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Changelog

Source: NEWS.md

Changes in version 1.0.0 released on 20 Jan 2026

New Features

  1. Family Assignment and Summary:
    • tidyped() now automatically assigns and includes a Family column, identifying full-sib groups.
    • summary.tidyped() has been updated to provide family statistics (count, sizes, top largest families) and richer offspring analysis.
  2. Pedigree Splitting (splitped): Added splitped() function to detect and split disconnected pedigree components. It efficiently identifies independent sub-populations (connected components) using graph theory, excludes isolated individuals, and returns a list of re-indexed tidyped objects ready for separate analysis or visualization.
  3. Comprehensive Matrix Support: pedmatrix() now fully supports 6 types of genetic relationship matrices: Additive (A, Ainv), Dominance (D, Dinv), and Additive-by-Additive Epistatic (AA, AAinv).
  4. Relationship Matrix Visualization (vismat): Added vismat() function for visualizing relationship matrices (A, D, AA, etc.) with heatmaps and histograms. It supports pedmatrix objects, tidyped objects (auto-calculates A matrix), and standard matrices. Heatmaps can be annotated with family groups when a pedigree is provided.

CRAN Submission & Internal Improvements

This release marks the first stable version 1.0.0, polished for CRAN.

  1. Portable Compilation: Standardized src/Makevars for cross-platform compatibility (removed GNU/platform-specific extensions).
  2. Dependencies: Moved RcppArmadillo to LinkingTo to optimize package structure.
  3. Documentation & S3: Fixed vignette generation, resolved diag S3 method dispatch, and cleaned up documentation for CRAN compliance.

Changes in version 0.7.3 released on 13 Jan 2026

New behavior (BREAKING)

  1. Simplified pedmatrix() return and single-method enforcement: pedmatrix() now requires a single method argument (e.g., method = "A"). When a single method is requested, the function returns the corresponding matrix or vector directly (not a named list). Requesting multiple methods in one call will now raise an error. Use repeated calls for multiple outputs.

New features

  1. High-Performance Genetic Relationship Calculations: Introduced pedmatrix() function implemented in Rcpp for efficient computation of:
    • Additive relationship matrix (A) using the tabular recursive algorithm.
    • Sparse inverse additive matrix (A-Inverse) using Henderson’s rules.
    • Dominance matrix (D) using the tabular approach.
    • Inbreeding coefficients (f) using the Meuwissen & Luo (1992) path-tracing algorithm.

Improvements

  1. Default Inbreeding Calculation Method: The inbreed() function now uses the native Rcpp implementation by default, moving the nadiv package to Suggests.
  2. Documentation and Website: Updated package documentation and vignettes to reflect new features and improvements. The official package website is available at https://luansheng.github.io/visPedigree/.

Changes in version 0.7.2 released on 12 Jan 2026

New features

  1. Flexible Generation Assignment: Added genmethod parameter to tidyped(). Users can now choose between "top" (top-aligned, default) and "bottom" (bottom-aligned) methods for generation inference.
    • The "top" method aligns founders at Generation 1, which is more appropriate for biological pedigrees and prevents “founder drift” in pedigrees with varying depths.
    • The "bottom" method aligns terminal nodes at the bottom, useful for visualizing introductions of unrelated exogenous parents.

Improvements

  1. Default Logic Change: Switched the default generation assignment method to "top" (top-down) for more intuitive biological visualization.
  2. Pkgdown Documentation: Generated and published the official package website at https://luansheng.github.io/visPedigree/.
  3. Automated CI/CD: Added GitHub Actions workflow for automatic documentation updates and deployment via GitHub Pages.

Changes in version 0.7.1 released on 11 Jan 2026

CRAN release: 2026-01-21

Performance optimizations

  1. Large Pedigree Performance: Optimized visped performance for displaying large pedigrees through efficient attribute handling and vectorized rendering. Computation time for 100k+ individuals reduced significantly by avoiding redundant igraph attribute lookups.
  2. Vectorized Tracing: Refactored trace_ped_candidates in tidyped to use vectorized igraph::neighborhood calls, achieving ~150x speedup for large candidate lists (e.g., 37k candidates in a 178k individual pedigree traced in ~1.2s).
  3. Early Filtering: Implemented unified early filtering of isolated individuals (Gen 0) in prepare_ped_graph to streamline downstream graph conversion and layout algorithms.

Improvements

  1. User Feedback: Standardized filtering notifications. The message “Note: Removed N isolated individuals…” now appears consistently for all pedigree sizes when Gen 0 individuals are present.
  2. Refined Tracing: Corrected trace = "all" logic in both tidyped and visped. It now correctly retrieves the union of ancestors and descendants (“up” + “down”) instead of the entire connected component (undirected search).

