NEWS

pegas 1.3 (2023-12-13)

NEW FEATURES

plot.haploNet() has a new argument 'col.lab' to change the colors of the haplotype labels. It can be changed through the option "labels.color" (see ?setHaploNetOptions).
The R code of mst() has been replaced by a C code which can be 1000 times faster with several 100s observations (this improves also rmst() and all other functions calling mst()). The code now scales very nearly as O(n^2) in practice.
rmst() now returns a network with a "backbone-MST" so that repeated analyses of the same data are likely to return graphically similar networks (see issue #82 on GitHub).

BUG FIXES

tajima.test() may use different sets of sites when computing the number of segregating sites and the mean pairwise distance. This has been fixed by adding pairwise.deletion = TRUE to the call to dist.dna (see issue #77 on GitHub).
The placement of mutation ticks on alternative links of haplotype networks has been fixed (see issue #77 on GitHub).

pegas 1.2 (2023-02-23)

NEW FEATURES

The new function nullAlleles2NA changes genotypes with at least one ‘null allele’ into NA.
MMD() now returns invisibly a list with the plotted data (i.e., histogram, empirical density, and expected curve under stable population).
dist.asd() has now the option 'pairwise.deletion = FALSE'.

BUG FIXES

The estimator variance in theta.s() has been corrected (thanks to Carsten Wiuf) and the help page has been updated.
plot.haploNet() did not handle correctly the 'bg' argument when it is a vector of colours. This also affected the plot of MJN networks.
VCF files with DOS-style end of lines (i.e., CRLF) are now supported.
Argument 'bg' was not always well interpreted in plot.haploNet() and plot.mjn().

OTHER CHANGES

There is a new (non-interactive) example in ?replot.
The help page of plot.mjn() has been clarified about the usage of the arguments 'shape' and 'bg'.

pegas 1.1 (2021-12-16)

BUG FIXES

plot.haploNet() did not use 'bg' correctly when 'pie' was used. The help page has been clarified that this argument could also be a function.
setHaploNetOptions(pie.colors.function = ) did not work correcly; similarly for 'pie.inner.segments.color'.
The argument 'scale.ratio' was not always passed correctly among internal functions when plotting "haploNet" objects (see issue #59 on GH).
haplotype.character() failed to work correctly (see issue #61).

OTHER CHANGES

amova() now accepts distance objects which inherit the class "dist" (instead of being strictly equal).
adegenet has been moved from 'Imports' to 'Suggests'.

pegas 1.0 (2021-04-08)

NEW FEATURES

The new function mutations() draws mutations on a network (with many options; see ?mutations).
The new function write.vcf writes an object of class "loci" into a VCF file.
There is a new cophenetic() method for objects of class "haploNet", and a new labels() method.
diffHaplo() has been simplified and gains the options 'strict' and 'trailingGapsAsN' which are passed to ape::seg.sites().
mjn() has a new option 'quiet = FALSE'; its code has been improved and is now 10 times faster (25 times with 100 sequences resulting in running times less than 15 sec). The returned object have the class c("mjn", "haploNet") and there is a new plot.mjn() method.
replot() has been improved: the instructions are more detailed, there is a new option 'col.identifier' to show the node to be moved, and the bounding box of the plot is now calculated correctly so the network does not "shrink" after each move.
plot.haploNet() has two new options: 'shape' and 'xy' to change the symbol shapes and their coordinates, respectively.
There are two new functions, getHaploNetOptions and setHaploNetOptions, to help users change the graphical paramaters when plotting haplotype networks.
There is a new as.loci() method for matrices.
rmst() implements a new algorithm to stop iterations after no new links are found: this is controlled by the new options 'stop.criterion' and 'iter.lim'. There is also a new option 'quiet = FALSE'.
Fst() now runs in the case of a single population, returning the Fis (and Fit which equates 1).
There is a new vignette "PlotHaploNet" detailing some aspects of plotting haplotype networks with pegas, including the new features and options.

BUG FIXES

A bug was fixed in geoTrans2().
as.loci.data.frame() now works with "tibble" objects (thanks to Jean-Baka Domelevo Entfellner for the fix).
allelicrichness(, method = "rarefaction") used to return the raw allelic richness: this is fixed and this function gains the option 'min.n' to work with this method (common sample size used for all populations).
haplotype() on an empty "DNAbin" object returns an empty "haplotype" object similarly to pegas 0.12 (see issue #53 on GH).

