R Under development (unstable) (2025-01-22 r87618 ucrt) -- "Unsuffered Consequences" Copyright (C) 2025 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. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(ComBatFamQC) > > test_check("ComBatFamQC") Google Chrome was not found. Try setting the `CHROMOTE_CHROME` environment variable to the executable of a Chromium-based browser, such as Google Chrome, Chromium or Brave. Error in initialize(...) : Invalid path to Chrome GAMLSS-RS iteration 1: Global Deviance = 11577.26 GAMLSS-RS iteration 2: Global Deviance = 11577.26 GAMLSS-RS iteration 3: Global Deviance = 11577.26 GAMLSS-RS iteration 1: Global Deviance = 11582.7 GAMLSS-RS iteration 2: Global Deviance = 11582.68 GAMLSS-RS iteration 3: Global Deviance = 11582.68 Google Chrome was not found. Try setting the `CHROMOTE_CHROME` environment variable to the executable of a Chromium-based browser, such as Google Chrome, Chromium or Brave. Error in initialize(...) : Invalid path to Chrome Starting data preparation for the batch effect diagnostic and harmonization stage... Taking the result from the visual preparation stage as input... No observation is dropped due to missing values. Starting Empirical Bayes assumption check... Starting data preparation for the batch effect diagnostic and harmonization stage... The result from the visual prepration stage is not provided! The required parameters should be specified... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: no batch level is dropped. Starting Empirical Bayes assumption check... Starting data preparation for the batch effect diagnostic and harmonization stage... The result from the visual prepration stage is not provided! The required parameters should be specified... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: no batch level is dropped. Starting first-time harmonization... Starting data preparation for the batch effect diagnostic and harmonization stage... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: no batch level is dropped. Starting data preparation for the batch effect diagnostic and harmonization stage... The result from the visual prepration stage is not provided! The required parameters should be specified... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: no batch level is dropped. Starting first-time harmonization... fixed-effect model matrix is rank deficient so dropping 1 column / coefficient fixed-effect model matrix is rank deficient so dropping 1 column / coefficient fixed-effect model matrix is rank deficient so dropping 1 column / coefficient fixed-effect model matrix is rank deficient so dropping 1 column / coefficient Starting data preparation for the batch effect diagnostic and harmonization stage... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: no batch level is dropped. Starting data preparation for the batch effect diagnostic and harmonization stage... The result from the visual prepration stage is not provided! The required parameters should be specified... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: no batch level is dropped. Starting first-time harmonization... Starting data preparation for the batch effect diagnostic and harmonization stage... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: no batch level is dropped. Starting data preparation for the batch effect diagnostic and harmonization stage... The result from the visual prepration stage is not provided! The required parameters should be specified... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: no batch level is dropped. Starting first-time harmonization... Starting data preparation for the batch effect diagnostic and harmonization stage... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: no batch level is dropped. Starting out-of-sample harmonization using the saved ComBat Model... Starting data preparation for the batch effect diagnostic and harmonization stage... The result from the visual prepration stage is not provided! The required parameters should be specified... