CHANGES in VERSION 1.21.2
-------------------------

o Allow writing of HaploPainter input files without a HaploPainter installation.


CHANGES in VERSION 1.21.1
-------------------------

o Add information on kinship-based relatedness to kinship sum test results.
o Keep memory consumption constant. This allows arbitrary long simulation
  runs without running out of memory. Fixes issue #22. Due to the solution
  of that problem, histograms and densities reported by the simulation
  functions may slightly deviate from comparable former runs on the same
  data.


CHANGES in VERSION 1.19.1
-------------------------

o Add kinshipPairs function


CHANGES in VERSION 1.17.1
-------------------------

o Fix issue #20 (binary trait drops names upon conversion).


CHANGES IN VERSION 1.13.3
-------------------------

o Fix cex issue when plotting pedigrees. Starts adding label1 text in the
  second line of individual ID text size and outputs this text at 80% size.

o Plot label2 and label3 text at 80% of the main text size.


CHANGES IN VERSION 1.13.2
-------------------------

o Big text blocks for label1 pedigree plotting generated by '\n' concatenation
  only grow towards the bottom of the canvas.

o Take into account cex when positioning label1 text.


CHANGES IN VERSION 1.13.1
-------------------------

o Parameters id.col, father.col, mother.col, family.col and sex.col for FAData
  allow now to specify the column names for the respective content also if
  a data.frame is provided.


CHANGES IN VERSION 1.11.5
-------------------------

o Ensure same ordering of pedigree and provided labels in buildPed (issue #19).


CHANGES IN VERSION 1.11.4
-------------------------

o Fix bug in buildPed with prune = TRUE that resulted in either a missing mother
  or father in some complicated family structures.


CHANGES IN VERSION 1.11.3
-------------------------

o Fixed bug in buildPed missing out mates in some special cases.
o Fixed bug in buildPed causing differences between individual IDs and rownames
  of the pedigree data.frame.


CHANGES IN VERSION 1.11.2
-------------------------

o Fix corner case in generating plotting data pedigree.
o Add -family parameter for haplopainter, got lost during refactoring
  (issue #16 aftermath).


CHANGES IN VERSION 1.11.1
-------------------------

o Fix issue with ids in the pedigree being factors.


CHANGES IN VERSION 1.9.1
------------------------

o Fix problem with custom plot title when using haplopainter (issue #16).


CHANGES IN VERSION 1.7.4
-------------------------

o Fix trait-related problem in binomial test.


CHANGES IN VERSION 1.7.3
-------------------------

o Deprecating the probability test because of problems with the gap package in
  MS Windows.


CHANGES IN VERSION 1.5.3
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES
    o plotPed with haplopaint plotting supports device = "txt" that just writes
      the data.frame for haplopaint and returns the file name, does however not
      call Haplopaint.


CHANGES IN VERSION 1.5.2
-------------------------

NEW FEATURES
    o New binomial test implemented (binomialTest and FABinTestResults object).


CHANGES IN VERSION 1.3.3
-------------------------

NEW FEATURES
    o Parameter id added to the findFounders method, which allows to find
      the founder couple for the pedigree of the specified individual.


CHANGES IN VERSION 1.3.2
-------------------------

BUG FIXES
    o FAData and pedigree<- ensure now that the IDs for individuals are unique,
      even across families.


CHANGES IN VERSION 1.3.1
-------------------------

NEW FEATURES
    o removeSingletons method for FAData objects.

SIGNIFICANT USER-VISIBLE CHANGES
    o Additional argument family in buildPed.


CHANGES IN VERSION 0.99.9
-------------------------

BUG FIXES
    o Fixes to the Vignette and addition of citation.


CHANGES IN VERSION 0.99.9
-------------------------

BUG FIXES
    o Small fixes mainly to the Vignette and one left over problem from the git/svn
      conflict merge.


CHANGES IN VERSION 0.99.8
-------------------------

NEW FEATURES
    o FAData constructor recognizes *.ped and *.fam files and imports their
      pedigree information correctly.
    o export method to export pedigree information from a FAData to a ped or fam file.
    o Add methods getFounders and getSingletons.

SIGNIFICANT USER-VISIBLE CHANGES
    o Founders are now represented by NA in columns 'father' and 'mother'. This fixed
      potential problems when IDs are character strings and not numeric.
    o Added column 'family' to the results of the probability test.
    o genealogicalIndexTest: renamed argument prune into rm.singletons.
    o Removed prune argument for methods calculating per-individual statistics.
    o Re-formated and re-structured the vignette.

BUG FIXES
    o Validation of pedigree information in FAData improved.
    o [ subsetting now ensures that father or mother IDs which are not available
      in column 'id' are set to NA.
    o clique names are no longer dropped when setting cliques(object) <- value.


CHANGES IN VERSION 0.99.6
-------------------------

NEW FEATURES
    o Monte Carlo simulation to assess significance of familial incidence
      rate and familial standardized incidence rates.
    o New FAIncidenceRateResults object along with its methods.
    o New FAStdIncidenceRateResults object along with its methods.
    o New function factor2matrix to convert a factor into a matrix.

