Changelog

Source: NEWS.md

Changes in version 1.9.0 released on 11 Jul 2026

New features

1. visped() SVG output: visped() now writes SVG files when file ends in .svg; other file names continue to use PDF output by default.
2. visped() custom labels: Added a labelvar argument to display labels from either a user-selected pedigree column or a row-aligned character vector. Compact full-sib family nodes continue to show family size.
3. visped() symbol schemes: Added a shapeby argument for choosing how node shapes are encoded. The default shapeby = "sex" uses circles for females, squares for males, diamonds for unknown sex, and hexagons for monoecious individuals. Set shapeby = "role" to keep the legacy role-based symbol scheme in which real individuals are circles and compact full-sib family summaries are rectangles.
4. Matrix-free relationship products: Added pedprod() to compute $Ax$, $AX$, $A^{-1}x$, and $A^{-1}X$ directly from a complete pedigree. The implementation uses the $A = TDT'$ factorization and avoids materializing the dense additive relationship matrix.
5. visped() custom generation labels: genlab now also accepts an unnamed character vector, assigning one user-provided label to each displayed generation from top to bottom. The existing logical values retain their behavior: TRUE draws the default G1, G2, … labels and FALSE omits them.

Improvements

1. Matrix-free pedrel() summaries: pedrel() now computes grouped mean relationships and coancestries from batched $Ag$ products. It traces the union of selected ancestors once and no longer constructs or scans a dense relationship matrix for each group.
2. Large-group support in pedrel(): The former dense and compact matrix size guards are no longer needed. The development-only force, max_dense, and max_compact no-op arguments were removed before release, while compact remains as a backward-compatible no-op argument. Status and Message continue to identify groups skipped because fewer than two individuals were selected or groups that failed during tracing.
3. Matrix-free coancestry analyses: pedne(method = "coancestry") now obtains sampled pair relationships from batched $AX$ products instead of constructing a dense triangular relationship matrix. pediv() reuses the same products for $N_e$ and founder genome equivalents, while pedhalflife() requests only the $f_g$ statistic it needs.
4. Matrix-free grouped heatmaps: vismat(tidyped_object, by = ...) now computes grouped additive relationships as $W' A W$ without first constructing the full individual-level relationship matrix.
5. Clearer compact full-sib family summaries in visped(): Compact full-sib family labels now use the explicit FS×N form instead of a bare number, avoiding confusion with an individual ID. Compact family summaries use a green-grey fill with a darker frame, while unknown-sex individuals use a neutral-grey fill with a grey frame.

Bug fixes

1. Selfing in Ainv: Corrected the sire-dam diagonal cross-term in Henderson’s inverse construction when the sire and dam are the same individual. pedmat(method = "Ainv") now remains the numerical inverse of A for pedigrees created with selfing = TRUE.

Documentation

1. Plant pedigree example in tidy-pedigree vignette: Added section 3.9 demonstrating selfing = TRUE for monoecious species, including sex inference, inbreeding coefficients under self-fertilization, and the summary() output for plant pedigrees.
2. Plant pedigree visualization in draw-pedigree vignette: Added section 1.1.3 showing a multi-generation self-pollinating pedigree with visped(). Monoecious individuals are drawn as hexagons with teal edges, selfing edges are shown in teal, and inbreeding coefficients are displayed with showf = TRUE.

Changes in version 1.8.1 released on 28 Mar 2026

CRAN release: 2026-03-30

New features

1. visped() generation labels: Added a genlab argument to visped() for drawing generation labels (G1, G2, …) on the left margin of pedigree plots. The default is FALSE, so existing plots are unchanged unless genlab = TRUE is requested.

Documentation

1. draw-pedigree vignette: Added an example showing how to display generation labels with visped(..., genlab = TRUE).