OTHER CHANGES

adegenet has been moved from 'Depends' to 'Imports'.
dist.snp() has been removed.

pegas 0.14 (2020-09-16)

NEW FEATURES

LDscan() gains the option 'what' with two possible choices: "r" (the default and previously only choice) and "Dprime".

BUG FIXES

haplotype.DNAbin() failed to assign correctly haplotypes in some situations with ambiguous bases. This is fixed and the code, which now relies on ape::seg.sites, is now 2 to 3 times faster if there are a few haplotypes in the data.

OTHER CHANGES

In VCFloci(), the option 'chunck.size' has been renamed 'chunk.size'.

pegas 0.13 (2020-03-10)

NEW FEATURES

haplotype.DNA() now handles ambiguities and gaps in an improved way (see the reference in ?haplotype.DNA). Two options have been added to control the behaviour of these analyses: strict = FALSE and trailingGapsAsN = TRUE.
The new functions geoTrans2 transforms latitudes and longitudes from values in decimal degree to character strings (optionally with LaTeX format).

BUG FIXES

VCFloci() crashed if a path starting with "~" was used.
VCF files with large header (> 1 MB) failed to be read.

pegas 0.12 (2019-10-05)

NEW FEATURES

The new functions F2, F3, and F4 implement the F-statistics developed by Patterson et al. (2012, Genetics, 192:1065).
The new function stairway implements the method from Polanski and Kimmel (2003, Genetics, 165:427) quantifying changes in population size from the site frequency spectrum (SFS). There are plot() and lines() method.
The new function loci2alleles does the reverse operation than alleles2loci().
The new function theta.tree.hetero estimates THETA from a non-ultrametric coalescent tree.
The new function Rst computes the R_ST index for microsatellites.
The new function loci2SnpMatrix converts SNPs from a "loci" object into the S4 class "SnpMatrix" of the BioConductor package snpStats.
The three new functions allelicrichness, rarefactionplot, and rhost analyse allelic richness with various methods.
There is a new default method sw() which can use genomic positions. sw() now returns an object of class "sw" for which there is a plot() method.
There are two new methods as.phylo() and as.evonet() for the class "haploNet".
site.spectrum() is now generic with methods for "DNAbin" (old code) and for "loci" (new code). The returned object now has an attribute "sample.size" (useful for folded spectra).
There is a new summary() method for the class "haplotype" to extract haplotype absolute frequencies.
There is a new by() method for the class "loci" that by default computes allele frequencies by population.
H() is now generic with a default method (with the old code) and a "loci" method.
Fst() has the new option 'na.alleles' ("" by default) to specify alleles coding for missing data.
LDscan() is now generic with methods for classes "DNAbin" (new code) and "loci" (old code). The latter has a new option, depth, to specify at what depth(s) (or lags) to compute r^2 values.

BUG FIXES

loci2genind() dropped row and column labels when converting an object with a single locus.
The 'dimnames' were not set correctly in sw().
all.equal.haploNet() failed depending on the order of the arguments.
hw.test() failed if some loci were ignored.
plotNetMDS(, k = 2) did not display the x-axis.
A bug was fixed in theta.tree() which multiplied the estimates of THETA by two.
LDmap() failed if there were NA's in the output from LDscan().
plot.haploNet(, show.mutation = 2) failed if the network had reticulations.
alleles2loci(, ploidy = 1) failed.
H.loci() did not use the correct values of 'n' (number of alleles; number of individuals was used before).

OTHER CHANGES

summary.loci() is around 4 times faster.
dist.snp() will be removed in the next release: its code has been incorporated in dist.asd(), and it now gives a warning.
The default of x[, 1] is now drop = FALSE for "loci" objects.
print.haplotype() now prints only the first 40 haplotype labels and frequencies (see the new summary.haplotype() above).
The BioConductor package snpStats is now suggested.

pegas 0.11 (2018-07-09)

NEW FEATURES

The new generic function sw computes sliding window averages. There is a method for "DNAbin" matrices with various options.
The new function dist.asd computes the allelic sharing distance (ASD) for all diploid genotypes (phased or unphased, with two alleles or more).
The new function dist.snp computes the ASD for strict SNPs (only for unphased, diploid genotypes).
The new function unphase unphases the genotypes and eventually pools those identical once unphased (e.g., A|T and T|A become A/T).
The new generic function hap.div computes haplotype diversity. There are methods for the "haplotype" and "DNAbin" classes.
The new function getPhi returns Phi-statistics from a vector of variance components.
The new function write.pegas.amova contributed by Brian Knaus writes outputs from amova() into files.
loci2gening() gains an option unphase (TRUE by default).
print.amova() now displays the Phi-statistics thanks to a contribution by Zhian Kamvar.
VCFloci() and read.vcf() can now read compressed files (.vcf.gz) remotely.
There is a new haplotype.numeric() method (for 0/1 sequences but not only).

