{ "_id": "6a1f51d7b401979e73429e2a", "Package": "fmridesign", "Type": "Package", "Title": "Design Matrix Construction for fMRI Analysis", "Version": "0.6.0", "Date": "2026-05-12", "Authors@R": "person(\"Bradley\", \"Buchsbaum\", role = c(\"aut\", \"cre\", \"cph\"), email = \"brad.buchsbaum@gmail.com\")", "Description": "Constructs and inspects design matrices for functional\nmagnetic resonance imaging (fMRI) analyses. Provides a formula\ninterface for specifying event-related designs with flexible\nhemodynamic response function (HRF) bases, parametric\nmodulators, and trialwise models. Includes facilities for\nbaseline/nuisance regressors, contrast specification, and\nutilities for naming, validation, and visualization. Intended\nto support the model-building stage prior to statistical\nfitting. Implements methods described in Friston et al. (1995)\n and Lindquist (2008)\n.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "Config/Needs/website": "github::bbuchsbaum/albersdown, albersdown", "URL": "https://github.com/bbuchsbaum/fmridesign,\nhttps://bbuchsbaum.github.io/fmridesign/", "BugReports": "https://github.com/bbuchsbaum/fmridesign/issues", "RoxygenNote": "7.3.3", "Roxygen": "list(markdown = TRUE)", "Collate": "'baseline_model.R' 'basis.R' 'condition_basis_list.R'\n'contrast.R' 'contrast_pipeline.R' 'covariate.R'\n'design_colmap.R' 'design_generics.R' 'design_map.R'\n'design_metadata.R' 'utils-internal.R' 'event-classes.R'\n'event_model_helpers.R' 'event_model.R' 'event_vector.R'\n'extension_registry.R' 'fmrihrf-imports.R'\n'fmrihrf-reexports.R' 'globals.R' 'hrf-formula.R'\n'namespace-imports.R' 'naming-utils.R' 'residualize.R'\n'sampling_frame.R' 'validate.R' 'zzz.R'", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libssl-dev", "Repository": "https://bbuchsbaum.r-universe.dev", "Date/Publication": "2026-06-02 18:40:14 UTC", "RemoteUrl": "https://github.com/bbuchsbaum/fmridesign", "RemoteRef": "HEAD", "RemoteSha": "89a475f2a49a1dfa15a9a0771b981e635ef7041c", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-02 21:53:27 UTC", "User": "root" }, "Author": "Bradley Buchsbaum [aut, cre, cph]", "Maintainer": "Bradley Buchsbaum ", "MD5sum": "813ca81e2aa52d62d999836c7ff8c937", "_user": "bbuchsbaum", "_type": "src", "_file": "fmridesign_0.6.0.tar.gz", "_fileid": "c6ed232c504eb44068404c592ffabc2d05f6fe97e8a7b8680fe71492e9364bab", "_filesize": 3501339, "_sha256": "c6ed232c504eb44068404c592ffabc2d05f6fe97e8a7b8680fe71492e9364bab", "_created": "2026-06-02T21:53:27.000Z", "_published": "2026-06-02T21:57:43.665Z", "_distro": "noble", "_jobs": [ { "job": 79180440449, "time": 204, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7370795126" }, { "job": 79180440472, "time": 182, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7370789374" }, { "job": 79180440463, "time": 103, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7370766596" }, { "job": 79180440467, "time": 160, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7370782693" }, { "job": 79179725042, "time": 288, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7370736165" }, { "job": 79180440464, "time": 128, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7370773145" }, { "job": 79180440460, "time": 157, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7370781544" }, { "job": 79180440491, "time": 147, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7370779196" }, { "job": 79180440485, "time": 141, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7370777051" } ], "_buildurl": "https://github.com/r-universe/bbuchsbaum/actions/runs/26850066498", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bbuchsbaum/fmridesign", "_commit": { "id": "89a475f2a49a1dfa15a9a0771b981e635ef7041c", "author": "bbuchsbaum ", "committer": "bbuchsbaum ", "message": "Add na_action to repair leading-NA nuisance regressors (#7)\n\nbaseline_model(nuisance_check=\"drop\") flagged any column with a single\nleading NA as non_finite and dropped it wholesale, silently removing\notherwise-valid fMRIPrep confounds (dvars, framewise_displacement,\n*_derivative1) that carry one NA in row 1. With nuisance_check=\"none\"\nthose NAs leaked straight into the design matrix.