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Changelog

Source: NEWS.md

fmrireg 0.2.0

New Features

  • write_results() now exports statistical maps as NIfTI volumes via format = "nifti" (or format = c("h5", "nifti")), reusing the same BIDS entity and filename machinery as the HDF5 backend. This removes the need to hand-roll loops over coef_image() + neuroim2::write_vol().
  • Added coef_images(), a plural companion to coef_image() that returns a named list of NeuroVols for every coefficient of a given type ("estimates", "contrasts", or "F") and statistic.

Bug Fixes

  • write_results() now labels F-contrast maps as fstat/fpval instead of reusing the tstat/pval labels. F statistics follow an F distribution (not Student’s t), so mixing them under a tstat label produced mislabeled maps and, under strategy = "by_stat", could collide t- and F-contrast outputs in a single file. t- and F-contrasts are now written to separate, correctly labeled files.

fmrireg 0.1.2

Changes

  • Moved PDF report generation (report.fmri_lm) to the standalone fmrireport package. Use fmrireport::report() for report rendering.

Bug Fixes

  • Fixed low-rank/sketch residual degrees of freedom to use original timepoints (T - p) instead of sketch rows.
  • Replaced placeholder fit_contrasts.fmri_lm() outputs with computed standard errors, test statistics, and p-values.
  • Consolidated duplicate meta-analysis pathways to shared implementations and removed inconsistent behavior across runwise/chunkwise pooling.
  • Fixed F-contrast meta pooling to combine evidence via p-values rather than averaging F statistics.
  • Fixed thread-safety issue in C++ meta kernels by deferring Paule-Mandel non-convergence warnings until after OpenMP regions.
  • Added bounds validation and safer inverse fallback in sketch kernels to prevent unsafe indexing and hard failures on ill-conditioned data.
  • Improved AR pipeline consistency for whitened covariance/fitted/residual handling and unified AR effective-df calculations.
  • Added regression coverage for fit_contrasts.fmri_lm() to prevent placeholder-stat regressions.

fmrireg 0.1.1

Bug Fixes

  • Fixed glm_lss() tests that incorrectly expected specific Cholesky decomposition errors.
  • Fixed convolution test with non-strictly-increasing onsets within blocks.
  • Fixed testthat API usage (expect_lt/expect_gt no longer use deprecated info argument).
  • Fixed latent_dataset API usage: now uses get_latent_scores() instead of deprecated get_data().
  • Changed glm_lss() use_cpp parameter default from TRUE to FALSE (C++ implementation retired; fmrilss package now used).
  • Added fmrireg.suppress_deprecation option check to all deprecated functions for cleaner test output.
  • Added tests/testthat/setup.R to suppress expected deprecation warnings during testing.
  • Suppressed expected kmeans convergence warnings in landmark SRHT tests.

Internal

  • Test warnings reduced from 129 to 31 (remaining warnings are from external packages).

fmrireg 0.1.0

Breaking Changes

  • Design Matrix Column Naming: The naming scheme for columns in design matrices generated by event_model() has been completely revised for consistency and clarity.
    • All column names now strictly follow the format: term_tag + _ + condition_tag + [_b## basis suffix].
    • term_tag: Automatically generated from variable names (e.g., var1_var2) or user-provided id= in hrf(), sanitized (dots become underscores), and made unique with # suffix if needed (e.g., cond, cond#1).
    • condition_tag: Represents factor levels (e.g., Factor.Level), continuous basis columns (e.g., poly_RT_01, z_RT), or interactions joined by _ (e.g., Factor.Level_poly_RT_01).
    • _b##: Optional suffix added only when the HRF has multiple basis functions (e.g., _b01, _b02).
    • The previous style argument ("compact", "qualified", "uid") in design_matrix() is removed. Only the single canonical format is produced.
    • Scripts or analyses that relied on matching previous column name formats (e.g., using Var[Level], Var:Level, :basis[]) will need to be updated to use the new term_tag_Condition.Tag_b## format.

Major Changes

  • Regressor System Refactoring:
    • Introduced a new internal S3 class Reg for representing regressors.
    • The main regressor() function now uses Reg internally but maintains backward compatibility (returns class c("regressor", "Reg", "list")).
    • Deprecated single_trial_regressor() and null_regressor() in favour of using regressor() directly.
    • Unified regressor evaluation under the evaluate.Reg S3 method, supporting different calculation methods (“fft”, “conv”, “loop”, “Rconv”).
    • Evaluation methods now consistently use the refactored evaluate.HRF for HRF sampling.
    • Refactored C++ evaluation code into a single wrapper (evaluate_regressor_cpp).
    • Removed redundant internal helper functions (fastevalreg, fastevalreg2, conform_len, dots).
    • Implemented autoplot.Reg (ggplot2) and print.Reg (cli) methods, deprecating older plot.regressor and print.regressor.
    • Improved input validation and recycling for regressor() arguments using vctrs.
    • Added optional sparse matrix output to evaluate.Reg.
    • Added memoization for HRF sampling within evaluation.

fmrireg 0.0.1

  • Initial CRAN release.