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.