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: no batch level is dropped. Starting first-time harmonization... fixed-effect model matrix is rank deficient so dropping 1 column / coefficient fixed-effect model matrix is rank deficient so dropping 1 column / coefficient fixed-effect model matrix is rank deficient so dropping 1 column / coefficient fixed-effect model matrix is rank deficient so dropping 1 column / coefficient Starting data preparation for the batch effect diagnostic and harmonization stage... The result from the visual prepration stage is not provided! The required parameters should be specified... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: no batch level is dropped. Starting first-time harmonization... fixed-effect model matrix is rank deficient so dropping 1 column / coefficient fixed-effect model matrix is rank deficient so dropping 1 column / coefficient fixed-effect model matrix is rank deficient so dropping 1 column / coefficient fixed-effect model matrix is rank deficient so dropping 1 column / coefficient Starting data preparation for the batch effect diagnostic and harmonization stage... The result from the visual prepration stage is not provided! The required parameters should be specified... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: 1 level(s) are dropped, corresponding to 2 observations. Starting out-of-sample harmonization using the reference dataset... Joining with `by = join_by(ID, site, subid, IMAGE_ID, VISIT, visit, EXAM_DATE, dateAcquired, timedays, timeyrs, AGE, baselineAge, SEX, DIAGNOSIS, MMSCORE, manufac, manufac.model, manufac.model.site, manufac.model.strength.site, manufac.model.coil.site, manufac.model.coil.strength.site, manufac.model.strength.site.indicator, manufac.model.coil.strength.site.indicator, strength, Field_Strength, Manufacturer, Mfg_Model, Weighting, Pulse_Sequence, Slice_Thickness, TE, TR, TI, Coil, Flip_Angle, Acquisition_Plane, Matrix_X, Matrix_Y, Matrix_Z, Pixel_Spacing_X, Pixel_Spacing_Y, X, thickness.left.fusiform, thickness.left.inferior.parietal, thickness.left.inferior.temporal, thickness.left.isthmus.cingulate, thickness.left.lateral.occipital, thickness.left.lateral.orbitofrontal, thickness.left.lingual, thickness.left.medial.orbitofrontal, thickness.left.middle.temporal, thickness.left.parahippocampal, thickness.left.paracentral, thickness.left.pars.opercularis, thickness.left.pars.orbitalis, thickness.left.pars.triangularis, thickness.left.pericalcarine, thickness.left.postcentral, thickness.left.posterior.cingulate, thickness.left.precentral, thickness.left.precuneus, thickness.left.rostral.anterior.cingulate, thickness.left.rostral.middle.frontal, thickness.left.superior.frontal, thickness.left.superior.parietal, thickness.left.superior.temporal, thickness.left.supramarginal, thickness.left.transverse.temporal, thickness.left.insula, thickness.right.caudal.anterior.cingulate, thickness.right.caudal.middle.frontal, thickness.right.cuneus, thickness.right.entorhinal, thickness.right.fusiform, thickness.right.inferior.parietal, thickness.right.inferior.temporal, thickness.right.isthmus.cingulate, thickness.right.lateral.occipital, thickness.right.lateral.orbitofrontal, thickness.right.lingual, thickness.right.medial.orbitofrontal, thickness.right.middle.temporal, thickness.right.parahippocampal, thickness.right.paracentral, thickness.right.pars.opercularis, thickness.right.pars.orbitalis, thickness.right.pars.triangularis, thickness.right.pericalcarine, thickness.right.postcentral, thickness.right.posterior.cingulate, thickness.right.precentral, thickness.right.precuneus, thickness.right.rostral.anterior.cingulate, thickness.right.rostral.middle.frontal, thickness.right.superior.frontal, thickness.right.superior.parietal, thickness.right.superior.temporal, thickness.right.supramarginal, thickness.right.transverse.temporal, thickness.right.insula)` The