Changes in version 1.8.0 released on 25 Mar 2026

Performance

1. Inbreeding calculation: Replaced the Meuwissen and Luo (1992) linear path-trace algorithm in cpp_calculate_inbreeding() with the Sargolzaei and Iwaisaki (2005) LAP (Longest Ancestral Path) bucket method. At N = 1,000,000, the C++ kernel completes in about 0.15 s (previously about 15 s), and the full inbreed() call returns in about 0.40 s. The implementation uses O(1) ancestor retrieval via bucket pop, O(1) duplicate suppression via the L[k] == 0 check, and O(m_i) path-coefficient reset. Results are numerically identical to the previous implementation (maximum difference < 2e-15).
2. tidyped() candidate tracing: When the input is already a tidyped object and cand is specified, the fast path now uses three C++ BFS functions (cpp_trace_ancestors(), cpp_trace_descendants(), and cpp_topo_order()) instead of rebuilding an igraph object. At N = 1,000,000 with 200 candidates, elapsed time drops from about 0.91 s to about 0.056 s. The fast path now also applies sibling and mate generation alignment for genmethod = "bottom", matching the output of the full path.
3. pedgenint() generation-interval lookup: Replaced the character-key data.table join used to look up each individual’s generation number with a pre-computed integer index array. Benchmark on a representative dataset: 4.24 s to 0.49 s.
4. pedmat(sparse = TRUE) matrix coercion: The conversion from a dense numeric matrix to a Matrix::dgeMatrix now bypasses the S4 dispatch overhead of as(mat, "dgeMatrix") via a direct methods::new() call backed by a package-level class cache. Benchmark on a representative subpedigree: 1.24 s to 0.60 s.
5. pedrel(compact = TRUE) safety guard: Added an early error when the number of reference individuals exceeds 200,000 in compact mode, preventing unintended O(N^2) matrix allocation.

Bug fixes

1. tidyped() fast path with addnum = FALSE and cand: When the input tidyped object was created with addnum = FALSE, passing cand could raise "None of the specified candidates were found in the pedigree." because the fast-path BFS looked up ped_dt$IndNum, which was NULL. The fix temporarily adds integer index columns for the BFS and removes them from the output when addnum = FALSE.
2. pediv() and pedne() coancestry outputs when ECG was not pre-computed: Internal merge(..., by = "Ind", all.x = TRUE) calls sorted output alphabetically by Ind, breaking the IndNum == row-index invariant used by the fast-path BFS in tidyped(). This could produce incorrect fg, MeanCoan, and NeCoancestry values, such as fg near 240 instead of about 19. Fixed by restoring IndNum order immediately after the merge.
3. summary_pedmat() density for dense Matrix subclasses: summary_pedmat() reported Density = 100% for all A, D, and AA matrices returned as Matrix::dgeMatrix objects. It now uses Matrix::nnzero() / (nrow * ncol) for all Matrix subclasses, giving the correct fill ratio for both dgeMatrix and dgCMatrix.

Documentation

1. Inbreeding references: Updated inbreed() and vignette references to cite Sargolzaei and Iwaisaki (2005) instead of Meuwissen and Luo (1992).

Internal changes

1. align_bottom_generations() helper: Consolidated the sibling and mate generation-alignment block previously duplicated between the main and fast paths of tidyped() into a single internal helper.
2. C++11 compatibility: Replaced two C++17 structured-binding usages in the BFS functions with explicit C++11 equivalents for compatibility with GCC 8.
3. methods dependency: Listed the methods package under Imports in DESCRIPTION, as required when methods::getClass() and methods::new() are called at runtime.

Changes in version 1.7.0 released on 23 Mar 2026

New features

1. pediv() retained genetic diversity (GeneDiv): pediv()$summary gains a GeneDiv = 1 - MeanCoan column, the pedigree-based retained genetic diversity of the reference population. Values lie in $[0, 1]$, with larger values indicating more diversity retained relative to an unrelated base population. print.pediv() displays it alongside fg and MeanCoan.
2. vismat() large-pedigree representative view: When the original pedigree has more than 5,000 individuals, vismat() no longer attempts a full N × N matrix expansion. It uses the compact K × K representative-individual matrix directly and adds sibling-count labels of the form ID (×n) to each axis tick. When compact = TRUE and by is supplied, group means are computed algebraically from the K × K matrix without expanding to N × N.

Internal changes

1. vismat() threshold constants: Hardcoded values controlling large-pedigree behavior (5000, 2000, and 50) were refactored into named constants (VISMAT_EXPAND_MAX, VISMAT_LABEL_MAX, and VISMAT_WARN_THRESHOLD) at the top of R/vismat.R.

Changes in version 1.6.2 released on 23 Mar 2026

New features

1. pedrel() coancestry scale: Added a scale parameter to pedrel() supporting "relationship" (default, returns mean $a_{ij}$) and "coancestry" (returns corrected mean coancestry $\bar{c}$). The coancestry scale uses the diagonal-corrected formula of Caballero and Toro (2000), accounting for self-coancestry within the reference group.

API changes

1. vispstat() internal-only backend: vispstat() is now the internal backend for plot.pedstats(). Users should call the standard S3 method with plot(stats_obj).

