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.