reference data is included in the new unharmonized dataset Joining with `by = join_by(ID, site, subid, IMAGE_ID, VISIT, visit, EXAM_DATE, dateAcquired, timedays, timeyrs, AGE, baselineAge, SEX, DIAGNOSIS, MMSCORE, manufac, manufac.model, manufac.model.site, manufac.model.strength.site, manufac.model.coil.site, manufac.model.coil.strength.site, manufac.model.strength.site.indicator, manufac.model.coil.strength.site.indicator, strength, Field_Strength, Manufacturer, Mfg_Model, Weighting, Pulse_Sequence, Slice_Thickness, TE, TR, TI, Coil, Flip_Angle, Acquisition_Plane, Matrix_X, Matrix_Y, Matrix_Z, Pixel_Spacing_X, Pixel_Spacing_Y, X, thickness.left.fusiform, thickness.left.inferior.parietal, thickness.left.inferior.temporal, thickness.left.isthmus.cingulate, thickness.left.lateral.occipital, thickness.left.lateral.orbitofrontal, thickness.left.lingual, thickness.left.medial.orbitofrontal, thickness.left.middle.temporal, thickness.left.parahippocampal, thickness.left.paracentral, thickness.left.pars.opercularis, thickness.left.pars.orbitalis, thickness.left.pars.triangularis, thickness.left.pericalcarine, thickness.left.postcentral, thickness.left.posterior.cingulate, thickness.left.precentral, thickness.left.precuneus, thickness.left.rostral.anterior.cingulate, thickness.left.rostral.middle.frontal, thickness.left.superior.frontal, thickness.left.superior.parietal, thickness.left.superior.temporal, thickness.left.supramarginal, thickness.left.transverse.temporal, thickness.left.insula, thickness.right.caudal.anterior.cingulate, thickness.right.caudal.middle.frontal, thickness.right.cuneus, thickness.right.entorhinal, thickness.right.fusiform, thickness.right.inferior.parietal, thickness.right.inferior.temporal, thickness.right.isthmus.cingulate, thickness.right.lateral.occipital, thickness.right.lateral.orbitofrontal, thickness.right.lingual, thickness.right.medial.orbitofrontal, thickness.right.middle.temporal, thickness.right.parahippocampal, thickness.right.paracentral, thickness.right.pars.opercularis, thickness.right.pars.orbitalis, thickness.right.pars.triangularis, thickness.right.pericalcarine, thickness.right.postcentral, thickness.right.posterior.cingulate, thickness.right.precentral, thickness.right.precuneus, thickness.right.rostral.anterior.cingulate, thickness.right.rostral.middle.frontal, thickness.right.superior.frontal, thickness.right.superior.parietal, thickness.right.superior.temporal, thickness.right.supramarginal, thickness.right.transverse.temporal, thickness.right.insula)` Joining with `by = join_by(ID, site, subid, IMAGE_ID, VISIT, visit, EXAM_DATE, dateAcquired, timedays, timeyrs, AGE, baselineAge, SEX, DIAGNOSIS, MMSCORE, manufac, manufac.model, manufac.model.site, manufac.model.strength.site, manufac.model.coil.site, manufac.model.coil.strength.site, manufac.model.strength.site.indicator, manufac.model.coil.strength.site.indicator, strength, Field_Strength, Manufacturer, Mfg_Model, Weighting, Pulse_Sequence, Slice_Thickness, TE, TR, TI, Coil, Flip_Angle, Acquisition_Plane, Matrix_X, Matrix_Y, Matrix_Z, Pixel_Spacing_X, Pixel_Spacing_Y, X, thickness.left.fusiform, thickness.left.inferior.parietal, thickness.left.inferior.temporal, thickness.left.isthmus.cingulate, thickness.left.lateral.occipital, thickness.left.lateral.orbitofrontal, thickness.left.lingual, thickness.left.medial.orbitofrontal, thickness.left.middle.temporal, thickness.left.parahippocampal, thickness.left.paracentral, thickness.left.pars.opercularis, thickness.left.pars.orbitalis, thickness.left.pars.triangularis, thickness.left.pericalcarine, thickness.left.postcentral, thickness.left.posterior.cingulate, thickness.left.precentral, thickness.left.precuneus, thickness.left.rostral.anterior.cingulate, thickness.left.rostral.middle.frontal, thickness.left.superior.frontal, thickness.left.superior.parietal, thickness.left.superior.temporal, thickness.left.supramarginal, thickness.left.transverse.temporal, thickness.left