| 02-21-2018 |
4.0 |
- read.pcadapt generates bed files instead of pcadapt files. |
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- Computation of PCA is based on the package RSpectra. |
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- Missing values are handled by specifying vector-matrix operation in RSpectra that accounts for missing values. |
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- Includes LD thinning to compute PCs. |
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- No more dependency to RcppArmadillo |
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- For Pooled-seq data, use Mahalanobis distances based on PCA loadings, no more simulations of individuals genotypes |
| 01-15-2017 |
3.1.0 |
- Switch from C/Lapack to Rcpp/RcppArmadillo. |
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- pcadapt can take genotype matrices as input. |
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- Modified code for binomial sampling. |
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- pcadapt argument clean.files is now deprecated. |
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- pcadapt argument output.filename is now deprecated. |
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- read.pcadapt argument local.env is now deprecated. |
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- Latest update of vcfR taken into account. |
| 12-20-2016 |
3.0.4 |
- Method based on sampling genotypes added to handle pooled-sequencing. |
| 10-06-2016 |
3.0.3 |
- Option type="vcfR" has been added to read.pcadapt to overcome some conversion issues occurring with VCF files. |
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- Argument transpose is now deprecated. Read section A for more details. |
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| 06-13-2016 |
3.0.2 |
- The function get.pc has been added. For each SNP, it returns the most correlated principal component. |
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| 06-01-2016 |
3.0.1 |
- The read4pcadapt is now deprecated, it is now called read.pcadapt. |
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- Using the pop option when plotting scores now provides the color legend. |
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| 04-04-2016 |
3.0 |
- All analyses are now included in the R package. Users should not use the C software PCAdapt fast anymore. |
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- Big datasets can be handled directly within the R session. |
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- read4pcadapt now converts files to the pcadapt format. |
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- The first argument of pcadapt can be either a small genotype matrix or the output of read4pcadapt. |
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| 02-12-2016 |
2.2 |
- The Mahalanobis distance is now estimated from the z-scores rather than the loadings. |
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- Make sure you have downloaded the latest version of the C software PCAdapt (last updated on February 11, 2016). |
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| 01-05-2016 |
2.1.1 |
- Bug fix: vignette header added. |
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| 12-18-2015 |
2.1 |
- 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. |
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- Bug fix: the genomic inflation factor has been corrected when K=1. |
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- Bug fix: a problem due to high proportion of missing data slowing the program has been fixed. |
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- Argument "minmaf" has been replaced with "min.maf". |
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2.0.1 |
- Vignette corrected: when reading output from the software PCAdapt, we do not mention the deprecated argument PCAdapt in the function pcadapt. |
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- Bug fix: an issue occurring when reading outputs from PCAdapt has been fixed. |
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- We mention in the vignette how to use Pool-seq data with the C software PCAdapt fast. |
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2.0 |
- The default test statistic is not the communality statistic anymore but the Mahalanobis distance. |
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- Test statistic for Pool-seq data. |