Bug fixes

1. Spurious subsetting warnings: Internal group-by slicing in pedrel(), pedne(), pediv(), pedhalflife(), and pedgenint() no longer triggers false-positive [.tidyped] warnings when the subset is only used for ID extraction.
2. Internal class-restoration messages: pedrel(compact = TRUE) no longer emits class-restoration messages caused by early-return branches in compact_ped_for_matrix(). Those branches now preserve the tidyped class by returning data.table::copy(ped).
3. vispstat() cleanup: Removed dead-code variables and added unit tests for the genint branch of vispstat().

Documentation

1. vispstat() generation-interval documentation: Updated the text to describe mean values accurately and remove the misleading “mean +/- SD” claim.
2. pedigree-analysis.Rmd section 9: Split the “Average Relationship Trends with pedrel()” section into two subsections covering both scale options. Added the Caballero and Toro (2000) diagonal-corrected coancestry formula, a worked scale = "coancestry" example, and guidance on choosing a scale.
3. relationship-matrix.Rmd updates: Added a compact-to-vismat() direct path, expanded the visualization examples, and replaced incorrect performance thresholds with a reference table.

Changes in version 1.6.1 released on 21 Mar 2026

Improvements

1. Diversity notation: Output columns in pedhalflife()$timeseries are now lowercase (fe, fa, fg, lnfe, lnfa, lnfg, lnfafe, and lnfgfa) to match population genetics notation.
2. plot.pedhalflife() log view: In type = "log" mode, the plot includes an OLS regression line for total diversity decay ($\ln f_g \sim \text{Time}$) and a vertical reference line for the diversity half-life $T_{1/2}$.
3. Time-unit labeling: plot.pedhalflife() and print.pedhalflife() now use the name of the timevar column, such as Gen or Year, for axis and summary labels.

Changes in version 1.6.0 released on 20 Mar 2026

New features

1. Information-theoretic diversity half-life (pedhalflife()): Added pedhalflife() to track $f_e$, $f_a$, and $f_g$ across time points and fit a log-linear decay model for the rate of genetic diversity loss. The total loss rate $\lambda_{total}$ is decomposed into foundation bottleneck ($\lambda_e$), breeding bottleneck ($\lambda_b$), and genetic drift ($\lambda_d$). The diversity half-life $T_{1/2} = \ln 2 / \lambda_{total}$ is reported in units of the timevar column. S3 print() and plot() methods are provided, with both log-scale (type = "log") and raw-scale (type = "raw") views.

Changes in version 1.5.0 released on 20 Mar 2026

New features

1. Shannon-entropy effective founders and ancestors (feH, faH): pedcontrib() and pediv() now compute two additional diversity statistics based on the Hill number of order $q = 1$ (Shannon entropy): feH, the effective number of founders under equal entropy weighting, and faH, the effective number of ancestors under equal entropy weighting. They satisfy $N_{\mathrm{Founder}} \ge f_e^H \ge f_e$ and $N_{\mathrm{Ancestor}} \ge f_a^H \ge f_a$, respectively. Both are computed as $\exp(-\sum p_i \ln p_i)$ and complement the classical quadratic ($q = 2$) effective numbers $f_e$ and $f_a$ (Lacy 1989; Boichard et al. 1997).

Changes in version 1.4.1 released on 15 Mar 2026

Bug fixes

1. Fail-fast incomplete-pedigree analysis: inbreed() and other completeness-sensitive analysis functions now error on row-truncated subsets with missing parent records. This prevents incorrect results, such as zero inbreeding, caused by calculating on partial ancestry data.

Changes in version 1.4.0 released on 15 Mar 2026

New features

1. tidyped class redesign: Refined the internal tidyped class architecture around a clearer metadata contract and safer S3/data.table interaction model for repeated downstream analysis and extension.
2. Safer tidyped workflows: Added is_tidyped(), pedmeta(), has_inbreeding(), and has_candidates() to make class checks and metadata inspection explicit.
3. Fast candidate tracing from existing tidyped objects: tidyped() now uses a fast path when the input is already a valid tidyped object and cand is supplied, avoiding repeated global validation and preprocessing.
4. Workflow coverage and developer documentation: Added a workflow vignette, a tidyped structure and extension vignette, and regression tests covering safe subsetting, := by-reference behavior, and split workflow semantics.

Bug fixes

1. By-reference mutation for tidyped: Replaced class and metadata attachment paths with data.table::setattr() so subsequent := operations keep true by-reference behavior instead of writing into shallow copies.
2. Safe row subsetting: Added [.tidyped interception so incomplete subsets degrade to plain data.table objects with a warning, while complete subsets preserve tidyped structure and rebuild pedigree indices.
3. Class recovery: Core analysis entry points now cooperate with ensure_tidyped() and validate_tidyped() to recover valid tidyped objects after common class-dropping operations.

