NEWS

Changes in version 1.7-7

* Maintainer email address updated.

* NEWS file reformatted according to CRAN specifications.

Changes in version 1.7-6

* A bug has been changed in genotypeProbs for compatibility with R 4.2.

Changes in version 1.7-5

* A bug has been fixed in calcPopDiff for estimating global Gst and Jost's D
  statistics.

* calcPopDiff now gives meaningful results for Gst and Rst if there are
  monomorphic markers in the dataset.

* The default value for loci in calcPopDiff is calculated in a (slightly) less
  confusing fashion.

* A bug in read.GeneMapper has been fixed to prevent empty strings from being
  counted as alleles when alleles are non-numeric.

Changes in version 1.7-4

* A "show" method has been added for "genambig" so that datasets print to
  the console in a more sensible manner.  Tyler Smith authored this method and
  has been added as a contributor.

* write.Structure now writes files that can be read directly by Structure without
  modification.  write.SPAGeDi no longer writes a temporary file to the working
  directory (tempdir() is used instead).

* A bug has been fixed in meandistance.matrix2 (via genotypeProbs) that caused
  errors when ploidy was equal to zero, which is a possible outcome of
  recodeAllopoly.

* Alistair Hall has been added as a contributor for coauthoring the SAS code
  used by deSilvaFreq.

Changes in version 1.7-3

* Fixed bug that would occur in a lot of functions (particularly functions 
  dealing with allele frequencies, as well as genbinary objects) if loci
  had overlapping names, e.g. "myloc1"" and "loc1".

* Minor speed and memory improvements for deSilvaFreq and meandistance.matrix2.

* PIC now returns NA if a marker is entirely missing for a population, rather
  than giving an error.

* Updated citation for Clark and Schreier (2017).  Acknowledgement of HN
  de Silva as contributor due to direct translation of his code from SAS
  into R for parts of this package.

Changes in version 1.7-2

* References to manuscripts describing polysat have been added to the 
  DESCRIPTION file.

* The PIC function has been updated to be compatible with R 3.5.

Changes in version 1.7-1

* Bug fixes in alleleCorrelations, testAlGroups, and mergeAlleleAssignments have
  been made so that these functions can accomodate loci with a very small number
  of alleles (one or two).

* Bug fixes in deSilvaFreq to help when allele names are very short, and to prevent
  the function from hanging.

* An option for estimating Slatkin's Rst has been added to calcPopDiff.

* Documentation for gendata.to.genind has been fixed so that the example can still
  run if adegenet is not installed.  (This change was made in order to prevent
  polysat from failing package checks on Solaris systems.)

Changes in version 1.7-0

* The function calcPopDiff has a new argument called "global" that can be used if 
  global rather than pairwise statistics are desired.  It also has an argument
  called "bootstrap" if replicates bootstrapped across loci are desired.

* A new function has been introduced, called "PIC", that estimates the 
  Polymorphic Information Content of loci.

* The function "genIndex" has been added for rapidly identifying all unique
  genotypes for a given locus.  meandistance.matrix and meandistance.matrix2
  now call this function, reducing their processing time several-fold.

* Bruvo.distance and Bruvo2.distance have been edited to speed processing several-fold.
  Package dependency on the combinat package has been removed since Bruvo.distance no
  longer requires combinat.

* Updated citation information with DOI for Molecular Ecology Resources.

Changes in version 1.6-0

* The allele swapping algorithm used by testAlGroups has changed.  Allele assignments
  should be more accurate in general, at the expense of processing time.

* A bug has been fixed in processDatasetAllo, affecting the contents of the missRate
  item in the function's output.

* testAlGroups now outputs an additional item called proportion.inconsistent.genotypes,
  which indicates the proportion of genotypes in the dataset that are inconsistent
  with the allele assignments output by the function.

