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compact = TRUE mode where relationship
values (A, D, AA) were incorrect for parent-offspring and avuncular
pairs due to improper merging of parent individuals with their
non-parent siblings.expand_pedmat() to correctly handle sibling off-diagonal
elements by dynamically calculating relationship values based on parent
kinship, rather than simply duplicating representative diagonal
values.tidyped(..., genmethod = "bottom") to prioritize
Sibling Consistency (P1) over Mate
Alignment (P2). This ensures that full siblings are always
aligned to the same generation.visped() edge highlighting: Fixed edge
highlighting logic so relationship edges are only emphasized when
trace is used.visped() layout: Fixed layout
optimization failure when showf = TRUE. The layout
algorithm now correctly uses immutable individual IDs.To provide a clean and intuitive API for v1.0.0, core function names
and behaviors have been standardized: -
pedmatrix is renamed to
pedmat. - pedmat
default method is now "A" (Additive
Relationship Matrix). Previously it was "f" (Inbreeding
Coefficients). - expand_pedmatrix is
renamed to expand_pedmat. -
summary_pedmatrix is renamed to
summary_pedmat. - The parameter
n_threads is standardized to
threads across all functions. - Legacy
function names (pedmatrix, etc.) have been removed. Please
use pedmat() directly.
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.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.pedmat()
(formerly pedmatrix) now fully supports 6 types of genetic
relationship matrices: Additive (A, Ainv), Dominance (D, Dinv), and
Additive-by-Additive Epistatic (AA, AAinv).vismat): Added vismat() function for
visualizing relationship matrices (A, D, AA, etc.) with heatmaps and
histograms. It supports pedmat objects,
tidyped objects (auto-calculates A matrix), and standard
matrices. Heatmaps can be annotated with family groups when a pedigree
is provided.This release marks the first stable version 1.0.0, polished for CRAN.
src/Makevars for cross-platform compatibility (removed
GNU/platform-specific extensions).RcppArmadillo to
LinkingTo to optimize package structure.vignette
generation, resolved diag S3 method dispatch, and cleaned
up documentation for CRAN compliance.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.pedmatrix() function implemented in Rcpp for
efficient computation of:
inbreed() function now uses the native Rcpp implementation
by default, moving the nadiv package to
Suggests.genmethod parameter to tidyped(). Users can
now choose between "top" (top-aligned, default) and
"bottom" (bottom-aligned) methods for generation inference.
"top" method aligns founders at Generation 1, which
is more appropriate for biological pedigrees and prevents “founder
drift” in pedigrees with varying depths."bottom" method aligns terminal nodes at the
bottom, useful for visualizing introductions of unrelated exogenous
parents."top" (top-down) for more
intuitive biological visualization.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.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).prepare_ped_graph to streamline downstream graph conversion
and layout algorithms.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).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.visped.R into functional modules:
visped_layout.R, visped_graph.R,
visped_style.R, and visped_render.R for better
maintainability.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.plot_ped_igraph() to ensure edges connect
exactly at node centers, eliminating visual gaps in vector PDF
outputs.trace
parameter in visped().outline = TRUE mode by
correcting attribute indexing in the graph object.testthat 3rd
edition, removing all legacy context() warnings.summary() method for tidyped objects
to provide quick pedigree statistics (number of individuals, founders,
sex distribution, etc.).tidyped(..., inbreed=TRUE) failed
due to incorrect class assignment order.visped(..., showf=TRUE) to gracefully handle
missing f columns by warning the user instead of
erroring.trace option to visped() to control
ancestry tracing direction.tidyped
objects with new_tidyped() constructor and
validate_tidyped() validator to ensure data integrity.highlight parameter to visped()
function. Users can now highlight specific individuals using a character
vector of IDs or a list for custom colors.showf parameter to visped() function
to display inbreeding coefficients on the pedigree graph.inbreed parameter to tidyped()
function to calculate inbreeding coefficients using the
nadiv package.inbreed() function as a standalone tool that
operates on tidyped objects.repeloverlap() function using
data.table for significantly better performance.visped() when combining
compact = TRUE, highlight, and
showf = TRUE by refactoring ped2igraph() to
delay label modification until after layout calculation.R CMD check notes related to
data.table non-standard evaluation by adding
R/globals.R.These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.