BUG FIXES

read.vcf(file = "~/chr.vcf") made R crash (apparently only under some OSs). Thanks to Frédéric Michaud for the fix.
plot.haploNet() failed with the default show.mutation = 1 if the distances were all less than one. A warning is now issued and show.mutation is changed to 3.
Fst() did not use correct sample size with respect to missing data: the correction is now done locus by locus.
Fst() failed when the data contained only a single locus.
amova() failed to compute P-values for the higher levels if the levels were not arranged as blocks: the data are now rearranged internally.
A bug was fixed in unphase().

OTHER CHANGES

summary.loci() is faster and scales better: 10 times faster with 1000 loci, 100 times faster with 10,000 loci.
The help page of theta.tree() has been clarified and its example extended.
mjn() gives a more explicit error message if failing because of duplicated sequences.
getPloidy() now returns a matrix of integers.

pegas 0.10 (2017-05-03)

NEW FEATURES

The new function mjn computes the median-joining network (Bandelt et al., 1999, Mol Biol Evol, 16:37).
The new function msn computes the minimum spanning network (Bandelt et al., 1999, Mol Biol Evol, 16:37).
The new function rmst computes the randomized minimum spanning tree (Paradis, in prep.)
The new function plotNetMDS plots a network (class "haploNet") using the coordinates of the haplotypes from an MDS done on the distance matrix.
The new function dist.hamming implements a general purpose Hamming distance. It can be used for many types of data, particularly the output of haplotype.character().
There is a new haplotype.character() method.
There is a new all.equal.haploNet() method to compare two haplotype networks.
haplotype.loci() has a new option (check.phase) to optionally skip the check of genotype phasing. The code is also now 2-5 times faster.
haploNet() has a new option, getProb = TRUE, to control whether to calculate Templeton's probabilities (in case of difficulties with very divergent sequences).
The option 'show.mutation' of plot.haploNet() now takes an integer between 0 and 3. The default (1) is to show the mutations with small segments on the links.
loci2genind() has the new option 'ploidy' which is by default taken from the data with getPloidy().
MMD() has a new option, bw, to specify the bandwidth of the empirical density curve.

BUG FIXES

plot.haploNet() failed with two haplotypes.
loci2genind() handles correctly missing alleles with a new option na.alleles = c("0", "."). The default value of 'ploidy' is now 2 (see explanation in the help page).
haplotype.DNAbin() failed with too many missing data.
A bug was fixed in na.omit.loci().

OTHER CHANGES

The arguments xlab and ylab in plot.haplotype can now be modified from the plot() call.

pegas 0.9 (2016-04-16)

NEW FEATURES

The new functions LDscan and LDmap analyse linkage disequilibrium with multiple loci and phased genotypes.
The new function na.omit.loci drops observations with unclearly identified genotypes. By default, "0" and "." are considered as missing alleles.
nuc.div() is now generic with methods for the classes "DNAbin" and "haplotype".
theta.s() is now generic with a default method (the previous code; the argument 's' has been renamed 'x') and a method for the class "DNAbin".
haplotype.loci() has a new option (compress) to return all observed haplotypes without checking their frequencies (mostly for internal use).

BUX FIXES

read.vcf() and VCFlabels() failed when the VCF file has a large header (> 1e5 bytes). The chunk read is now 1 Mb.
read.vcf() made R crash when reading files with 1000s of loci for a single individual.
loci2genind() now treats '.' as a missing allele.
amova() with three levels did not work correctly: several bugs were fixed.
read.vcf() failed to read correctly the last genotype in a row if the previous one was different from all the others and if only the genotypes are in the file.
alleles2loci() now returns the 'population' column as a factor.

OTHER CHANGES

haplotype.loci() is 5 to 10 times faster.

pegas 0.8-2 (2015-09-25)

NEW FEATURES

There is now a print method for objects of class "haploNet".
as.igraph.haploNet() and as.network.haploNet() gains a new option, altlinks, to output the alternative links in the converted object (TRUE by default).