Changes in version 1.5-0

* The functions processDatasetAllo, plotSSAllo, and plotParamHeatmap have been added
  to simplify the workflow when using alleleCorrelations and testAlGroups.

* The function calcPopDiff has been added to allow estimation of Gst and Jost's D.

* gendata validity function edited to prevent locus names from containing periods.

* fixloci function added to clean up locus names so that they can be column headers.
  This has the consequence that characters such as spaces, hyphens, and parentheses
  will be automatically removed from locus names.  Underscores are allowed.

* Genotype and Genotypes assignment methods for the "genambig" class edited to 
  prevent empty vectors or NA values from being assigned to genotypes.

* deSilvaFreq edited to be compatible with ploidymatrix format.

* gendata.to.genind edited to allow multiple ploidies in the dataset, to be compatible
  with newer versions of adegenet.

* Broken URLs in documentation fixed or removed.

Changes in version 1.4-1

* Documentation for freq.to.genpop and gendata.to.genind updated to be compatible with
  adegenet 2.0.

* Edited Description and Namespace to import from stats and utils for compatibility
  with R 3.3.

* Validation function for gendata, as well as Samples and Loci replacement functions,
  edited to prevent samples and loci from having non-unique names.

* Validation functions for genambig and genbinary edited to call the validation function
  from gendata.

* All data import functions now call validObject immediately before returning the
  object, in order to confirm that genambig objects are formatted correctly.

Changes in version 1.4

* Polysat 1.4 introduces a set of functions for assigning alleles to isoloci in
  allopolyploids and diploidized autopolyploids, and recoding datasets so that
  they can be analyzed under the assumption of random segregation.  New functions
  include simAllopoly, alleleCorrelations, testAlGroups, catalanAlleles,
  mergeAlleleAssignments, and recodeAllopoly.

* meandistance.matrix edited to throw an error if a "genambig" object is not provided.

* meandist.from.array edited to reduce computation time.  meandistance.matrix
  and meandistance.matrix2 edited to call meandist.from.array.

* find.na.dist edited to reduce computation time.

* read.GeneMapper edited to throw an error if it encounters any rows with
  blank spaces or NA in the first allele position, or any rows with -9 outside
  of the first allele position.

* Documentation for FCRinfo and testgenotypes updated to include citation for dataset.

Changes in version 1.3-3

* Fixed an error that would occor if ploidies were in "ploidymatrix" format but
  there was only one sample or only one locus.  (In the "pld" method for class
  "ploidymatrix".)  Fixing this bug introduced another bug in simpleFreq, which
  has also been fixed.

* Fixed PopInfo replacement method for the "gendata" class so that a warning
  would not be issued if all values are NA after replacement.

* Copied all example files for data import into the "extdata" folder so that
  they will once again be part of the installation.

* Edited the documentation of assignClones to suggest excluding samples with
  missing data.

* Added an error message to the Ploidies<- replacement function if any
  individuals are being assigned a negative number as a ploidy.  Added a
  warning to the same function if any individuals are being assigned a ploidy
  greater than 12.

* genotypeProbs is edited to allow for missing genotypes to have a ploidy of zero.

* read.Structure and read.STRand have been edited to prevent periods from being
  inserted into loci names.

* read.Structure now has several options for assigning ploidy to the output
  dataset.  (1) The ploidy of the file can be used as the ploidy of the entire
  dataset, (2) the maximum number of alleles per sample can be used to assign
  ploidy to each sample, or (3) the ploidies can be output as a matrix of
  allele counts for each sample*locus genotype, as in versions 1.3-0 through
  1.3-2.

* read.STRand documentation has been edited so that the example files produced
  more closely resemble files produced by STRand.

* Package "combinat" changed from "Depends" to "Suggests" since it is only needed
  by the Bruvo.distance function.  Package "methods" changed from "Depends" to
  "Imports".  The functions Bruvo.distance and gendata.to.genind have been
  modified to have the correct syntax for package dependencies.