Documentation

1. Pkgdown article navigation: Reorganized vignette order, restored draw-pedigree to the recommended reading sequence, and exposed tidyped developer notes through a dedicated pkgdown developer-documentation entry.

Changes in version 1.3.5 released on 14 Mar 2026

New features

1. S3 class protection: Added as_tidyped() and an internal ensure_tidyped() mechanism to handle cases where R operations such as merge(), rbind(), and dplyr verbs strip the custom S3 class from data.table objects. Major analysis functions can restore the class when the underlying data structure is still valid and inform the user.

Bug fixes

1. Analysis entry points: Updated core analysis functions, including pedstats(), pedne(), pediv(), and pedrel(), to use the class-recovery logic.

Changes in version 1.3.4 released on 14 Mar 2026

Bug fixes

1. data.table return visibility: Functions returning data.table or tidyped objects now explicitly return with [] so results auto-print in the R console and knitted documents after internal data.table operations such as := and set*. Affected functions included pedancestry(), pedpartial(), pedne(), pedrel(), and tidyped().
2. Side-effect prevention: Updated calc_ne_demographic() to operate on a copy of the input pedigree instead of modifying the user’s data by reference.

Documentation

1. Coding standard: Added a data.table return-visibility rule to Positron.md.

Changes in version 1.3.3 released on 14 Mar 2026

Bug fixes

1. Vignette API synchronization: Replaced outdated pedinbreed_class() calls in the pedigree analysis vignette with the current pedfclass() interface and aligned examples with the current reference, foundervar, and cycle argument names.

Documentation

1. pedigree-analysis.Rmd rewrite: Reorganized the main pedigree analysis vignette into thematic sections covering pedigree overview, pedigree completeness (pedecg()), generation intervals (pedgenint()), subpopulation structure (pedsubpop()), diversity indicators (pediv()), effective population size (pedne()), average relationship trends (pedrel()), inbreeding classification (pedfclass()), and ancestry / partial inbreeding diagnostics.
2. Theory expansion: Added formulas, interpretation notes, and breeding-use explanations for Equivalent Complete Generations (ECG), generation intervals, effective numbers of founders / ancestors / founder genomes (f_e, f_a, f_g), three effective population size definitions (N_e by demographic, inbreeding, and coancestry methods), and average additive relationship (MeanRel).
3. Reference update: Expanded the vignette bibliography to include Wright (1922, 1931), Lacy (1989), Boichard et al. (1997), Caballero and Toro (2000), Cervantes et al. (2011), and Gutierrez et al. (2008, 2009).

Internal changes

1. Analysis regression coverage: Added unit tests verifying that pedancestry() proportions sum to 1 in a multi-line admixture pedigree and that pedrel() returns identical results between compact = TRUE and compact = FALSE on the same pedigree.

Changes in version 1.3.2 released on 13 Mar 2026

New features

1. Core analysis examples: Added @examples to pedne(), pedecg(), and pedsubpop().
2. Pedigree connectivity analysis (pedsubpop()): Enhanced pedsubpop() to distinguish pedigree splitting via splitped() from grouping and summary analysis. It now reports counts of total individuals, sires, dams, and founders within subgroups or connected components.

API changes

1. pedfclass() rename: Renamed pedinbreedclass() to pedfclass() to align with the package naming guide and provide a shorter API.
2. pedfclass() output refinement: Renamed the returned class column from F_Class to FClass and added user-defined inbreeding class breakpoints through breaks and labels.
3. pedgenint() parameter rename: Renamed cycle_length to cycle.
4. pedgenint() and pedstats() unit parameter: Removed "gen" from unit options. The unit parameter now accepts "year", "month", "day", or "hour".
5. pedgenint() timevar definition: Clarified timevar as a birth-date column. Numeric year inputs are converted to Date values using "YYYY-07-01" with an informational message. Character date strings are parsed with as.POSIXct(..., tz = "UTC").

Improvements

1. pedsubpop() documentation: Refined internal documentation to clarify its use cases alongside splitped().
2. .parse_to_numeric_time() rewrite: Rewrote the internal time parser to handle Date, POSIXct, character date strings, and numeric years. POSIXct conversions now use tz = "UTC" to avoid DST-related artifacts.

Bug fixes

1. vispstat() pathway filter: Fixed an issue where the generation-interval bar chart could drop pathways because of an overly broad factor() filter. The filter now uses explicit %in% c("SS", "SD", "DS", "DD") subsetting.