Changes in version 0.7.0 released on 10 Jan 2026

Breaking changes & Major Refactoring

  1. Graph-based tidyped Core: Reimplemented the pedigree tidying engine using formal graph theory principles (Directed Acyclic Graphs). Improved loop detection and generation inference accuracy using topological sorting.
  2. Modular Architecture: Split the monolithic visped.R into functional modules: visped_layout.R, visped_graph.R, visped_style.R, and visped_render.R for better maintainability.

New features

  1. New Parameters in visped():
    • pagewidth: Allows users to specify the PDF page width (default 200 inches) to accommodate different pedigree scales.
    • symbolsize: A scaling factor (default 1) to adjust node sizes relative to label dimensions, providing finer control over whitespace.
  2. Two-Pass Rendering Engine: Introduced a two-pass strategy in plot_ped_igraph() to ensure edges connect exactly at node centers, eliminating visual gaps in vector PDF outputs.
  3. Enhanced Highlighting: Added support for real-time ancestry and descendant highlighting via the trace parameter in visped().

Bug fixes

  1. Fixed rendering failure in outline = TRUE mode by correcting attribute indexing in the graph object.
  2. modernized the unit testing suite to testthat 3rd edition, removing all legacy context() warnings.
  3. Improved coordinate calculation precision to prevent overlapping in high-density generations.

Changes in version 0.6.2 released on 01 Jan 2026

New features

  1. Added summary() method for tidyped objects to provide quick pedigree statistics (number of individuals, founders, sex distribution, etc.).

Bug fixes

  1. Fixed an issue where tidyped(..., inbreed=TRUE) failed due to incorrect class assignment order.
  2. Fixed visped(..., showf=TRUE) to gracefully handle missing f columns by warning the user instead of erroring.
  3. Fixed broken internal navigation links in package vignettes.

Changes in version 0.6.1 released on 30 Dec 2025

New features

  1. Implemented opaque highlighting effects for better visualization clarity.
  2. Added trace option to visped() to control ancestry tracing direction.

Changes in version 0.6.0 released on 28 Dec 2025

New features

  1. Implemented strict S3 class structure for tidyped objects with new_tidyped() constructor and validate_tidyped() validator to ensure data integrity.

Changes in version 0.5.0 released on 26 Dec 2025

New features

  1. Added highlight parameter to visped() function. Users can now highlight specific individuals using a character vector of IDs or a list for custom colors.
  2. Added showf parameter to visped() function to display inbreeding coefficients on the pedigree graph.
  3. Added inbreed parameter to tidyped() function to calculate inbreeding coefficients using the nadiv package.
  4. Refactored inbreed() function as a standalone tool that operates on tidyped objects.
  5. Optimized repeloverlap() function using data.table for significantly better performance.

Bug fixes

  1. Fixed a critical crash in visped() when combining compact = TRUE, highlight, and showf = TRUE by refactoring ped2igraph() to delay label modification until after layout calculation.
  2. Fixed documentation grammar and phrasing across all functions for CRAN compliance.
  3. Fixed R CMD check notes related to data.table non-standard evaluation by adding R/globals.R.

Changes in version 0.4.1 released on 25 Dec 2025

Changes in version 0.2.6 released on 31 Mar 2020

New features

Bug fixes

  1. Fixed a bug that the number of generations for candidates would be traced to n+1 when tracegen=n. This bug is found by Mianyu Liu.

Changes in version 0.2.5 released on 25 Feb 2020

New features

Bug fixes

  1. The tidyped() does not work with trace=‘all’ in certain cases

Changes in version 0.2.4.1 released on 24 Feb 2020

New features

Bug fixes

  1. An unexpected column with the name as NA occured when a tidyped object is tidyed again using the tidyped()

Changes in version 0.2.4 released on 12 June 2019

New features

Bug fixes

  1. The data.table used as the input parameter ‘ped’ may be changed in tidyped() and visped().

Changes in version 0.2.3 released on 05 Mar 2019

New features

Bug fixes

  1. The generation number of individuals is not inferred rightly.

Changes in version 0.2.2 released on 28 Jan 2019

New features

Bug fixes

  1. The tidied pedigree will not include the candidates which are not in the Ind column of the origin pedigree when the cand parameter is not NULL.

Changes in version 0.2.1 released on 17 Nov 2018

New features

Bug fixes

  1. Repel the overlapping nodes due to very small differences (digits > 7) among x positions of nodes