CHANGES IN ADEGENET VERSION 1.2-3 NEW FEATURES o implement handling of presence/absence markers. genind and genpop object now have a 'type' attribute to differentiate between codominant markers (e.g. microsatellite), which is the default type, and presence/absence data (e.g. AFLP). Functions in adegenet now behave according to the type of markers being used. o SNP can now be obtained from sequence data, stored as DNAbin (see E. Paradis's package 'ape'). They can be selected to verify any given degree of polymorphism. o 'hybridize' can now be used for genotypes having any even degree of ploidy (e.g. tetraploid genotypes). o the new function 'isPoly' checks which loci are polymorphic, or which alleles contribute to polymorphism. o the new function 'pop' can be used to retrieve and set the pop slot of genind object. o the new function 'selPopSize' allows one to select a subset of genotypes belonging to well-sampled populations, as defined by a threshold sample size. o the new accessor 'locNames' can be used to retrieve real labels of markers and/or alleles. o the loadingplot has been modified to allow specifying x axis, so that scoring SNPs along their sequence is now possible. BUG FIXES o no bug to fix this version! CHANGES IN ADEGENET VERSION 1.2-2 NEW FEATURES o implement different levels of ploidy in genind / genpop objects (new slot @ploidy). Now, any level of ploidy can be handled by input function df2genind, which has been recoded almost entierely. Different levels of ploidy are now handled by different functions. o a "sep" argument is now handled by df2genind: this allows reading many data formats. o implemented a method "scaleGen" for genind / genpop objects, which scales allelic data using different methods. o colorplot: a generic function, with a method for spca objects. Represents up to three principal components based on RGB representation of Cavalli-Sforza. o loadingplot for plotting loadings of one axis o adegenetTutorial function which opens the online tutorials o allow for the use of na.replace and scaleGen in spca function o added rupica dataset o enable reading data from URL (import2genind, read.[...]) o permit specification of a matrix of spatial weights in spca BUG FIXES o fixed bug 1.2-2.01 (read.structure issue): was due to the default of "onerowperind" argument. o fixed bug 1.2-2.02 (read.genetix issue): was due to an error in the data file (wrong nloc); now read.genetix corrects that automatically and issues a warning. o fixed bug 1.2-2.03 (monmonier issue): was a non-detected code 2 due to intersection check with previously drawn segment (was not always removed). o fixed bug 1.2-2.05 (a few fixes/improvement for monmonier) CHANGES IN ADEGENET VERSION 1.2-1 NEW FEATURES o documentation of scaleGen provides an example of usefulness of an appropriate scaling in PCA BUG FIXES o fixed the recognition of NAs in df2genind o fixed the call to inherits in spca (returned value changes in R-devel) CHANGES IN ADEGENET VERSION 1.2-0 NEW FEATURES o implement different levels of ploidy in genind / genpop objects. Make necessary adaptations throughout the package. o put some stop where needed when ploidy!=2 is not handled. o implement a "sep" argument in df2genind. o implement accessor for genind/genpop: nLoc. o implement "scaleGen" for genind/genpop, which allows for different types of scaling. o added several coercion methods, from genind/genpop to data.frame, matrix and ktab objects. o implemented propTyped, a function giving the proportion of non-missing data in different ways. BUG FIXES o missing data indicated in summary corrected (loci with more alleles had more weight in the computations). CHANGES IN ADEGENET VERSION 1.1-3 NEW FEATURES o 'as' methods for genind/genpop objects to matrix, data.frame, and ktab objects. Now, ordination implemented as dudi functions in ade4 (like dudi.pca) can be performed directly using genind/genpop as inputs. CHANGES IN ADEGENET VERSION 1.1-2 NEW FEATURES o significant improvement in the speed of genind2df (more than twice as fast as before). o function propShared added: computes the proportion of shared alleles among a set of genotypes (core computations in C). o A warning is issued when NAs exist in the input of sPCA. o improvement of the validity checking for genind/genpop: validObject now detects duplicates in any kind of names (ind.names, pop.names, etc.) and prints the corresponding items. BUG FIXES o genind2df does now handles the pop argument correctly. o df2genind does no longer bug when there is an entirely non-typed locus. CHANGES IN ADEGENET VERSION 1.1-1 NEW FEATURES o I/O: df2genind no longer fails when entirely non-type individuals exist. o Monmonier: optimize.monmonier now computes the 'best' boundary only once instead of twice. The whole code was re-thought and optimized for speed. Monmonier's boundaries can now form loops. Instead of stoping at a given threshold, it is also possible to ask for a given length of boundary (argument bd.length). o The function chooseCN has a new option to return a list of spatial weights defined as the inverse of spatial distances, at a given exponent. o A wrapper for glob.varcomp has been implemented for genind objects, through the new function fstat. o The elements of the @other slot are now proceeded wisely when objects are subsetted using the '[' operator. BUG FIXES o I/O: df2genind no longer fails when entirely non-type individuals exist. o monmonier no longer fails when coordinates are drawn from a regular grid. The matched call of the returned object has been fixed. CHANGES IN ADEGENET VERSION 1.1-0 NEW FEATURES o Data representation: S4 classes in replacement of old S3 classes. o Spatial genetics: the spatial Principal Component Analysis (Jombart et al, 2008, Heredity), two multivariate spatial tests, and new functionalities for Monmonier's algorithm. o I/O: functions to import data are now 'read' functions; available for formats of GENETIX, Fstat, Genepop, STRUCTURE and from data.frames of genotypes. Export from genind to data.frame of genotypes. o Data: five new simulated geo-referenced datasets o Simulations: a hybridize function, which creates hybrids from two parent datasets. Can output to STRUCTURE format. o Data manipulation: new function to separate data by population. Accessors to genind and genpop object like with matrices using 'foo[ chosenGenotypes, chosenAlleles]'. CHANGES IN ADEGENET VERSION 1.0-2 NEW FEATURES o adegenetWeb is a simple function opening the adegenet website in the default web browser. o sim2pop is a dataset obtained by simulation using the software Easypop. It contains 130 georeferenced genotypes sampled from two distinct populations. o monmonier documentation was improved by adding a genetic example, using sim2pop data. BUG FIXES o some bugs corrected in optimize.monmonier CHANGES IN ADEGENET VERSION 1.0-1 NEW FEATURES o chooseCN is a simple interactive tool for choosing and building a connection network from spatial coordinates. This tool is called by monmonier function. o monmonier, optimize.monmonier, plot.monmonier and print.monmonier implement the Monmonier algorithm. While not restrained to genetic data analysis, this method can be used to find genetic boundaries among individuals or populations based on their allelic frequencies and spatial coordinates. BUG FIXES o several bugs fixed in I/O functions