Ginv                    Compute Generalized Inverse of Input Matrix
arp.fit                 Fitted values for an ARP type
arp.gof                 Find 'r-squared' as the goodness-of-fit of an
                        arp.ibd model
arp.ibd                 Estimate the trait locus position
                        simultaneously with trait locus effects for
                        Affected Relative Pairs
arp.ibd.fitter          For internal use within arp.ibd.
c.ls                    Estimate C-coefficient for an ARP type by
                        least squares
c2lambda                Convert C-coefficient to lambda for a
                        specified type of ARP
derivC2lambda           Derivative of lambda with respect to the
                        C-coefficient
example.share           Example IBD sharing values for Affected
                        Relative Pairs
finish.objects          Finish making objects that have been read by
                        read.objects
finish.objects.default
                        finish.object is to finish making objects that
                        have been read by read.objects
finish.objects.genehunter.ibd
                        Method to finish an object of class
                        genehunter.ibd, as read by read.objects
finish.objects.merlin   Method to finish an object of class merlin, as
                        read by read.objects
get.genehunter.ibd      Compute IBD matrices by Genehunter and read
                        into S
get.object              Retreive an object from a data file
ibd.df                  Create and return a dataframe of ped, per1,
                        per2, and ibd information
ibd.df.merlin           Create and return a dataframe of ped, per1,
                        per2, and ibd information from merlin
ibd.peaks               Find positions corresponding to ibd sharing
                        peaks
ibd.share.genehunter    Make an ibd.share object from Genehunter data
ibd.share.merlin        Make an ibd.share object from Merlin data
lambda.equal.arp        Score statistic to test equal lambda's for
                        different type of ARP's
lambda2c                Convert lambda to C-coefficient for a
                        specified type of ARP
mergeIbdCovar           Merge ibd and pedigree information
parse.genehunter.ibd.pl
                        Lines of a perl script used to process results
                        from Genehunter or Merlin.
plot.arp.ibd            Plot results of an arp.ibd object.
plot.ibd.share          Plot mean ibd share values for an ibd.share
                        object
print.arp.ibd           Print the results of an arp.ibd object
printBanner             Print a nice banner
read.objects            Read an s-tagged file and create an oldClass
                        object
relpair.type            Determine relative pair types
setupData               Set up an example dataset provided within the
                        library.
summary.arp.ibd         Summarize the results of an arp.ibd object,
                        including details of the Newton-Raphson
                        estimation process and parameter estimates.
summary.ibd.share       Summary of an ibd.share object