.insula, thickness.right.caudal.anterior.cingulate, thickness.right.caudal.middle.frontal, thickness.right.cuneus, thickness.right.entorhinal, thickness.right.fusiform, thickness.right.inferior.parietal, thickness.right.inferior.temporal, thickness.right.isthmus.cingulate, thickness.right.lateral.occipital, thickness.right.lateral.orbitofrontal, thickness.right.lingual, thickness.right.medial.orbitofrontal, thickness.right.middle.temporal, thickness.right.parahippocampal, thickness.right.paracentral, thickness.right.pars.opercularis, thickness.right.pars.orbitalis, thickness.right.pars.triangularis, thickness.right.pericalcarine, thickness.right.postcentral, thickness.right.posterior.cingulate, thickness.right.precentral, thickness.right.precuneus, thickness.right.rostral.anterior.cingulate, thickness.right.rostral.middle.frontal, thickness.right.superior.frontal, thickness.right.superior.parietal, thickness.right.superior.temporal, thickness.right.supramarginal, thickness.right.transverse.temporal, thickness.right.insula)` fixed-effect model matrix is rank deficient so dropping 1 column / coefficient fixed-effect model matrix is rank deficient so dropping 1 column / coefficient fixed-effect model matrix is rank deficient so dropping 1 column / coefficient fixed-effect model matrix is rank deficient so dropping 1 column / coefficient Starting data preparation for the batch effect diagnostic and harmonization stage... The result from the visual prepration stage is not provided! The required parameters should be specified... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: 1 level(s) are dropped, corresponding to 2 observations. Starting out-of-sample harmonization using the reference dataset... Joining with `by = join_by(ID, site, subid, IMAGE_ID, VISIT, visit, EXAM_DATE, dateAcquired, timedays, timeyrs, AGE, baselineAge, SEX, DIAGNOSIS, MMSCORE, manufac, manufac.model, manufac.model.site, manufac.model.strength.site, manufac.model.coil.site, manufac.model.coil.strength.site, manufac.model.strength.site.indicator, manufac.model.coil.strength.site.indicator, strength, Field_Strength, Manufacturer, Mfg_Model, Weighting, Pulse_Sequence, Slice_Thickness, TE, TR, TI, Coil, Flip_Angle, Acquisition_Plane, Matrix_X, Matrix_Y, Matrix_Z, Pixel_Spacing_X, Pixel_Spacing_Y, X, thickness.left.fusiform, thickness.left.inferior.parietal, thickness.left.inferior.temporal, thickness.left.isthmus.cingulate, thickness.left.lateral.occipital, thickness.left.lateral.orbitofrontal, thickness.left.lingual, thickness.left.medial.orbitofrontal, thickness.left.middle.temporal, thickness.left.parahippocampal, thickness.left.paracentral, thickness.left.pars.opercularis, thickness.left.pars.orbitalis, thickness.left.pars.triangularis, thickness.left.pericalcarine, thickness.left.postcentral, thickness.left.posterior.cingulate, thickness.left.precentral, thickness.left.precuneus, thickness.left.rostral.anterior.cingulate, thickness.left.rostral.middle.frontal, thickness.left.superior.frontal, thickness.left.superior.parietal, thickness.left.superior.temporal, thickness.left.supramarginal, thickness.left.transverse.temporal, thickness.left.insula, thickness.right.caudal.anterior.cingulate, thickness.right.caudal.middle.frontal, thickness.right.cuneus, thickness.right.entorhinal, thickness.right.fusiform, thickness.right.inferior.parietal, thickness.right.inferior.temporal, thickness.right.isthmus.cingulate, thickness.right.lateral.occipital, thickness.right.lateral.orbitofrontal, thickness.right.lingual, thickness.right.medial.orbitofrontal, thickness.right.middle.temporal, thickness.right.parahippocampal, thickness.right.paracentral, thickness.right.pars.opercularis, thickness.right.pars.orbitalis, thickness.right.pars.triangularis, thickness.right.pericalcarine, thickness.right.postcentral, thickness.right.posterior.cingulate, thickness.right.precentral, thickness.right.precuneus, thickness.right.rostral.anterior.cingulate, thickness.right.rostral.middle.frontal, thickness.right.superior.frontal, thickness.right.superior.parietal, thickness.right.superior.temporal, thickness.right.supramarginal, thickness.right.transverse.temporal, thickness.right.insula)` The