Changes in version 1.3.1 released on 12 Mar 2026

New features

1. Selfing support in tidyped(): Added the selfing argument to support plant and aquaculture pedigrees where an individual can appear as both sire and dam, resolving sex-conflict errors for biologically valid selfing pedigrees (#10).
2. pedrel() ancestral tracing: pedrel() now uses full ancestral tracing via tidyped(ped, cand = ...) when calculating subgroup relationships, avoiding underestimation caused by ancestor truncation in deep-inbred populations.

API changes

1. pedancestry() parameter rename: Renamed labelvar to foundervar and labels to target_labels to make the ancestry-tracing interface more explicit. Old argument names are no longer supported because the function was still under active development.
2. pedecg() parameter cleanup: Removed the short-lived reference argument, which only filtered rows after a full ECG pass and did not define a reference population or prune the pedigree before calculation.

Improvements

1. Academic nomenclature alignment: Updated documentation for pedrel() and pedne() to distinguish additive genetic relationship ($a_{ij}$) from coancestry ($f_{ij}$). pedrel() now states that it returns $a_{ij} = 2f_{ij}$, and pedne() documents that its "coancestry" method is based on $f_{ij}$.
2. Monoecious individuals: Individuals acting as both parents are identified as "monoecious" in the Sex column.
3. visped() monoecious styling: visped() uses teal (#26a69a) for "monoecious" individuals.
4. Role-specific pedigree edges: Pedigree edges are colored by the parent’s role in each mating (sire, dam, or selfing) rather than invariant node sex.
5. tidyped summary methods: summary() and print() methods for tidyped objects now report the count and percentage of monoecious individuals.
6. pedancestry() initialization: Optimized initialization on large pedigrees by using vectorized matrix indexing, reducing overhead for pedigrees with more than 25,000 nodes.

Bug fixes

1. pedrel() deep-inbreeding regression coverage: Added a unit test verifying relationship calculation in deep-inbreeding scenarios, including Gen 4 relationships reaching 1.0.

Changes in version 1.3.0 released on 10 Mar 2026

New features

1. Founder genome equivalents (fg): Integrated calculation of founder genome equivalents into pediv(). The implementation evaluates mean coancestry with diagonal intra-cohort correction through adaptive scaling, keeping computational costs linear relative to the reference cohort size.
2. Reproducible parameter inference: Added a seed argument to pedne() and pediv() for reproducible sampling in effective population size and fg calculations that use Monte Carlo approximations.

Changes in version 1.2.3 released on 08 Mar 2026

Bug fixes

1. Trace edge highlighting in visped(): Fixed incorrect edge highlighting when using trace = "all". When a node was highlighted as both an ancestor and a parent of descendants, cross-path edges could be highlighted incorrectly. The fix separates upward and downward trace paths and uses trace_edges to control highlighted edges.
2. Focal-node upward edge in trace = "down": Fixed an issue where the focal node’s upward connection to its parents’ family node was highlighted when tracing downward only. Individual-to-family edges are now highlighted only when the individual appears as a child in the traced path.

Changes in version 1.2.2 released on 08 Mar 2026

New features

1. Unified diversity analysis (pediv()): Added pediv() as a single entry point that aggregates founder contributions (f_e), ancestor contributions (f_a), and three N_e estimates (coancestry, inbreeding, and demographic) into a pediv S3 object. A print.pediv() method provides a formatted summary table.
2. complex_ped dataset: Added complex_ped, a multi-generation pedigree dataset for testing deeper ancestry tracing and cross-generation diversity analyses.

API changes

1. Reference-population parameter rename: Standardized the reference population parameter name across relevant analysis functions: pedne(..., reference = NULL), pedcontrib(..., reference = NULL), and pedrel(..., reference = NULL). These previously used cand. Old cand arguments are no longer supported in those functions.

Documentation

1. pedigree-analysis.Rmd rewrite: Restructured the pedigree analysis vignette with expanded theory explanations for f_e, f_a, and N_e, updated examples using pediv() and reference, and additional interpretation for breeding decisions.
2. Workspace organization: Moved development-only files (MACOS_OPENMP_FIX.md, manuscript.md, and analysis scripts) into sandbox/, with corresponding .gitignore and .Rbuildignore rules.