SIGNIFICANT USER-VISIBLE CHANGES
    o Vignette: extended content and adapted to use Bioconductor style.
    o Results from the kinship sum test are now, in addition to the p-value, also
      sorted by the kinship sum.

BUG FIXES
    o Fixed some problems in the documentation.


CHANGES IN VERSION 0.99.5
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES
    o Some changes related to the github repository.
    o Added a readme.org file.


CHANGES IN VERSION 0.99.4
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES
    o Renamed genealogicalIndex method into genealogicalIndexTest to conform the
      naming convention that all methods ending with Test use simulations to
      assess signifcance levels.



CHANGES IN VERSION 0.99.3
-------------------------

NEW FEATURES
    o Stratified sampling for kinship group test.

BUG FIXES
    o Fixed a bug in plotPed related to optional labels.
    o Fixed a bug in familialIncidenceRate: self-self kinship was not excluded.



CHANGES IN VERSION 0.99.2
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES
    o Vignette streamlining.



CHANGES IN VERSION 0.99.1
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES
    o Fixed pdf export of vignette.

BUG FIXES
    o Removed the Haplopaint requirement checking during package loading as
      this resulted in errors on some systems.



CHANGES IN VERSION 0.99.0
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES
    o Improved the vignette.
    o Fixed several issues in the documentation.



CHANGES IN VERSION 0.6.0
------------------------

NEW FEATURES
    o sliceAge function to define the time an individual spent per age stratum.


SIGNIFICANT USER-VISIBLE CHANGES
    o Removed the obsolete FAResult object; all result objects now inherit
      directly from FAData, that contains now also the trait information.
    o kinship returns now the kinship matrix with columns and rows corresponding
      to the ids in the internal pedigree.
    o Renamed the "kinship test" and FAKinshipResult in "kinship group test" and
      FAKinGroupResults.
    o Renamed the "kinship cluster test" and FAKinClustResult in "kinship sum test"
      and FAKinSumResults.
    o Renamed FAProbResult in FAProbResults.
    o Renamed FAGenIndexResult in FAGenIndexResults.
    o Renamed familialRate into familialIncidenceRate.



CHANGES IN VERSION 0.5.1
------------------------

BUG FIXES
    o Fixed the vignette reducing the number of permutations and the pedigree size.



CHANGES IN VERSION 0.5.0
------------------------

NEW FEATURES
    o plotRes for FAKinshipResult.
    o Stratified sampling for kinshipClusterTest.


BUG FIXES
    o The range of data values to be plotted includes now also the observed
      mean kinship value, thus, for results with an p-value=0 are also displayed
      correctly in plotRes for FAGenIndexResult.
    o Removed all CHRIS data sources and the related unit tests to compare new
      and old code.
    o Fixed a bug in the subsetting method ([) of FAData that did not return the
      correct kinship matrix.


SIGNIFICANT USER-VISIBLE CHANGES
    o Added parameter "only.phenotyped" to the plotPed method.
    o Added some more use cases and examples to the vignette.
    o Removed a lot of un-needed warnings.
    o Results methods of all analysis methods return now a p-value sorted data.frame.



CHANGES IN VERSION 0.4.0
------------------------

NEW FEATURES
    o Implemented the "familial incidence ratio" from Kerber (1995).


SIGNIFICANT USER-VISIBLE CHANGES
    o Removed warnings and "cleaned" analysis methods.




CHANGES IN VERSION 0.3.0
------------------------

NEW FEATURES
    o New methods to extract matched controls for given ids from the pedigree:
      getAll, getExternalMatched, getGenerationMatched, getGenerationSexMatched,
      getSexMatched.
    o Implemented the "genealogical index" method: FAGenIndexResult and related
      methods.
    o Implemented the plotting method plotRes to visualize simulation results (thus
      far only for FAGenIndexResult).


BUG FIXES
    o Kinships of 0.5 were by default removed in the kinship and the kinship cluster
      test to avoid considering self-self kinships. This resulted in erroneous kinship
      estimates if twins (also having a kinship of 0.5) were in the pedigree.
      Thus, now only the self-self kinship (i.e. diagonal of the kinship matrix) is
      excluded prior to the kinship aggregations.



SIGNIFICANT USER-VISIBLE CHANGES
    o Using kinship2 with device="plot" plotting by default.
    o New section in the vignette describing a genealogical index use-case.




CHANGES IN VERSION 0.2.0
------------------------

NEW FEATURES
    o Implemented methods countGenerations, estimateGenerations, generationsFrom,
      getSiblings, findFounders for FAData, data.frame, pedigree and pedigreeList.
    o Most pedigree functions (e.g. getChildren, getAncestors) can also be applied
      to data.frame, pedigree or pedigreeList objects.


SIGNIFICANT USER-VISIBLE CHANGES
    o Implemented the following methods for data.frame, pedigree and pedigreeList
      objects: getAncestors
    o Added arguments label1, label2 and label3 to plotPed that allow to further
      customize pedigree plots.
    o Some more examples added to the vignette.



CHANGES IN VERSION 0.1.0
------------------------

SIGNIFICANT USER-VISIBLE CHANGES
    o Added support for argument is.proband in kinship2 plotting.


BUG FIXES
    o In plotPed, argument cex is passed down to plotting functions.
