══ DONE ════════════════════════════════════════════════════════════════════════ > > proc.time() user system elapsed 4.42 0.48 20.09