Changes in version 1.3-2

* read.GeneMapper has been edited to prevent the import of alleles as factors.
  The forceInteger argument has also been added to this function to prevent users
  from accidentally importing alleles as character strings.

* read.STRand has been edited to fix a bug that caused an error when a given locus
  had a maximum of one allele per individual.

* Lynch.distance has been edited to be robust to alleles being repeated in a
  genotype (e.g. if a tetraploid homozygote is coded as AAAA instead of A).

* The function Simpson.var, which calculates the variance of the Simpson index and
  can be used with the genotypeDiversity function, has been added.

Changes in version 1.3-1

* The internal function .ulal1loc has been added.  This function finds all
  unique alleles at a single locus.  genambig.to.genbinary has been changed to
  use this function, resulting in about a 3% reduction in processing time.

* The function alleleDiversity has been added.  alleleDiversity finds and counts
  unique alleles in a dataset.

* The functions read.STRand and gendata.to.genind have been added.

Changes in version 1.3-0

* Ploidies can now be indexed by sample, locus, both, or neither.  To accomplish
  this, the 'Ploidies' slot of a "gendata" object must now be an object
  of the class "ploidysuper", a virtual class which includes four new classes
  called "ploidymatrix", "ploidysample", "ploidylocus", and "ploidyone".  Generic
  functions 'pld', 'pld<-', and 'plCollapse' have been defined with methods for
  these four new classes, in order to access and replace ploidy values and convert
  ploidy data between classes, respectively.  The 'Ploidies' function now has
  'sample' and 'locus' arguments so that ploidies can be retrieved in the same way
  regardless of how they are stored.  'reformatPloidies' is a new function for use
  on "gendata" objects, to change the class of the 'Ploidies' slot.  The 'Loci'
  function now has a "ploidies" argument so that loci can be retrieved by ploidy,
  as could be done with samples in previous versions.  Most functions in polysat
  have undergone minor changes in order to utilize the new flexibility in
  ploidy indexing.

* genotypeDiversiy, Simpson, Shannon functions: Calculations are now based on
  counts rather than frequencies, which in the case of the Simpson index, allows
  correction for sample size.

* genotypeDiversity: bug fix for cases in which a population only has one sample
  with non-missing data at a given locus.

* assignClones: bug fix for cases in which there is just one sample.

* 'Genotypes' method of "genbinary" class: Bug fixed that would have simplified the
  genotypes matrix to a vector if a locus had only one allele.  This also
  fixes an issue that came up with 'genbinary.to.genambig'.

* 'genambig.to.genbinary' and 'genbinary.to.genambig' functions:  Minor bug fix
  to prevent warning messages if nothing has been stored to the 'PopInfo' slot.
  Also, bug fix in 'genambig.to.genbinary' to allow for loci at which all data is
  missing.

Changes in version 1.2-1

* Bruvo2.distance function has been added.  This calculates an alternate version
  of the distance measure of Bruvo et al. (2004), under the models of genome
  loss and/or addition.

* genotypeDiversity function: Default value of d has been changed to being
  calculated with Lynch.distance, since the default threshold value is 0 and
  Lynch.distance is faster.

* Bruvo.distance function: If both genotypes are equal to the missing data value,
  the distance returned is now NA instead of 0.

* read.GenoDive: Now correctly finds the "Individual" column, and uses it to
  extract sample names, whether or not a "Clones" column is included.

* read.GeneMapper: Sample and locus names may now consist of any combination of
  letters and numbers.  (There had been a bug that caused an error if samples or
  loci were named with non-consecutive numbers.)

* Locus names are now allowed to be shorter versions of other locus names,
  e.g. "ABC1" and "ABC12".  Fixed: 'Genotypes' method of "genbinary" class
  (this affects 'simpleFreq' and 'genbinary.to.genambig'), 'deleteLoci' method
  of "genbinary" class, 'Loci<-' method of "genbinary" class, 'deSilvaFreq',
  'calcFst', 'write.freq.SPAGeDi', and 'freq.to.genpop'.

