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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.
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