`read.pcadapt()`

generates`bed`

files instead of`pcadapt`

files.Computation of PCA is now based on R package

`RSpectra`

.Missing values are handled by specifying matrix-vector operations in

`RSpectra`

that accounts for missing values.Includes LD thinning to compute PCs.

No more dependency to R package RcppArmadillo.

For Pooled-seq data, use Mahalanobis distances based on PCA loadings, no more simulations of individual genotypes.

Switch from C/Lapack to Rcpp/RcppArmadillo.

`pcadapt()`

can take genotype matrices as input.Modified code for binomial sampling.

`pcadapt()`

argument`clean.files`

is now deprecated.`pcadapt()`

argument`output.filename`

is now deprecated.`read.pcadapt()`

argument`local.env`

is now deprecated.Latest update of R package

`vcfR`

taken into account.

- Method based on sampling genotypes added to handle pooled-sequencing.

Option

`type = "vcfR"`

has been added to`read.pcadapt()`

to overcome some conversion issues occurring with VCF files.Argument

`transpose`

is now deprecated. Read section A for more details.

- The function
`get.pc()`

has been added. For each SNP, it returns the most correlated principal component.

Function

`read4pcadapt()`

is now deprecated, it is now called`read.pcadapt()`

.Using the

`pop`

option when plotting scores now provides the color legend.

All analyses are now included in the R package. Users should not use the C software PCAdapt fast anymore.

Big datasets can be handled directly within the R session.

`read4pcadapt()`

now converts files to the`pcadapt`

format.The first argument of

`pcadapt()`

can be either a small genotype matrix or the output of`read4pcadapt()`

.

The Mahalanobis distance is now estimated from the z-scores rather than the loadings.

Make sure you have downloaded the latest version of the C software PCAdapt (last updated on February 11, 2016).

The scaling of the SNP before computing PCA has been changed. Instead of using standard deviation, we now use the square root of \(p(1-p)\) (haploid data) or of \(2p(1-p)\) (diploid data) where \(p\) is the minimum allele frequency.

Bug fix: the genomic inflation factor has been corrected when

`K=1`

.Bug fix: a problem due to high proportion of missing data slowing the program has been fixed.

Argument

`"minmaf"`

has been replaced with`"min.maf"`

.

The default test statistic is not the communality statistic anymore but the Mahalanobis distance.

Test statistic for Pool-seq data.