Changes in version 1.2.1 released on 07 Mar 2026

New features

1. Ancestral analysis (pedcontrib()): Added algorithms for assessing genetic diversity through gene-origin probabilities. pedcontrib() computes effective number of founders (f_e) through recursive gene derivation and effective number of ancestors (f_a) through Boichard’s iterative algorithm.
2. Missing-parent conservation in pedcontrib(): Single missing parents are augmented with temporary phantom parents before processing so probability mass is conserved for half-founder records.
3. Ancestry proportions (pedancestry()): Added pedancestry() to trace line origins and monitor surviving gene proportions from specified historic founder lines or strains to descendants.
4. Partial inbreeding (pedpartial()): Added pedpartial() to decompose the overall inbreeding coefficient into fractions attributed to targeted ancestors, following Meuwissen and Luo (1992).
5. half_founder_ped dataset: Added half_founder_ped, an ENDOG-derived dataset containing records with a single known parent for testing phantom-parent corrections.

Performance

1. Peeling core engine: Rebuilt the C++ array engine backing the f_a and f_e calculations. The bounded O(K × N) array-state implementation avoids excessive latency on deep pedigrees with more than 180,000 nodes.

Documentation

1. Reference index: Expanded _pkgdown.yml mappings to expose pedigree statistical functions such as pedancestry(), pedcontrib(), pedpartial(), and pedecg() in the reference documentation.
2. Analysis vignette: Updated vignettes/pedigree-analysis.Rmd with Boichard-style genetic bottleneck interpretations (f_e versus f_a) and examples for targeted lineage flow.

Changes in version 1.2.0 released on 04 Mar 2026

New features

1. Effective population size methods in pedne(): Expanded pedne() to support three methods for estimating N_e: "coancestry" based on the rate of coancestry ($\Delta c$), "inbreeding" based on the individual rate of inbreeding ($\Delta F$), and "demographic" based on the numbers of breeding males ($N_m$) and females ($N_f$). The coancestry method is now the default and may provide earlier signals of diversity loss in selected populations than inbreeding-based estimates.
2. Parallel and sampled coancestry estimation: Added OpenMP multi-threading for the method = "coancestry" path via ncores, and added nsamples for sampled estimation on large pedigrees.

Performance

1. Coancestry backend: Implemented the C++ backend cpp_calculate_sampled_coancestry_delta() using RcppArmadillo, replacing previous R-level coancestry calculations for larger datasets.

Documentation

1. pedne() parameter scopes: Documented that ncores and nsamples apply to method = "coancestry".
2. pedne() method descriptions: Expanded documentation for the three N_e calculation methods to support method selection.

Changes in version 1.1.1 released on 02 Mar 2026

New features

1. pedgenint() sex-independent pathways: Added SO (sire-to-offspring) and DO (dam-to-offspring) generation intervals alongside the standard four pathways. These pathways support settings such as aquaculture or early-stage screening where offspring sex may be unknown.

API changes

1. pedne() interface standardization: Renamed timevar to by and cohort to cand; removed unused or misleading parameters (unit, cycle_length, and maxgen). Old timevar and cohort arguments are retained with deprecation warnings.
2. vismat() parameter alignment: Renamed grouping to by for grouping consistency. The old grouping argument is retained with a deprecation warning.

Bug fixes

1. pedrel() correctness: Fixed an error where mean average relatedness was calculated by summing the full relationship matrix, including traced ancestors, and dividing by only the target subgroup size. The function now subsets the relationship matrix and handles NUsed < 2. Output columns N and MeanRel were replaced with NTotal, NUsed, and MeanRel.
2. pedgenint() aggregation: pedgenint() now outputs the appropriate unweighted mixture standard deviation for generation intervals alongside the unweighted four-pathway average.
3. pedgenint() sample size: Fixed underestimation of the Average pathway N by evaluating all parent-offspring pairs through calc_all_pathway().
4. pedcontrib() effective numbers: Standardized effective founder (Ne_f) and effective ancestor (Ne_a) calculations so they use the full untruncated cohort before reporting the top-ranked rows. The result list now includes total and reported count variables.
5. pedcontrib() deep-pedigree latency: Replaced a string-named-vector backward pass with a pure integer-indexed backward pass for large and deep pedigrees, including cases with more than 200,000 records.
6. pedpartial() and pedancestry() input compatibility: Missing numeric identifier columns in incoming pedigrees, such as objects created with addnum = FALSE, no longer break pedpartial() or pedancestry(). The pedigree propagation loop in pedancestry() was also simplified to use direct vector lookup.
7. pedne() performance bottleneck: Removed obsolete O(N^2) individual traversal in calc_ancestral_f(), using the direct formula by Gutierrez et al.

Changes in version 1.1.0 released on 01 Mar 2026

New features

1. Pedigree analysis module: Added pedigree analysis and population-genetics functions: pedstats() for summary and demographic statistics; pedrel() for average relatedness within groups; pedgenint() for sire-sire, sire-dam, dam-sire, dam-dam, and overall generation intervals; pedcontrib() for founder and ancestor genetic contributions; pedancestry() for ancestral-lineage proportions; and pedpartial() for partial inbreeding attributed to specified ancestors.
2. Pedigree analysis visualization: Added vispstat() for plotting generation-interval bar charts and depth-related distributions such as Equivalent Complete Generations.