\n\nAdd na_action = c(\"drop\",\"zero\",\"median\") to baseline_model(),\ncheck_nuisance(), and clean_nuisance():\n- \"drop\" (default): unchanged behavior, fully backward compatible.\n- \"zero\": replace NA with 0 (fMRIPrep leading-row convention).\n- \"median\": replace NA with the column median.\n\nOnly pure NA is repaired; NaN and Inf are left in place so genuinely\ncorrupt columns are still dropped as non-finite. Repair runs up front in\nbaseline_model() so both the diagnostics and make_nuisance_term() see the\nrepaired matrices, and it applies even when nuisance_check=\"none\",\nclosing the NA-leak path. All-NA columns still drop (zero -> zero\nvariance; median -> stays NA -> non-finite).\n\nTests cover retention under zero/median, Inf/NaN still dropped, all-NA\ndropped, no NA leak under \"none\", and check/clean_nuisance pass-through.\n\nCloses #7\n\nCo-Authored-By: Claude Opus 4.8 (1M context) \n", "time": 1780425614 }, "_maintainer": { "name": "Bradley Buchsbaum", "email": "brad.buchsbaum@gmail.com", "login": "bbuchsbaum", "description": "", "uuid": 53819 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "fmrihrf", "version": ">= 0.3.0", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "assertthat", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": 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"_exports": [ "as_hrf", "baseline", "baseline_model", "baseline_terms", "basis_suffix", "block", "blockids", "blocklens", "boxcar_hrf_gen", "BSpline", "cells", "check_collinearity", "check_nuisance", "clean_nuisance", "column_contrast", "columns", "condition_basis_list", "condition_map", "conditions", "construct", "contrast", "contrast_from_mask", "contrast_mask", "contrast_set", "contrast_weights", "contrasts", "convolve", "convolve_design", "correlation_map", "covariate", "design_colmap", "design_map", "design_matrix", "design_meta", "duration_hrf_gen", "durations", "elements", "evaluate", "event_basis", "event_conditions", "event_factor", "event_matrix", "event_model", "event_table", "event_term", "event_terms", "event_variable", "events", "Fcontrasts", "feature_suffix", "gen_hrf", "get_all_external_hrf_functions", "get_basis_entry", "get_external_hrfspec_functions", "get_external_hrfspec_info", "global_onsets", "hrf", "HRF", "hrf_spmg1", "Ident", "interaction_contrast", 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"baseline_terms", "baseline_terms.baseline_model" ] }, { "page": "basis_suffix", "title": "Create Basis Function Suffix", "topics": [ "basis_suffix" ] }, { "page": "block", "title": "Create a Block Variable", "topics": [ "block" ] }, { "page": "boxcar_hrf_gen", "title": "Create duration-based boxcar HRF generator", "topics": [ "boxcar_hrf_gen" ] }, { "page": "BSpline", "title": "B-spline basis", "topics": [ "BSpline" ] }, { "page": "cells", "title": "Extract cells from a design object", "topics": [ "cells", "cells.baseline_model", "cells.covariate_convolved_term", "cells.event", "cells.event_term" ] }, { "page": "check_collinearity", "title": "Check design matrix for multicollinearity", "topics": [ "check_collinearity" ] }, { "page": "check_nuisance", "title": "Check nuisance regressors for rank and column problems", "topics": [ "check_nuisance" ] }, { "page": "clean_nuisance", "title": "Clean nuisance regressors by dropping rank-useless columns", "topics": [ "clean_nuisance" ] }, { "page": "column_contrast", "title": "Column Contrast Specification", "topics": [ "column_contrast" ] }, { "page": "columns", "title": "Extract columns", "topics": [ "columns", "columns.RobustScale", "columns.Scale", "columns.ScaleWithin" ] }, { "page": "condition_basis_list", "title": "Convert an 'event_term' to a per-condition basis list", "topics": [ "condition_basis_list" ] }, { "page": "condition_map", "title": "Map Display and Canonical Condition Names", "topics": [ "condition_map" ] }, { "page": "conditions", "title": "Extract conditions from a design object", "topics": [ "conditions", "conditions.event_term" ] }, { "page": "construct", "title": "Construct method", "topics": [ "construct", "construct.baselinespec", "construct.covariatespec" ] }, { "page": "contrast", "title": "Contrast Specification", "topics": [ "contrast" ] }, { "page": "contrast_from_mask", "title": "Package a base mask into a 'contrast' object", "topics": [ "contrast_from_mask" ] }, { "page": "contrast_mask", "title": "Build a base contrast mask", "topics": [ "contrast_mask" ] }, { "page": "contrast_set", "title": "Create a Set of Contrasts", "topics": [ "contrast_set" ] }, { "page": "contrast_weights", "title": "Unit Contrast Weights", "topics": [ "contrast_weights", "contrast_weights.column_contrast_spec", "contrast_weights.contrast_diff_spec", "contrast_weights.contrast_formula_spec", "contrast_weights.contrast_set", "contrast_weights.convolved_term", "contrast_weights.event_model", "contrast_weights.interaction_contrast_spec", "contrast_weights.oneway_contrast_spec", "contrast_weights.pair_contrast_spec", "contrast_weights.poly_contrast_spec", "contrast_weights.unit_contrast_spec" ] }, { "page": "contrasts", "title": "Extract contrasts", "topics": [ "contrasts" ] }, { "page": "contrasts.event_model", "title": "Retrieve contrast definitions for an event model", "topics": [ "contrasts.event_model" ] }, { "page": "contrasts.event_term", "title": "Retrieve contrast definitions for an event term", "topics": [ "contrasts.event_term" ] }, { "page": "contrasts.hrfspec", "title": "Retrieve contrast specifications from an hrfspec", "topics": [ "contrasts.hrfspec" ] }, { "page": "convolve", "title": "Convolve events with a hemodynamic response function", "topics": [ "convolve", "convolve.event_term" ] }, { "page": "convolve_design", "title": "Convolve HRF with Design Matrix.", "topics": [ "convolve_design" ] }, { "page": "correlation_map", "title": "Compute correlation map", "topics": [ "correlation_map" ] }, { "page": "correlation_map.baseline_model", "title": "correlation_map.baseline_model", "topics": [ "correlation_map.baseline_model" ] }, { "page": "correlation_map.event_model", "title": "Visualize Regressor Correlations", "topics": [ "correlation_map.event_model" ] }, { "page": "covariate", "title": "Construct a Covariate Term", "topics": [ "covariate" ] }, { "page": "design_colmap", "title": "Column Metadata Map", "topics": [ "design_colmap" ] }, { "page": "design_colmap.event_model", "title": "Column metadata for a design matrix", "topics": [ "design_colmap.event_model" ] }, { "page": "design_map", "title": "Compute design map", "topics": [ "design_map" ] }, { "page": "design_map.baseline_model", "title": "Heatmap visualization of the baseline_model design matrix", "topics": [ "design_map.baseline_model" ] }, { "page": "design_map.event_model", "title": "Visualize Event Model Design Matrix", "topics": [ "design_map.event_model" ] }, { "page": "design_matrix", "title": "Extract or construct a design matrix", "topics": [ "design_matrix", "design_matrix.baseline_model", "design_matrix.baseline_term", "design_matrix.event_model", "design_matrix.event_term" ] }, { "page": "design_meta", "title": "Accessor: column metadata for a design matrix", "topics": [ "design_meta" ] }, { "page": "duration_hrf_gen", "title": "Create duration-aware normalized HRF generator", "topics": [ "duration_hrf_gen" ] }, { "page": "elements", "title": "Extract elements from an object", "topics": [ "elements", "elements.event", "elements.event_term" ] }, { "page": "event_basis", "title": "Create an event set from a ParametricBasis object.", "topics": [ "event_basis" ] }, { "page": "event_conditions", "title": "Retrieve per-event condition assignments", "topics": [ "event_conditions" ] }, { "page": "event_factor", "title": "Create a categorical event sequence from a factor.", "topics": [ "event_factor" ] }, { "page": "event_matrix", "title": "Create a continuous event set from a matrix.", "topics": [ "event_matrix" ] }, { "page": "event_model", "title": "Generic functions for fmridesign package", "topics": [ "event_model" ] }, { "page": "event_table", "title": "Extract event table", "topics": [ "event_table" ] }, { "page": "event_term", "title": "Create an event model term from a named list of variables.", "topics": [ "event_term" ] }, { "page": "event_terms", "title": "Extract event terms", "topics": [ "event_terms" ] }, { "page": "event_variable", "title": "Create a continuous event sequence from a numeric vector.", "topics": [ "event_variable" ] }, { "page": "events", "title": "Retrieve canonical event information", "topics": [ "events" ] }, { "page": "Fcontrasts", "title": "Compute F-contrasts", "topics": [ "Fcontrasts", "Fcontrasts.convolved_term", "Fcontrasts.event_model" ] }, { "page": "feature_suffix", "title": "Create Feature Suffix", "topics": [ "feature_suffix" ] }, { "page": "get_all_external_hrf_functions", "title": "Get All External HRF Function Names", "topics": [ "get_all_external_hrf_functions" ] }, { "page": "get_basis_entry", "title": "Look Up a Registered Basis Entry", "topics": [ "get_basis_entry" ] }, { "page": "get_external_hrfspec_functions", "title": "Get the HRF Function Name for External Specifications", "topics": [ "get_external_hrfspec_functions" ] }, { "page": "get_external_hrfspec_info", "title": "Get Information About a Registered External HRF Specification", "topics": [ "get_external_hrfspec_info" ] }, { "page": "hrf", "title": "hemodynamic regressor specification function for model formulas.", "topics": [ "hrf" ] }, { "page": "Ident", "title": "Ident", "topics": [ "Ident" ] }, { "page": "interaction_contrast", "title": "Interaction Contrast", "topics": [ "interaction_contrast" ] }, { "page": "is_categorical", "title": "Check if categorical", "topics": [ "is_categorical", "is_categorical.event" ] }, { "page": "is_continuous", "title": "Check if continuous", "topics": [ "is_continuous", "is_continuous.event" ] }, { "page": "is_external_hrfspec", "title": "Check if a Class is a Registered External HRF Specification", "topics": [ "is_external_hrfspec" ] }, { "page": "labels.event", "title": "Get Formatted Labels for a Single Event", "topics": [ "labels.event" ] }, { "page": "levels.event", "title": "Extract Levels from fmrireg Objects", "topics": [ "columns.event", "levels.event", "levels.RobustScale", "levels.Scale", "levels.ScaleWithin" ] }, { "page": "list_external_hrfspecs", "title": "List All Registered External HRF Specifications", "topics": [ "list_external_hrfspecs" ] }, { "page": "list_registered_bases", "title": "List Registered Parametric Basis Classes", "topics": [ "list_registered_bases" ] }, { "page": "longnames", "title": "Extract longnames", "topics": [ "longnames" ] }, { "page": "nbasis.hrfspec", "title": "Get number of basis functions from hrfspec", "topics": [ "nbasis.hrfspec" ] }, { "page": "nuisance", "title": "Create a Nuisance Specification", "topics": [ "nuisance" ] }, { "page": "one_against_all_contrast", "title": "One Against All Contrast", "topics": [ "one_against_all_contrast" ] }, { "page": "oneway_contrast", "title": "One-way Contrast", "topics": [ "oneway_contrast" ] }, { "page": "pair_contrast", "title": "Pair Contrast", "topics": [ "pair_contrast" ] }, { "page": "pairwise_contrasts", "title": "Pairwise Contrasts", "topics": [ "pairwise_contrasts" ] }, { "page": "plot_contrasts", "title": "plot_contrasts", "topics": [ "plot_contrasts" ] }, { "page": "plot_contrasts.event_model", "title": "plot_contrasts.event_model", "topics": [ "plot_contrasts.event_model" ] }, { "page": "plot.event_model", "title": "Plot Event Model", "topics": [ "plot.event_model" ] }, { "page": "Poly", "title": "Polynomial basis", "topics": [ "Poly" ] }, { "page": "poly_contrast", "title": "Polynomial Contrast", "topics": [ "poly_contrast" ] }, { "page": "predict", "title": "Predict from a ParametricBasis object", "topics": [ "predict.BSpline", "predict.Ident", "predict.ParametricBasis", "predict.Poly", "predict.RobustScale", "predict.Scale", "predict.ScaleWithin", "predict.Standardized" ] }, { "page": "print", "title": "Print a Baseline Model", "topics": [ "print.baseline_model", "print.contrast", "print.contrast_diff_spec", "print.contrast_set", "print.contrast_spec", "print.convolved_term", "print.event", "print.event_model", "print.event_term", "print.fmri_term", "print.poly_contrast_spec" ] }, { "page": "print.sampling_frame", "title": "Print and Plot for sampling_frame", "topics": [ "plot.sampling_frame", "print.sampling_frame" ] }, { "page": "register_basis", "title": "Register a Parametric Basis Class", "topics": [ "register_basis" ] }, { "page": "register_hrfspec_extension", "title": "Register an External HRF Specification Type", "topics": [ "register_hrfspec_extension" ] }, { "page": "regressors", "title": "Extract regressors", "topics": [ "regressors", "regressors.event_term" ] }, { "page": "requires_external_processing", "title": "Check if an Object Requires External Processing", "topics": [ "requires_external_processing" ] }, { "page": "residualize", "title": "Residualize Data Against a Design", "topics": [ "residualize" ] }, { "page": "residualize-methods", "title": "Residualize methods", "topics": [ "residualize-methods", "residualize.baseline_model", "residualize.event_model", "residualize.matrix" ] }, { "page": "RobustScale", "title": "Robust Scaling (Median/MAD)", "topics": [ "RobustScale" ] }, { "page": "sanitize", "title": "Sanitize Strings for Use in R Names", "topics": [ "sanitize" ] }, { "page": "Scale", "title": "Z-score (global) basis", "topics": [ "Scale" ] }, { "page": "ScaleWithin", "title": "Z-score within groups", "topics": [ "ScaleWithin" ] }, { "page": "shortnames", "title": "Extract shortnames", "topics": [ "shortnames" ] }, { "page": "sliding_window_contrasts", "title": "Sliding-Window Contrasts (Disjoint)", "topics": [ "sliding_window_contrasts" ] }, { "page": "split_by_block", "title": "Split by block", "topics": [ "split_by_block", "split_by_block.event_model" ] }, { "page": "split_onsets", "title": "Split onsets", "topics": [ "split_onsets", "split_onsets.event_term" ] }, { "page": "Standardized", "title": "Standardized basis", "topics": [ "Standardized" ] }, { "page": "sub_basis", "title": "sub_basis", "topics": [ "sub_basis", "sub_basis.RobustScale", "sub_basis.Scale", "sub_basis.ScaleWithin" ] }, { "page": 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