reference data is included in the new unharmonized dataset Joining with `by = join_by(ID, site, subid, IMAGE_ID, VISIT, visit, EXAM_DATE, dateAcquired, timedays, timeyrs, AGE, baselineAge, SEX, DIAGNOSIS, MMSCORE, manufac, manufac.model, manufac.model.site, manufac.model.strength.site, manufac.model.coil.site, manufac.model.coil.strength.site, manufac.model.strength.site.indicator, manufac.model.coil.strength.site.indicator, strength, Field_Strength, Manufacturer, Mfg_Model, Weighting, Pulse_Sequence, Slice_Thickness, TE, TR, TI, Coil, Flip_Angle, Acquisition_Plane, Matrix_X, Matrix_Y, Matrix_Z, Pixel_Spacing_X, Pixel_Spacing_Y, X, thickness.left.fusiform, thickness.left.inferior.parietal, thickness.left.inferior.temporal, thickness.left.isthmus.cingulate, thickness.left.lateral.occipital, thickness.left.lateral.orbitofrontal, thickness.left.lingual, thickness.left.medial.orbitofrontal, thickness.left.middle.temporal, thickness.left.parahippocampal, thickness.left.paracentral, thickness.left.pars.opercularis, thickness.left.pars.orbitalis, thickness.left.pars.triangularis, thickness.left.pericalcarine, thickness.left.postcentral, thickness.left.posterior.cingulate, thickness.left.precentral, thickness.left.precuneus, thickness.left.rostral.anterior.cingulate, thickness.left.rostral.middle.frontal, thickness.left.superior.frontal, thickness.left.superior.parietal, thickness.left.superior.temporal, thickness.left.supramarginal, thickness.left.transverse.temporal, thickness.left.insula, thickness.right.caudal.anterior.cingulate, thickness.right.caudal.middle.frontal, thickness.right.cuneus, thickness.right.entorhinal, thickness.right.fusiform, thickness.right.inferior.parietal, thickness.right.inferior.temporal, thickness.right.isthmus.cingulate, thickness.right.lateral.occipital, thickness.right.lateral.orbitofrontal, thickness.right.lingual, thickness.right.medial.orbitofrontal, thickness.right.middle.temporal, thickness.right.parahippocampal, thickness.right.paracentral, thickness.right.pars.opercularis, thickness.right.pars.orbitalis, thickness.right.pars.triangularis, thickness.right.pericalcarine, thickness.right.postcentral, thickness.right.posterior.cingulate, thickness.right.precentral, thickness.right.precuneus, thickness.right.rostral.anterior.cingulate, thickness.right.rostral.middle.frontal, thickness.right.superior.frontal, thickness.right.superior.parietal, thickness.right.superior.temporal, thickness.right.supramarginal, thickness.right.transverse.temporal, thickness.right.insula)` Joining with `by = join_by(ID, site, subid, IMAGE_ID, VISIT, visit, EXAM_DATE, dateAcquired, timedays, timeyrs, AGE, baselineAge, SEX, DIAGNOSIS, MMSCORE, manufac, manufac.model, manufac.model.site, manufac.model.strength.site, manufac.model.coil.site, manufac.model.coil.strength.site, manufac.model.strength.site.indicator, manufac.model.coil.strength.site.indicator, strength, Field_Strength, Manufacturer, Mfg_Model, Weighting, Pulse_Sequence, Slice_Thickness, TE, TR, TI, Coil, Flip_Angle, Acquisition_Plane, Matrix_X, Matrix_Y, Matrix_Z, Pixel_Spacing_X, Pixel_Spacing_Y, X, thickness.left.fusiform, thickness.left.inferior.parietal, thickness.left.inferior.temporal, thickness.left.isthmus.cingulate, thickness.left.lateral.occipital, thickness.left.lateral.orbitofrontal, thickness.left.lingual, thickness.left.medial.orbitofrontal, thickness.left.middle.temporal, thickness.left.parahippocampal, thickness.left.paracentral, thickness.left.pars.opercularis, thickness.left.pars.orbitalis, thickness.left.pars.triangularis, thickness.left.pericalcarine, thickness.left.postcentral, thickness.left.posterior.cingulate, thickness.left.precentral, thickness.left.precuneus, thickness.left.rostral.anterior.cingulate, thickness.left.rostral.middle.frontal, thickness.left.superior.frontal, thickness.left.superior.parietal, thickness.left.superior.temporal, thickness.left.supramarginal, thickness.left.transverse.temporal, thickness.left.insula, thickness.right.caudal.anterior.cingulate, thickness.right.caudal.middle.frontal, thickness.right.cuneus, thickness.right.entorhinal, thickness.right.fusiform, thickness.right.inferior.parietal, thickness.right.inferior.temporal, thickness.right.isthmus.cingulate, thickness.right.lateral.occipital, thickness.right.lateral.orbitofrontal, thickness.right.lingual, thickness.right.medial.orbitofrontal, thickness.right.middle.temporal, thickness.right.parahippocampal, thickness.right.paracentral, thickness.right.pars.opercularis, thickness.right.pars.orbitalis, thickness.right.pars.triangularis, thickness.right.pericalcarine, thickness.right.postcentral, thickness.right.posterior.cingulate, thickness.right.precentral, thickness.right.precuneus, thickness.right.rostral.anterior.cingulate, thickness.right.rostral.middle.frontal, thickness.right.superior.frontal, thickness.right.superior.parietal, thickness.right.superior.temporal, thickness.right.supramarginal, thickness.right.transverse.temporal, thickness.right.insula)` fixed-effect model matrix is rank deficient so dropping 1 column / coefficient fixed-effect model matrix is rank deficient so dropping 1 column / coefficient fixed-effect model matrix is rank deficient so dropping 1 column / coefficient fixed-effect model matrix is rank deficient so dropping 1 column / coefficient Starting data preparation for the batch effect diagnostic and harmonization stage... The result from the visual prepration stage is not provided! The required parameters should be specified... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: no batch level is dropped. Starting data preparation for the batch effect diagnostic and harmonization stage... The result from the visual prepration stage is not provided! The required parameters should be specified... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: no batch level is dropped. Starting data preparation for the batch effect diagnostic and harmonization stage... The result from the visual prepration stage is not provided! The required parameters should be specified... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: no batch level is dropped. Starting data preparation for the batch effect diagnostic and harmonization stage... Taking the result from the visual preparation stage as input... No observation is dropped due to missing values. Starting data preparation for the post-harmonization stage... No existing model is provided. Fitting the regression model from scratch! No observation is dropped due to missing values. Starting data preparation for the post-harmonization stage... No existing model is provided. Fitting the regression model from scratch! No observation is dropped due to missing values. Starting data preparation for the post-harmonization stage... No existing model is provided. Fitting the regression model from scratch! No observation is dropped due to missing values. Starting data preparation for the post-harmonization stage... No observation is dropped due to missing values. Template moved to: D:\temp\2025_01_24_20_40_16_23077\Rtmp8mrRjv\file2a2c050cf7e24/diagnosis_report.qmd processing file: diagnosis_report.qmd output file: diagnosis_report.knit.md pandoc --output diagnosis_report.html to: html standalone: true self-contained: true section-divs: true html-math-method: mathjax wrap: none default-image-extension: png number-sections: true toc: true metadata document-css: false link-citations: true date-format: long lang: en title: Batch Effect Diagnostics editor: visual date: '`r Sys.Date()`' title-block-banner: true page-layout: full toc-title: Contents toc-location: left theme: minty cap-location: bottom Output created: diagnosis_report.html Starting data preparation for the batch effect diagnostic and harmonization stage... The result from the visual prepration stage is not provided! The required parameters should be specified... