NEWS
FamAgg 1.21.2
- Allow writing of HaploPainter input files without a HaploPainter installation.
FamAgg 1.21.1
- Add information on kinship-based relatedness to kinship sum test results.
- 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.
FamAgg 1.19.1
- Add kinshipPairs function
FamAgg 1.17.1
- Fix issue #20 (binary trait drops names upon conversion).
FamAgg 1.13.3
- 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.
- Plot label2 and label3 text at 80% of the main text size.
FamAgg 1.13.2
- Big text blocks for label1 pedigree plotting generated by '\n' concatenation
only grow towards the bottom of the canvas.
- Take into account cex when positioning label1 text.
FamAgg 1.13.1
- 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.
FamAgg 1.11.5
- Ensure same ordering of pedigree and provided labels in buildPed (issue #19).
FamAgg 1.11.4
- Fix bug in buildPed with prune = TRUE that resulted in either a missing mother
or father in some complicated family structures.
FamAgg 1.11.3
- Fixed bug in buildPed missing out mates in some special cases.
- Fixed bug in buildPed causing differences between individual IDs and rownames
of the pedigree data.frame.
FamAgg 1.11.2
- Fix corner case in generating plotting data pedigree.
- Add -family parameter for haplopainter, got lost during refactoring
(issue #16 aftermath).
FamAgg 1.11.1
- Fix issue with ids in the pedigree being factors.
FamAgg 1.9.1
- Fix problem with custom plot title when using haplopainter (issue #16).
FamAgg 1.7.4
- Fix trait-related problem in binomial test.
FamAgg 1.7.3
- Deprecating the probability test because of problems with the gap package in
MS Windows.
FamAgg 1.5.3
SIGNIFICANT USER-VISIBLE CHANGES
- 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.
FamAgg 1.5.2
NEW FEATURES
- New binomial test implemented (binomialTest and FABinTestResults object).
FamAgg 1.3.3
NEW FEATURES
- Parameter id added to the findFounders method, which allows to find
the founder couple for the pedigree of the specified individual.
FamAgg 1.3.2
BUG FIXES
- FAData and pedigree<- ensure now that the IDs for individuals are unique,
even across families.
FamAgg 1.3.1
NEW FEATURES
- removeSingletons method for FAData objects.
SIGNIFICANT USER-VISIBLE CHANGES
- Additional argument family in buildPed.
FamAgg 0.99.9
BUG FIXES
- Fixes to the Vignette and addition of citation.
- Small fixes mainly to the Vignette and one left over problem from the git/svn
conflict merge.
FamAgg 0.99.8
NEW FEATURES
- FAData constructor recognizes *.ped and *.fam files and imports their
pedigree information correctly.
- export method to export pedigree information from a FAData to a ped or fam file.
- Add methods getFounders and getSingletons.
SIGNIFICANT USER-VISIBLE CHANGES
- Founders are now represented by NA in columns 'father' and 'mother'. This fixed
potential problems when IDs are character strings and not numeric.
- Added column 'family' to the results of the probability test.
- genealogicalIndexTest: renamed argument prune into rm.singletons.
- Removed prune argument for methods calculating per-individual statistics.
- Re-formated and re-structured the vignette.
BUG FIXES
- Validation of pedigree information in FAData improved.
- [ subsetting now ensures that father or mother IDs which are not available
in column 'id' are set to NA.
- clique names are no longer dropped when setting cliques(object) <- value.
FamAgg 0.99.6
NEW FEATURES
- Monte Carlo simulation to assess significance of familial incidence
rate and familial standardized incidence rates.
- New FAIncidenceRateResults object along with its methods.
- New FAStdIncidenceRateResults object along with its methods.
- New function factor2matrix to convert a factor into a matrix.
SIGNIFICANT USER-VISIBLE CHANGES
- Vignette: extended content and adapted to use Bioconductor style.
- Results from the kinship sum test are now, in addition to the p-value, also
sorted by the kinship sum.
BUG FIXES
- Fixed some problems in the documentation.
FamAgg 0.99.5
SIGNIFICANT USER-VISIBLE CHANGES
- Some changes related to the github repository.