BUX FIXES

haplotype.DNAbin() ignored alignment gaps so that identical sequences were considered as different if they contained gaps.
haplotype.DNAbin() failed with very short sequences (1 or 2 nucleotides).
alleles2loci() did not handle correctly its 'population' option.
amova() could not be called within a function. This is fixed.

OTHER CHANGES

Updated NAMESPACE file for r-devel.
haplotype.loci() is now 2-8 times faster and gains a new option (quiet = FALSE) to display or not a message of the progress of the analysis.

pegas 0.8-1 (2015-06-24)

OTHER CHANGES

Minor correction in Fst.Rd.

pegas 0.8 (2015-05-20)

NEW FEATURES

Seven new functions (VCFloci, VCFheader, VCFlabels, rangePOS, is.snp.VCFinfo, selectQUAL, getINFO) are provided to read information from VCF files.
The new function alleles2loci transforms a matrix of alleles (typical for microsatellites) into an object of class "loci".
read.vcf() has been completely rewritten with new options.
hw.test() is now generic with methods for classes "loci" and "genind" (contributed by Thibaut Jombart).
is.snp() is now generic with methods for classes "loci" and "VCFinfo".
There is now a subset method for objects of class "haplotype" giving the possibility to select haplotypes with respect to their absolute frequency and/or frequency of missing data.
There is a new data set (jaguar) with microsatellites from four populations of jaguars.

BUG FIXES

Subsetting "loci" objects failed when some column names were the same (often when reading VCF files).
haploNet() failed when no alternative links were found.
amova() failed when the factors in the rhs of the formula were in a data frame. Thanks to Zhian Kamvar for the fix.

OTHER CHANGES

The vignette "ReadingFiles" has been revised and extended.

pegas 0.7 (2015-03-05)

NEW FEATURES

The new function geod calculates geodesic (aka great-circle) distances from coordinates in (decimal) degrees.
The new function geoTrans transforms strings such as 43°12'34" into a numerical value.
The new function replot edits the layout of a haplotype network interactively or with specified coordinates (typically from a previous call to replot).
The new function diffHaplo outputs details of the differences between two haplotypes.
haploNet() now outputs alternative links of a haplotype network.
plot.haploNet() has been improved (a bit faster) and has a new option 'threshold' to control how alternative links of the network are displayed.
The option 'show.mutation' of plot.haploNet() has been extended.

OTHER CHANGES

haplotype() now takes base ambiguities into account when comparing sequences. For consistency, haploNet() now uses pairwise deletion when comparing sequences of haplotypes.
The attribute "CHR" returned by read.vcf() is now character (was integer before).

pegas 0.6 (2014-08-21)

NEW FEATURES

The new function read.vcf reads VCF files.
The new function is.snp tests whether a locus is a SNP.
The new function is.phased tests whether a genotype is phased.
The new function proba.genotype computes expected genotype probabilities under Hardy-Weinberg equilibrium for all levels of ploidy and any number of alleles.
The new function haplotype.loci extracts haplotypes from phased genotypic data.
The new function dist.haplotype.loci computes distances among haplotypes extracted from loci data.
Two new functions, LD and LD2, test for linkage disequilibrium with phased and unphased genotypes, respectively.
haplotype() is now generic with methods for "DNAbin" and "loci" objects.
There is a sort() method for objects of class "haplotype".
expand.genotype() now works with all levels of ploidy and any number of alleles.

BUG FIXES

site.spectrum( , folded = FALSE) dit not work correctly.
Genotypes with alleles not separated by the default slash (e.g., a|A) were not read correctly.
Reordering of alleles has been improved: alleles are now always sorted alphabetically within an unphased genotype, e.g., a/A is changed to A/a even if A/a was not observed (this was not the case before).
hw.test() now checks more carefully for ploidy level and accepts data with mixed levels of ploidy.

OTHER CHANGES

amova() now checks that the term(s) in the rhs of the formula is (are) factor(s).
Plotting haplotype networks with pies can now be done with user-chosen colours for the slices (thanks to Marius Wenzel for pointing this out).
tajima.test() now returns a warning with less than 4 observations as this test cannot be done in this situation (an error occured before).

pegas 0.5-1 (2014-01-10)

NEW FEATURES

MMD() now plots the expected distribution of mismatches under the assumption of a stable population together with the empirical curve (contribution by David Winter). The new option 'lty' can specify the types of lines. The legend is now at the top of the plot.

