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forrel 1.7.0

New features

  • The function checkPairwise() has undergone substantial revision, with plots implemented in both ggplot2 and plotly in addition to the default base plot. A summary of the main changes are:

    • a new argument plotType can be either "base" (default), "ggplot" or "plotly"
    • the plotting is now done in a separate function plotCP() which is also exported
    • a new argument ids, which when given restricts the checks to those individuals
    • the output column LR is renamed to GLR (generalised likelihood ratio)
    • new output column pedrel describing (in words) each relationship according to the pedigree. The descriptions are obtained with the verbalisr package
    • estimation of P-values for each pairwise relationship, by parametric bootstrap simulations. This feature is controlled through new arguments nsim, pvalThreshold and seed. By default nsim = 0, meaning that no simulations are performed. The P-values are stored in the output column pval.

  • New function quickLR() performs the most common kinship tests (paternity and sibship) for a pair of individuals.

  • New function ibdLoglik() computes the pairwise likelihood for given set IBD coefficients (kappa or delta).

  • Improved progress bars using the pbapply package.

Other

  • Removed (long deprecated) IBDtriangle(), replaced by ribd::ibdTriangle().

  • Improved missingPersonPlot() appearance.

  • In ibdEstimate(), more efficient data prep, and better removal of missing data.

  • Refresh code in examples.

forrel 1.6.1

  • Functions facilitating interaction with the Familias software have been moved to a dedicated package, pedFamilias. However, readFam() and writeFam() will continue to be re-exported from forrel for some time.

  • Remove dependency of pedmut.

  • In kinshipLR(), improve checking of argument markers.

forrel 1.6.0

New features

  • New function writeFam().

  • readFam() gains argument fallbackModel to be applied if the function encounters unrecognisable mutation models in the .fam file.

Other

  • Remove use of packageVersion() (thereby sidestepping CRAN issue).

  • Use pedtools::setMutmod() instead of pedprobr::setMutationModel().

  • Update version requirements for imported packages.

forrel 1.5.2

New features

  • readFam() includes more input checks and gives better error/warning messages.

forrel 1.5.1

New features

  • readFam() now handle all mutation models available in the Familias software.

  • readFam() and Familias2ped() gain argument prefixAdded.

Bug fixes

  • Fixed bug in missingPersonLR() manifesting when POI and MP have identical names.

Other

  • Added license statement GPL (>=2).

  • Expanded README, adding an example with conditional simulation.

  • Updated package documentation.

  • Fixed CRAN note by avoiding ibdsim2:::.

forrel 1.5.0

Breaking change

  • The default output of profileSim(x, N = 1) is now a single pedigree, instead of a list of length 1 (containing the pedigree). This is usually the desired output of N = 1 in interactive use. To override this behaviour, set simplify1 = FALSE.

New features

  • Added dataset FORCE describing the FORCE snp panel (Tillmar et al, 2021, doi:10.3390/genes12121968).

  • profileSim() has a new argument simplify1 (by default TRUE) controlling the output when N = 1.

  • profileSim() now allows markers to be a list of frequency vectors, simplifying the code in unconditional simulations. For instance, the following command now works: nuclearPed() |> profileSim(markers = NorwegianFrequencies). Previously this required an intermediate step of setMarkers().

  • In kinshipLR() the treatment of linked markers (with MERLIN) has been rewritten and is substantially more efficient. A new argument keepMerlin allows to keep merlin files for debugging.

  • missingPersonLR() was overhauled, making it more user friendly.

  • missingPersonPlot() has been modified and updated in sync with changes in pedtools.

forrel 1.4.1

  • Fix CRAN complaint: Use inherits() instead of class().

forrel 1.4.0

New features

  • New function findExclusions() for identifying incompatible markers in identification cases.

  • powerPlot() gains a logical argument jitter, which can be switched on to avoid overplotting.

  • checkPairwise() gains an argument excludeInbred, which is TRUE by default. This is sensible since the plot shows estimated kappa coefficients, which are well-behaved only for pairs of noninbred individuals.

Other changes

  • forrel now requires R version 4.1 and recent versions of pedtools and ribd. This allowed many simplifications in code and examples.

  • Added scales as a suggested package.

forrel 1.3.0

New features

  • The new function ibdEstimate() replaces the previous IBDestimate() (note the name change). This is a complete rewrite, which optimises the log-likelihood using a projected gradient descent algorithm, combined with a version of Armijo line search.

  • The function ibdBootstrap() replaces the previous kappaBootstrap() and deltaBootstrap(), and is considerably faster. This function implements both parametric and non-parametric bootstrap, controlled with the method parameter.

  • The output of ibdEstimate() now has a class attribute "ibdEst", with its own print and subsetting methods.

forrel 1.2.0

New features

  • kinshipLR() now handles linked markers by wrapping MERLIN.

  • New functions kappaBootstrap() and deltaBootstrap() for assessing the uncertainty of pairwise relatedness estimates.

  • New function randomPersonEP() handling a common special case of exclusionPower().

Other changes

  • forrel now depends on version 0.9.6 (or later) of pedtools.

  • Deprecated arguments id.labels and frametitles in missingPersonPlot() has been removed.

forrel 1.1.0

New features

  • Implement parallelisation in profileSim().

  • Partial rewrite of kinshipLR(), including new argument source.

  • Added the NorwegianFrequencies dataset, containing allele frequencies for 35 STR markers.

  • New function missingPersonLR().

  • New function checkPairwise() replaces the (long obsolete) examineKinships().

  • New functions markerSimParametric() and profileSimParametric() for simulating marker data for two individuals with given kappa (or condensed identity) coefficients.

Bug fixes

  • In profileSim(), fix bug resulting in identical seeds given to each parallel cluster.

forrel 1.0.1

New features

  • readFam() now has a parameter Xchrom which can be used to indicate that the markers included in the file are on the X chromosome

  • MPPsims() is more flexible, and allows subsetting of its output.

  • powerPlot() is more flexible and allows finer control of the plot contents

Bug fixes

  • Fixed several glitches in readFam(). It is more robust now, and fails gracefully in certain situations which cannot currently be handled (e.g. if the file contains twins).

forrel 1.0.0

  • Initial CRAN release