Changes in version 1.2-0

* The internal functions .G, .indexg, .genlist, .ranmul, and .selfmat have been
  added.  Previously, these existed only within the environment of the
  deSilvaFreq function.  They have been moved to the polysat package environment
  in order to be used for the calculation of genotype probabilities in
  additional functions (i.e. meandistance.matrix2).

* Functions genotypeProbs and meandistance.matrix2 have been added.  This allows
  ambiguous genotypes to be dealt with in a more sophisticated way, calculating
  the probabiliity of each possible unambiguous genotype based on allele
  frequencies and selfing rate.

* Functions assignClones, genotypeDiversity, Shannon, and Simpson have been added.
  These use distance matrices to assign individuals to clonal groups, and
  calculate diversity indices based on genotype frequencies.

* Bruvo.distance function: Before any calculation is done, the function checks
  to see if usatnt is NA.  If so, an error message is given telling the user
  to fill in the Usatnts slot.  The error that the function would previously
  give in this case was not particularly informative.

* deSilvaFreq function: Now checks to see if the 'self' argument is missing
  before performing any calculations.  This means that a more informative
  error message is given if the selfing rate is not provided.  Also, the line
  smatt <- smat/smatdiv has been moved out of the while loop and is now
  performed immediately after the calculation of smat, to reduce computation time.

* Bug fix in write.GeneMapper.  It can now write files correctly when there are
  more alleles than the ploidy of the individual.

Changes in version 1.1-0

* read.POPDIST, write.POPDIST, and freq.to.genpop functions added.

* read.Tetrasat function changed so that the comment line can't be accidentally
  read as a "Pop" line if it contains the letters "pop".  The documentation for
  this function now also instructs the user not to have any locus name contain
  the letters "pop" adjacent to each other.

* write.Tetrasat function changed so that if the 'samples' argument excludes
  some populations, there won't be a "Pop" line for these populations.

Changes in version 1.0-1

* Bug fixed in the 'editGenotypes' method for "genambig" objects.
  stringsAsFactors=FALSE was added for the data frame that is sent to the
  'edit' function, so that samples and loci are indexed correctly when genotypes
  are written back to the object that is returned.  Version 1.0 would rearrange
  the genotypes if the samples or loci were not in alphabetical order.

Changes in version 1.0

* The S4 classes "gendata", "genambig", and "genbinary" and their accompanying
  methods have been added.  This allows genotypes, population identities,
  population names, ploidies, microsatellite repeat lengths, and a description
  to all be stored in one object, while in version 0.1 they had to be stored in
  separate objects.  Because of this, many of the functions require fewer
  arguments, and user error should be reduced.

* The functions 'viewGenotypes' and 'editGenotypes' have been added so that
  genotypes can be more neatly printed to the console, and can be edited with
  the Data Editor as an alternative to command-line genotype editing.

* The 'isMissing' function is added to simplify the identification of missing
  genotypes.

* The function 'estimatePloidy' now directly opens the Data Editor and then
  returns the ploidies to the appropriate slot in the "gendata" object.
  Previously, the function produced an array from which ploidies had to be
  manually extracted.

* The function 'distance.matrix.1locus' no longer exists since it has been
  consolidated into the 'meandistance.matrix' function.  'Lynch.distance' has a
  'usatnt' argument added to it for the sake of simplifying the code for
  'meandistance.matrix'; this argument is ignored by 'Lynch.distance'.

* The new function 'deSilvaFreq' performs an iterative computation to estimate
  allele freqencies in populations with uniform, even-numbered ploidy and a
  known selfing rate.  The old function 'estimate.freq' is renamed 'simpleFreq'.

* A function 'write.freq.SPAGeDi' is added to export allele frequencies to
  SPAGeDi.