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: no batch level is dropped. Starting first-time harmonization... Starting data preparation for the post-harmonization stage... No existing model is provided. Fitting the regression model from scratch! No observation is dropped due to missing values. New names: * `residual_y` -> `residual_y...1` * `residual_y` -> `residual_y...2` * `residual_y` -> `residual_y...3` * `residual_y` -> `residual_y...4` Starting data preparation for the post-harmonization stage... No existing model is provided. Fitting the regression model from scratch! No observation is dropped due to missing values. New names: * `X3` -> `X3...1` * `X3` -> `X3...2` * `X3` -> `X3...3` * `X3` -> `X3...4` Starting data preparation for the post-harmonization stage... No observation is dropped due to missing values. Starting data preparation for the post-harmonization stage... No existing model is provided. Fitting the regression model from scratch! No observation is dropped due to missing values. New names: * `residual_y` -> `residual_y...1` * `residual_y` -> `residual_y...2` * `residual_y` -> `residual_y...3` * `residual_y` -> `residual_y...4` Starting data preparation for the post-harmonization stage... No observation is dropped due to missing values. Starting data preparation for the post-harmonization stage... No observation is dropped due to missing values. New names: * `residual_y` -> `residual_y...1` * `residual_y` -> `residual_y...2` * `residual_y` -> `residual_y...3` * `residual_y` -> `residual_y...4` Starting data preparation for the post-harmonization stage... No existing model is provided. Fitting the regression model from scratch! No observation is dropped due to missing values. New names: * `residual_y` -> `residual_y...1` * `residual_y` -> `residual_y...2` * `residual_y` -> `residual_y...3` * `residual_y` -> `residual_y...4` Starting data preparation for the batch effect diagnostic and harmonization stage... The result from the visual prepration stage is not provided! The required parameters should be specified... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: no batch level is dropped. Statistic Numer.DF Pseudo.R2 Analytic.p.value (Omnibus) 0.0495 2 0.0472 < 1e-20 *** manufacs 0.0495 2 0.0472 < 1e-20 *** --- Signif. codes: 0 "***" 0.001 "**" 0.01 "*" 0.05 "." 0.1 " " 1Starting data preparation for the batch effect diagnostic and harmonization stage... The result from the visual prepration stage is not provided! The required parameters should be specified... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: no batch level is dropped. Statistic Numer.DF Pseudo.R2 Analytic.p.value (Omnibus) 0.363 2 0.266 < 1e-20 *** manufacs 0.363 2 0.266 < 1e-20 *** --- Signif. codes: 0 "***" 0.001 "**" 0.01 "*" 0.05 "." 0.1 " " 1refitting model(s) with ML (instead of REML) refitting model(s) with ML (instead of REML) refitting model(s) with ML (instead of REML) refitting model(s) with ML (instead of REML) Starting data preparation for the batch effect diagnostic and harmonization stage... The result from the visual prepration stage is not provided! The required parameters should be specified... No observation is dropped due to missing values. Batch levels that contain less than 3 observations are dropped: no batch level is dropped. Statistic Numer.DF Pseudo.R2 Analytic.p.value (Omnibus) 0.0534 2 0.0507 < 1e-20 *** manufacs 0.0534 2 0.0507 < 1e-20 *** --- Signif. codes: 0 "***" 0.001 "**" 0.01 "*" 0.05 "." 0.1 " " 1[ FAIL 0 | WARN 97 | SKIP 2 | PASS 215 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • `shinytest2::AppDriver` can not be initialized as {chromote} can not be started (2): 'test-age_shiny.R:6:3', 'test-comfam_shiny.R:5:3' [ FAIL 0 | WARN 97 | SKIP 2 | PASS 215 ] > > proc.time() user system elapsed 71.84 3.73 90.90