ibdsim2 2.3.2

• plotSegmentDistribution() gains argument merge.
• Allow parameters ids and skipRecomb to be functions.
• Brush up documentation of ibdsim().
• App: Warn (instead of crash) when empty seed input.

ibdsim2 2.3.1

App changes

• The number of simulations are restricted to minimum 5, maximum 5000.

Other

• Make plot code compatible with ggplot2 v4.0.0.

ibdsim2 2.3.0

Breaking change

• The default built-in recombination map “decode19” has been updated. As before, this is a thinned version of the map from Halldorsson et al. (2019), using GRCh38 coordinates, but the new version has more accurate physical chromosome endpoints. It also uses a better thinning algorithm, which allowed reducing the number of data points from ~38 000 to ~14 000 without losing accuracy.

App changes

• The app now uses the updated built-in map as described above. This may lead to (usually very slightly) different results when the length unit is set to “Mb”.
• A new switch button “Origin” has been added in the bottom left corner of the plot region. This can be used to enforce the scatter plot axes to start at the origin (0,0).
• In the “Total IBD” distribution plot, the x-axis now show percentages of the total (autosomal or X) genome length, in addition to the absolute lengths. When the unit is “cM”, the total length is taken as the average length for males and females (unless for X, when the female length is used).

Package changes

• The realised...() functions gain argument simplify1 for simplifying the output when N = 1. This is useful for interactive use.
• Fixed a bug in profileSimIBD(), which sometimes affected markers in the telomeric regions.
• Added internal helper functions for taking unions and intersections of IBD segments.

ibdsim2 2.2.0

App updates

• launchApp() now opens the app in the default browser.
• The app now stops automatically when the browser is closed (locally).
• Minor appearance tweaks.

Other

• Added merge = TRUE argument to realisedKappa() and other realised... functions. Previously, IBD segment merging was handled inconsistently, sometimes causing unexpected results. (Thanks, @mkruijver.)
• Added all required packages for the app to ‘Suggests’.
• Remove unused shinyBS import

ibdsim2 2.1.1

App updates

• Tweaked the labels of the built-in pedigrees (some were confusingly named).
• Added a few more inbred built-in pedigrees.
• Revised the default individuals to be selected for each built-in pedigree.
• Changed the pedigree shown at startup to half siblings.

Package updates

• Fixed a bug in haploDraw() causing an additional empty plot in some situations.

ibdsim2 2.1.0

This version includes a major update of the shiny app frontend to ibdsim2. Previously developed in a separate repository (accessible at https://github.com/magnusdv/ibdsim2-legacy/), the app is now included as part of the ibdsim2 package, and can be run locally with ibdsim2::launchApp(). The live version is available at https://magnusdv.shinyapps.io/ibdsim2-shiny/.

New app features

• The simulations are now much faster than before. As a result, the default number of simulations has been increased from 50 to 500.

• X-chromosomal IBD simulations are now supported.

• The user can now choose the length unit for IBD segments; either centiMorgan (“cM”, default) or megabytes (“Mb”).

• Fixed buggish unit conversion in the previous version: In some cases the segments were measured in Mb while the plot labels said “cM”.

• The random number seed can now be selected by the user.

• More coherent layout and better pedigree plots.

• New function launchApp() for running the app from within R.

Other

• findPattern() now works as intended also for X-chromosomal simulations.
• Various updates of docs and examples.

ibdsim2 2.0.0

Breaking changes

• As of version 2.0.0, the main data structure for IBD segments includes both megabase (MB) and centiMorgan (CM) coordinates. This allows the user to choose length unit in all downstream analyses. However, the new format is not compatible with previous versions of the package.

• ibdsim() has a new argument simplify1, by default TRUE. This means that ibdsim(..., N = 1) now simply returns a matrix, without the outer list layer. This typically the desired behaviour in interactive use, especially when piping. To enforce a list output, add simplify1 = FALSE.

New features

• All downstream functions depending on segment lengths (e.g. segmentStats() and plotSegmentDistribution()) have a new argument unit, allowing the user to choose between “cm” (centiMorgan) and “mb” (megabases).

• haploDraw() has nicer default colours and automatically produces sensible margins.

• New (experimental) function karyoHaploid() for visualising IBD segments in karyogram plots.

• convertPos() has been rewritten using Rcpp, making it much more efficient.

• General overhaul of documentation, examples and README.

ibdsim2 1.5.0

New features

• X-chromosomal simulations are now implemented.

• haploDraw() now handles and displays X-chromosomal simulations.

Other

• Fix labelling bug in haploDraw().

• profileSimIBD() has been overhauled, fixing several glitches and with significant speed improvements. Note: Simulations with a given seed may differ across versions.

• The internal dataset decode19 has been recompiled, updating some attributes. This should not affect regular users.

ibdsim2 1.4.0

New features

• New function segmentStats() for summarising the segments identified by findPattern().

• findPattern() has a new argument cutoff for excluding short segments.

• findPattern() can detect more patterns: the argument pattern now accepts entries autozygous and heterozygous.

• findPattern() is much faster now, mostly due to a new implementation of the internal mergeSegments()

• New function extractIds() replaces the previous (non-exported) extractIdsFromSegmentSummary().

• Updated README, including links to Shiny app.

Bug fixes

• Fixed wrong length attribute of loadMap() when uniform = F and sexAverage = T.

ibdsim2 1.3.0

New features

• ibdsim() now allows map to be a list of chromosome maps.

• New function findPattern() for identifying IBD patterns in simulation outputs.

• New function convertPos() for converting between genetic and physical positions.

• New functions mapLen() and physRange() for retrieving map info.

• profileSimIBD() now sorts the genotypes before returning.

• README is updated and expanded.

Bug fixes

• Fix bug in estimateTwoLocusInbreeding()

• Fix issue with negative segment lengths

ibdsim2 1.2

Breaking changes

• The previous built-in recombination map (based on Kong et al., 2010) is replaced with one based on Halldorsson et al. (2019), using GRCh38 coordinates. For reasons of speed and efficiency, the built-in map is a thinned version of the published map, keeping around 60 000 data points.

New features

• New function haploDraw() for visualising IBD patterns

• The internal data structure for genetic maps has been rewritten.

• New functions loadMap() and customMap() for loading built-in and user-prepared maps.

Bug fixes

• Fixed CRAN warnings about self-assignment in Rcpp code.

ibdsim2 1.1

• Initial CRAN release