\name{NEWS}
\title{NEWS file for the kinship2 package}
\section{Changes in version 1.8.0}{
  \itemize{
    \item Make all functions extracted into R/, no longer from noweb files
    \item All documentation from pedigree.shrink.Rnw moved into Rd and R
    files
  }
}
\section{Changes in version 1.8.0}{
  \itemize{
    \item legendPlot: added function to make a plot with a legend at
    the bottom, which is a separate sibship, whose parents are plotted
    over by the pedigree of interest.
    \item update documentation (Rd and vignette) on specifying
    relation matrix in pedigreeList objects.
    \item vignette now written in Rmd, will convert to html
  }
} 
\section{Changes in version 1.7.2}{
  \itemize{
    \item fixParents: added new function to add parents when they don't
    exist, but listed in momid/dadid, or fixes gender of them if it is
    wrong in the parent id row. Returns a valid pedigree
    object. Suggested by Tomos Potter.
    \item adding plot tests to tests suite: test.plot.pedigree.R
  }
} 
\section{Changes in version 1.7.0}{
  \itemize{
    \item plot.pedigree: fixed kindepth problem when there are many
    multiple marriages
    \item plot.pedigree: fixed bug when affection status is only NA and 1
    \item pedigree.legend: fixed for when radius not given, and when
    only one affection status
  }
} 
\section{Changes in version 1.6.6}{
  \itemize{
    \item plot.pedigree: if no subjects in a generation, don't try to
    plot. This is making plot work for an error that exists in aligning
  }
}  
\section{Changes in version 1.6.3}{
  \itemize{
    \item Change factors to character in pedigree
    \item Fix kinship for all unrelateds to not iterate 1:0
  }
}    
\section{Changes in version 1.5.8}{
  \itemize{
    \item For some complex non-human pedigrees, multiple sires for a
    female cause errors in autohint.  For these cases, we put a
    try-catch around the call to autohint and supress error messages,
    allowing the plot to proceed with ped$hints=1:nrow(ped), and thus
    drawing lots of lines
    \item Add dim.pedigree method, which allows nrow to work as well. It
    returns the number of subjects in the pedigree
    \item Add pconnect arg for plot.pedigree to give flexibility to plot
    children directly under their parents, or loosen this restriction
  }
}
\section{Changes in version 1.5.6}{
  \itemize{
    \item Bug found in pedigree.shrink when character ids used and
    stringsAsFactors set to TRUE. Fix: when making data.frame()s in
    findUnavail and findAvalNonInform, add stringsAsFactors=FALSE
    \item Add pconnect option to plot.pedigree.  This gives more control
    over the lines from parent to child.
  }
}
\section{Changes in version 1.5.4}{
  \itemize{
    \item bug introduced in kinship.pedigree in making other updates in
    version 1.5.0: if(duplicated(id)) set back to be if(duplicated(id$id))
    \item vignette added to vignettes directory, no more need for
    inst/doc dir in source version    
  }  
}
\section{Changes in version 1.5.0}{
  \itemize{
    \item kinship function allows chrtype="X" for X chromosome kinship 
    matrices, will have NA for any relationships that include a subject
    with sex code 3 or 4
    \item add test script for X-chromosome kinship matrix, with and
    without unknown sex codes
    \item plot.pedigree: fixed indexing bug in dog pedigree for sire in
    multiple generations
    \item pedigree.shrink and pedigree.trim now properly update indices
    in relation matrix after subjects are removed
  }
}

\section{Changes in version 1.3.8}{
\itemize{
     \item When subscripting a pedigreeList object, the relationship
     matrix was not properly computed.
 }}
 
\section{Changes in version 1.3.7}{
  \itemize{
    \item Add monzygotic twins computation to the kinship matrix

    \item Add a test for the new monozygote kinship code

    \item Add the ibdMatrix function
}}
\section{Changes in version 1.3.5}{
  \itemize{
    \item Add the ibdMatrix routine, a replacement for bdsmatrix.ibd.
    
    \item The dimnames of a kinship matrix were in the wrong order if
    a. it was created from a pedigreeList and b. the original data set
    that created the pedigreeList was not sorted by family blocks
    (all of one family, then all of the next, ...).  Pointed out by 
    Claus Thorn Ekstrom.
}}

\section{Changes in version 1.3.4}{
  \itemize{
    \item The dimnames on kinship matrices had both row and column names 
    some instances, only column names in others.   Changed to always 
    return both.
    }
}
		

\section{Changes in version 1.3.3}{
  \itemize{
    \item Per a query from Alex Cunningham, checked the return list of
    x,y values from plot.pedigree.  Indeed, they were not in a useful
    order (to the user).  Updated them to be in the same order as the
    input data, and added more information to the help page.
    
    \item Took some families out of minnbreast that did not belong

    \item Compress example data files
  }
}
\section{Changes in version 1.3.0}{
  \itemize{
    \item Added a Minnesota Breast Cancer dataset
    
    \item Add missid as a code for the parents of founder subjects if the code 
    is not one of the defaults (0 or NA for numeric ids, "" or NA for 
    character)
    
    \item Fixed some findex/mindex problems in findUnavailable and 
    excludeUnavailFounders, both used within pedigree.shrink.
    
    \item Updated plot.pedigree.shrink to plot available subjects as red, and 
    included a simple legend to indicate availability coloring. A new 
    parameter, xlegend, can now control the placing of the legend.
    
    \item Fixed a minor indexing bug in "[.pedigree"
    
    \item Fixed typing and grammatical problems in error messages in pedigree()
    
    \item Fixed row/column names in kinship function (Shannon/Terry, please 
    give more details)
    
    \item Allow pedigree.trim to trim all subjects and return an empty pedigree 
    object
    
    \item pedigree.legend to show which portions of a subject's plot
    symbol indicate which affection status
    
    \item aligning of pedigrees now more robust to handle subjects in
    multiple marriages
  }
}
\section{Release Notes for kinship2, version 1.2.1}{
  \itemize{
    
    \item Summary: kinship2 is a branch from the original kinship package with 
    some key updates for the pedigree and kinship functions, with some additional
    functions that work with the pedigree object.
    
    \item pedigree and pedigreeList objects implemented with S3 methods 
    print and "[,"
    \item pedigree plotting routine re-written, now more robust
    \item kinship matrices now implemented with Matrix package classes
    \item utilities to trim the pedigree object with various criteria
  }
}