BUG FIXES

theta.tree() returned estimates of Theta divided by 2 (scaled on Nu). The estimates are now correct (ie, scaled on 2Nu).

pegas 0.5 (2013-10-08)

NEW FEATURES

The new function theta.msat computes THETA from micro-satellite data using three different estimators.
The new function haploFreq extracts the haplotype frequencies, possibly using the labels of the original sequences; see ?haploFreq for details.
plot.haploNet() has the new option 'show.mutation' to display the mutations on the links of the network.

OTHER CHANGES

Improved DESCRIPTION and NAMESPACE files.
The packages igraph and network are no more required.

pegas 0.4-5 (2013-06-06)

OTHER CHANGES

Improved NAMESPACE file.

pegas 0.4-4 (2013-01-23)

NEW FEATURES

theta.tree() has a new option, analytical = TRUE, to compute THETA and its standard-error with analytical formulae. If FALSE, a numerical optimisation is done (as in previous versions).
The function mst (minimum spanning tree) has been moved from ape to pegas with a new code.

BUG FIXES

hw.test() should have one less ddl to its chi2 tests (thanks to Gabriel Terraz for the fix).
Extracting sequence(s) from an object of class "haplotype" could not be printed correctly: this is fixed with a new '[' method for this class.
The reference to Chakraborty and Weiss (1991) was corrected thanks to Kari Vepsäläinen.

pegas 0.4-3 (2012-07-31)

OTHER CHANGES

Changed some coding in summary.loci().

pegas 0.4-2 (2012-05-11)

BUG FIXES

amova() did not randomize correctly at the highest level, resulting in P-values that were always equal to 1.

pegas 0.4-1 (2012-01-19)

BUG FIXES

site.spectrum(, folded = FALSE) failed.
The variances returned by nuc.div() were inflated (thanks to Paulina Ossa for the report).

pegas 0.4 (2011-07-23)

NEW FEATURES

The new function rr.test by Alastair Potts performs Tajima's test of a molecular clock (Genetics, 1993, 135:599).
haploNet() has a new argument 'd = NULL' to specify an alternative distance matrix among haplotypes.
There are two new functions, as.network.haploNet() and as.igraph.haploNet() for converting networks of class "haploNet" towards other packages.

BUG FIXES

plot.haploNet() has now by default asp = 1.

pegas 0.3-4 (2011-04-01)

OTHER CHANGES

The help command ?loci now points to the man page of read.loci() where this class is described.

pegas 0.3-3 (2010-11-26)

BUG FIXES

read.loci() failed with haploid data. It also failed in some situations with the population column. The default behaviour is now more flexible and more reliable.
Variance components were not correctly computed by amova() in the single-level case.
print.amova() did not work correctly when amova() was called with 'nperm = 0'.

pegas 0.3-2 (2010-06-10)

BUG FIXES

A bug was fixed in Fst().

pegas 0.3-1 (2010-05-19)

OTHER CHANGES

The default of 'loci.sep' in read.loci() is now "".

pegas 0.3 (2009-12-03)

NEW FEATURES

The new function edit.loci allows to edit allelic data frame while keeping the attributes correct (which edit.data.frame doesn't).
There are new rbind() and cbind() methods for objects of class "loci".
There is a print 'method' for the class "haplotype".
‘[.loci' has now an option ’drop = TRUE'.
There is a vignette detailing how to read allelic data files of various formats into R: type vignette("ReadingFiles") in R.

BUG FIXES

amova() did not compute SSD correctly with a single level.
getAlleles() did not work correctly.
read.loci() did not work when 'col.pop' was used.
Checking for ordered alleles did not work (i.e, A/a and a/A were treated as different genotypes: they are now pooled).
The display of haplotype labels by plot.haploNet() was not effective.

OTHER CHANGES

read.loci() loses the 'skip' option which is replaced by '...'.

pegas 0.2 (2009-10-07)

NEW FEATURES

The new function site.spectrum computes the (un)folded site frequency spectrum of a set of DNA sequences.
The new function theta.tree estimates THETA from a phylogenetic tree under a simple coalescent model by maximum likelihood.
There is now a "[" method for the class "loci".
haplotype() has now an option 'labels' to give as rownames of the returned object.
amova() has a new option 'is.squared' to specify whether the distance matrix has been squared beforefand (FALSE by default).
write.loci() has a new argument '...' passed to write.table().
The functions heterozygosity, nuc.div, theta.h, theta.k and theta.s have been moved from ape to pegas.

BUG FIXES

amova() did not compute SSD correctly.
summary.loci() failed in the presence of NA's.