Changes in version 1.0.1 released on 31 Jan 2026

CRAN release: 2026-02-23

Bug fixes

1. Compact matrix correctness: Fixed incorrect A, D, and AA relationship values in compact = TRUE mode for parent-offspring and avuncular pairs caused by merging parent individuals with their non-parent siblings.
2. Pedigree compression strategy: Updated compaction logic to preserve the genetic identity of any individual that appears as a sire or dam, ensuring parents have unique entries in the relationship matrix.
3. Sibling row and column expansion: Fixed expand_pedmat() so sibling off-diagonal elements are calculated from parent kinship rather than by duplicating representative diagonal values.
4. Generation alignment: Fixed tidyped(..., genmethod = "bottom") so sibling consistency is prioritized over mate alignment, ensuring full siblings are aligned to the same generation.
5. visped() edge highlighting: Fixed edge highlighting so relationship edges are only emphasized when trace is used.
6. Shared-parent and shared-child paths: Corrected edge highlighting for cases where a parent has multiple families or a family has multiple children.
7. visped() layout with showf = TRUE: Fixed a layout optimization failure by using immutable individual IDs.

Changes in version 1.0.0 released on 24 Jan 2026

Breaking changes

1. Matrix API names: Renamed pedmatrix() to pedmat(), expand_pedmatrix() to expand_pedmat(), and summary_pedmatrix() to summary_pedmat(). Legacy function names were removed.
2. pedmat() default method: Changed the default method of pedmat() from "f" to "A".
3. Thread argument name: Standardized n_threads to threads across functions.

New features

1. Family assignment and summary: tidyped() now assigns a Family column identifying full-sib groups. summary.tidyped() reports family counts, sizes, largest families, and offspring summaries.
2. Pedigree splitting (splitped()): Added splitped() to detect disconnected pedigree components, exclude isolated individuals, and return re-indexed tidyped objects for separate analysis or visualization.
3. Relationship matrix support: pedmat() supports additive (A, Ainv), dominance (D, Dinv), and additive-by-additive epistatic (AA, AAinv) relationship matrices.
4. Relationship matrix visualization (vismat()): Added vismat() for heatmaps and histograms of pedmat objects, tidyped objects, and standard matrices. Heatmaps can be annotated with family groups when a pedigree is provided.

Documentation

1. CRAN preparation: Updated vignette generation, S3 method dispatch, and documentation for CRAN submission.

Internal changes

1. Portable compilation: Standardized src/Makevars for cross-platform compatibility.
2. Dependencies: Moved RcppArmadillo to LinkingTo.

Changes in version 0.7.3 released on 13 Jan 2026

Breaking changes

1. pedmatrix() return value and method selection: pedmatrix() now requires a single method value, such as method = "A". It returns the requested matrix or vector directly instead of a named list. Requesting multiple methods in one call now raises an error; use repeated calls for multiple outputs.

New features

1. Rcpp relationship calculations: Added pedmatrix() with Rcpp implementations for the additive relationship matrix (A), sparse inverse additive matrix (Ainv) using Henderson’s rules, dominance matrix (D), and inbreeding coefficients (f) using the Meuwissen and Luo (1992) path-tracing algorithm.

Improvements

1. Default inbreeding backend: inbreed() now uses the native Rcpp implementation by default, moving nadiv to Suggests.
2. Documentation and website: Updated package documentation and vignettes. The 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 the genmethod parameter to tidyped(). Users can choose "top" (top-aligned, default) or "bottom" (bottom-aligned) generation inference. The "top" method aligns founders at generation 1; the "bottom" method aligns terminal nodes at the bottom for visualization of unrelated introduced parents.

Improvements

1. Default generation assignment: Changed the default generation assignment method to "top".
2. Pkgdown website: Generated and published the package website at https://luansheng.github.io/visPedigree/.
3. Automated documentation deployment: Added a GitHub Actions workflow for documentation updates and GitHub Pages deployment.

Changes in version 0.7.1 released on 11 Jan 2026

CRAN release: 2026-01-21

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. Trace semantics: Corrected trace = "all" in tidyped() and visped() so it returns the union of ancestors and descendants ("up" plus "down") instead of the entire connected component.

Performance

1. Large-pedigree visped() rendering: Optimized visped() for large pedigrees through attribute handling and vectorized rendering, reducing repeated igraph attribute lookups for 100,000+ individuals.
2. Vectorized tracing: Refactored trace_ped_candidates() in tidyped() to use vectorized igraph::neighborhood() calls. In one benchmark, 37,000 candidates in a 178,000-individual pedigree were traced in about 1.2 s.
3. Early isolated-individual filtering: Implemented early filtering of isolated Gen 0 individuals in prepare_ped_graph() to streamline graph conversion and layout.

Changes in version 0.7.0 released on 10 Jan 2026

Breaking changes

1. Graph-based tidyped() core: Reimplemented the pedigree tidying engine around a directed acyclic graph representation, with cycle detection and generation inference based on topological sorting.
2. Modular visped() architecture: Split the previous monolithic visped.R implementation into visped_layout.R, visped_graph.R, visped_style.R, and visped_render.R.

New features

1. visped() layout parameters: Added pagewidth to control PDF page width and symbolsize to scale node sizes relative to label dimensions.
2. Two-pass rendering: Added a two-pass strategy in plot_ped_igraph() so edges connect at node centers in vector PDF outputs.
3. Highlight tracing: Added ancestry and descendant highlighting through the trace parameter in visped().

Bug fixes

1. outline = TRUE rendering: Fixed rendering failure by correcting graph attribute indexing.
2. Coordinate precision: Improved coordinate calculation precision to reduce overlap in high-density generations.

Internal changes

1. Testing framework: Modernized the unit testing suite to testthat 3rd edition and removed legacy context() warnings.

Changes in version 0.6.2 released on 01 Jan 2026

New features

1. summary.tidyped(): Added a summary() method for tidyped objects to report counts of individuals, founders, sex distribution, and related pedigree statistics.

Bug fixes

1. tidyped(..., inbreed = TRUE): Fixed failure caused by incorrect class assignment order.
2. visped(..., showf = TRUE): Added a warning when the f column is missing instead of erroring.
3. Vignette navigation: Fixed broken internal navigation links in package vignettes.

Changes in version 0.6.1 released on 30 Dec 2025

New features

1. Highlight styling: Implemented opaque highlighting effects for clearer visualization.
2. visped() trace direction: Added the trace option to visped() to control ancestry tracing direction.

Changes in version 0.6.0 released on 28 Dec 2025

New features

1. Strict tidyped S3 class structure: Added the new_tidyped() constructor and validate_tidyped() validator for tidyped objects.

Changes in version 0.5.0 released on 26 Dec 2025

New features

1. visped() highlighting: Added the highlight parameter to visped() for highlighting specific individuals with a character vector of IDs or a list of custom colors.
2. visped() inbreeding display: Added the showf parameter to visped() to display inbreeding coefficients on the pedigree graph.
3. tidyped() inbreeding calculation: Added the inbreed parameter to tidyped() to calculate inbreeding coefficients using nadiv.
4. Standalone inbreed(): Refactored inbreed() as a standalone tool that operates on tidyped objects.

Performance

1. repeloverlap(): Optimized repeloverlap() with data.table.

Bug fixes

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

Changes in version 0.4.1 released on 25 Dec 2025

Bug fixes

1. Edge overlap detection: Fixed overlapping edge detection for small pedigree graphs.
2. Compact-mode coloring: Improved coloring consistency for compact mode.

Changes in version 0.2.6 released on 31 Mar 2020

Bug fixes

1. Candidate generation tracing: Fixed a bug where candidates were traced to generation n + 1 when tracegen = n. Reported by Mianyu Liu.

Changes in version 0.2.5 released on 25 Feb 2020

Bug fixes

1. trace = "all" in tidyped(): Fixed cases where tidyped() did not work with trace = "all" (issue comment).

Changes in version 0.2.4.1 released on 24 Feb 2020

Bug fixes

1. Repeated tidyped() calls: Fixed an unexpected column named NA when a tidyped object was tidied again with tidyped().

Changes in version 0.2.4 released on 12 Jun 2019

Bug fixes

1. Input mutation: Fixed a bug where a data.table supplied as ped could be changed by tidyped() or visped().

Changes in version 0.2.3 released on 05 Mar 2019

Bug fixes

1. Generation inference: Fixed incorrect generation-number inference for individuals.

Changes in version 0.2.2 released on 28 Jan 2019

Bug fixes

1. Candidate retention: Fixed a bug where a tidied pedigree did not include candidates absent from the original Ind column when cand was not NULL.

Changes in version 0.2.1 released on 17 Nov 2018

Bug fixes

1. Node overlap: Repelled overlapping nodes caused by very small differences (digits > 7) among node x positions.