- Added a readme.org file.
FamAgg 0.99.4
SIGNIFICANT USER-VISIBLE CHANGES
- Renamed genealogicalIndex method into genealogicalIndexTest to conform the
naming convention that all methods ending with Test use simulations to
assess signifcance levels.
FamAgg 0.99.3
NEW FEATURES
- Stratified sampling for kinship group test.
BUG FIXES
- Fixed a bug in plotPed related to optional labels.
- Fixed a bug in familialIncidenceRate: self-self kinship was not excluded.
FamAgg 0.99.2
SIGNIFICANT USER-VISIBLE CHANGES
FamAgg 0.99.1
SIGNIFICANT USER-VISIBLE CHANGES
- Fixed pdf export of vignette.
BUG FIXES
- Removed the Haplopaint requirement checking during package loading as
this resulted in errors on some systems.
FamAgg 0.99.0
SIGNIFICANT USER-VISIBLE CHANGES
- Improved the vignette.
- Fixed several issues in the documentation.
FamAgg 0.6.0
NEW FEATURES
- sliceAge function to define the time an individual spent per age stratum.
SIGNIFICANT USER-VISIBLE CHANGES
- Removed the obsolete FAResult object; all result objects now inherit
directly from FAData, that contains now also the trait information.
- kinship returns now the kinship matrix with columns and rows corresponding
to the ids in the internal pedigree.
- Renamed the "kinship test" and FAKinshipResult in "kinship group test" and
FAKinGroupResults.
- Renamed the "kinship cluster test" and FAKinClustResult in "kinship sum test"
and FAKinSumResults.
- Renamed FAProbResult in FAProbResults.
- Renamed FAGenIndexResult in FAGenIndexResults.
- Renamed familialRate into familialIncidenceRate.
FamAgg 0.5.1
BUG FIXES
- Fixed the vignette reducing the number of permutations and the pedigree size.
FamAgg 0.5.0
NEW FEATURES
- plotRes for FAKinshipResult.
- Stratified sampling for kinshipClusterTest.
BUG FIXES
- 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.
- Removed all CHRIS data sources and the related unit tests to compare new
and old code.
- Fixed a bug in the subsetting method ([) of FAData that did not return the
correct kinship matrix.
SIGNIFICANT USER-VISIBLE CHANGES
- Added parameter "only.phenotyped" to the plotPed method.
- Added some more use cases and examples to the vignette.
- Removed a lot of un-needed warnings.
- Results methods of all analysis methods return now a p-value sorted data.frame.
FamAgg 0.4.0
NEW FEATURES
- Implemented the "familial incidence ratio" from Kerber (1995).
SIGNIFICANT USER-VISIBLE CHANGES
- Removed warnings and "cleaned" analysis methods.
FamAgg 0.3.0
NEW FEATURES
- New methods to extract matched controls for given ids from the pedigree:
getAll, getExternalMatched, getGenerationMatched, getGenerationSexMatched,
getSexMatched.
- Implemented the "genealogical index" method: FAGenIndexResult and related
methods.
- Implemented the plotting method plotRes to visualize simulation results (thus
far only for FAGenIndexResult).
BUG FIXES
- 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
- Using kinship2 with device="plot" plotting by default.
- New section in the vignette describing a genealogical index use-case.
FamAgg 0.2.0
NEW FEATURES
- Implemented methods countGenerations, estimateGenerations, generationsFrom,
getSiblings, findFounders for FAData, data.frame, pedigree and pedigreeList.
- Most pedigree functions (e.g. getChildren, getAncestors) can also be applied
to data.frame, pedigree or pedigreeList objects.
SIGNIFICANT USER-VISIBLE CHANGES
- Implemented the following methods for data.frame, pedigree and pedigreeList
objects: getAncestors
- Added arguments label1, label2 and label3 to plotPed that allow to further
customize pedigree plots.
- Some more examples added to the vignette.
FamAgg 0.1.0
SIGNIFICANT USER-VISIBLE CHANGES
- Added support for argument is.proband in kinship2 plotting.
BUG FIXES
- In plotPed, argument cex is passed down to plotting functions.