# pcadapt 3.0 to 4.4.1 (CRAN)

Two releases side by side, the earlier on the left.

Part of: [pcadapt](/cran/pcadapt.md)

[Compare these two releases](/cran/pcadapt/compare/3.0...4.4.1.md)

- Time between: 3,388 days (12 releases in between)
- Advisories: None known (for either release)
- Exports: 9 removed (12 added as well)
- Files changed: 330 (+27,453 −87,260 lines)

Record made 29 Oct 2026, 10:00 UTC from data release v2026-10-28, merged 23:10 UTC. Project DOI 10.5281/zenodo.21843040. Address: https://r-observatory.thecoatlessprofessor.com/cran/pcadapt/compare/3.0...4.4.1?view=record

This record reports what R Observatory measured for these two releases. It is not a validation, and it does not say whether either release is fit for your intended use.

Key: "yes" under Differs marks a row whose values differ between the two releases, and – marks a row that is not on that release's record.

## Release

| Measure | 3.0 | 4.4.1 | Differs |
| --- | --- | --- | --- |
| Published | 15 Apr 2016 | 25 Jul 2025 |  |
| Status | Replaced by 3.0.1 on 14 Jun 2016 | Current release |  |
| Previous | 2.2, 13 Feb 2016 | 4.4.0, 24 Sep 2024 |  |
| Releases | – | 20 since 5 Sep 2015 |  |
| License | GPL (>= 2), OSI approved | GPL (>= 2), OSI approved |  |
| Maintainer | Keurcien Luu | Florian Privé | yes |
| Download size | 993 KB | 1.6 MB | yes |
| Authors | Keurcien Luu, Michael G.B. Blum, Nicolas Duforet-Frebourg | Keurcien Luu, Michael Blum, Florian Privé, Eric Bazin, Nicolas Duforet-Frebourg | yes |
| Source code | Not kept for this release | [https://github.com/bcm-uga/pcadapt](https://github.com/bcm-uga/pcadapt) |  |

## Advisories

[Method](/about/advisories.md)

| Measure | 3.0 | 4.4.1 | Differs |
| --- | --- | --- | --- |
| This release | [None known](/about/advisories.md) | [None known](/about/advisories.md) |  |

## CRAN checks

[Method](/about/checks-health.md)

| Measure | 3.0 | 4.4.1 | Differs |
| --- | --- | --- | --- |
| Results | Kept only for the current release | 13 OK |  |
| Release checked | – | 4.4.1 on 13 platforms |  |

## Code

[Method](/about/code-metrics.md)

| Measure | 3.0 | 4.4.1 | Differs |
| --- | --- | --- | --- |
| Public exports | 11 | 14 | yes |
| Internal functions | 1 | 26 | yes |
| Lines of R code | 696 | 1,297 | yes |
| Lines of compiled code | 60,815, 97.7% of code | 1,252, 40.1% of code | yes |
| Complexity | mean 7.5, highest 30 | mean 3.5, highest 14 | yes |
| Exports changed since 2.2 | 8 added, 11 removed | – |  |

**Exports added (12)**

- `bed2matrix`
- `get.pc`
- `get.pop.names`
- `hist_plot`
- `manhattan_plot`
- `qq_plot`
- `read.pcadapt`
- `run.pcadapt`
- `score_plot`
- `scree_plot`
- `vcf2pcadapt`
- `writeBed`

**Exports removed (9)**

- `compute.pval`
- `corpca`
- `create.pcadapt`
- `manhattan.plotting`
- `neutral.plotting`
- `pvalqq.plotting`
- `read4pcadapt`
- `score.plotting`
- `scree.plotting`

**Most changed files (12 of 330)**

| File | Lines added | Lines deleted |
| --- | ---: | ---: |
| `src/src_Lapack/clapack.h` | 0 | 7,267 |
| `inst/extdata/missing.bim` | 4,000 | 2,000 |
| `inst/extdata/missing.pcadapt` | 4,000 | 2,000 |
| `inst/extdata/geno3pops.bim` | 3,000 | 1,500 |
| `inst/extdata/geno3pops.pcadapt` | 3,000 | 1,500 |
| `src/src_Lapack/dgesvd.c` | 0 | 4,052 |
| `inst/testdata/novar.bim` | 2,000 | 1,000 |
| `inst/doc/pcadapt.html` | 933 | 1,269 |
| `src/src_Lapack/dgesdd.c` | 0 | 1,596 |
| `inst/extdata/geno3pops.loadings` | 0 | 1,500 |
| `inst/extdata/geno3pops.maf` | 0 | 1,500 |
| `inst/extdata/geno3pops.zscores` | 0 | 1,500 |

## Tests

[Method](/about/coverage.md)

| Measure | 3.0 | 4.4.1 | Differs |
| --- | --- | --- | --- |
| Tests | No | No |  |
| Test lines per line of code | 0.00 | 0.00 |  |
| Coverage | Not measured for this release | No tests to run |  |
| Exports named in tests | 0% | 0% |  |
| Help pages with running examples | 1 of 10 | 1 of 4 | yes |

## Documentation

[Method](/about/code-metrics.md)

| Measure | 3.0 | 4.4.1 | Differs |
| --- | --- | --- | --- |
| Help pages | 13 | 19 | yes |
| Exports documented | 100% | 100% |  |
| Exports with examples | 72.7% | 21.4% | yes |
| Arguments documented | 95.5% | 98.7% | yes |
| Return value documented | 9.1% | 21.4% | yes |
| Vignettes | 1 | 0 | yes |
| NEWS | No | Yes, does not mention 4.4.1 | yes |
| Citation file | No | Yes, cites a publication | yes |
| Website | Not kept for this release | No, not declared in DESCRIPTION |  |

## Dependencies

[Method](/about/reverse-dependencies.md)

| Measure | 3.0 | 4.4.1 | Differs |
| --- | --- | --- | --- |
| Depends | robust, MASS | None | yes |
| Imports | ggplot2 | bigutilsr (>= 0.3), data.table, ggplot2 (>= 3.4), magrittr, mmapcharr (>= 0.3), Rcpp (>= 0.12.8), RSpectra | yes |
| LinkingTo | None | mmapcharr, Rcpp, rmio | yes |
| Suggests | knitr, qvalue, rmarkdown | plotly, shiny, spelling, testthat, vcfR | yes |
| Install tree | Kept only for the current release | 40 packages, 22 with compiled code, 42.9 MB of source tarballs |  |
| Advisories in the install tree | Kept only for the current release | [None known](/about/advisories.md) |  |

## Today

| Measure | 3.0 | 4.4.1 | Differs |
| --- | --- | --- | --- |
| CRAN downloads, past year | – | 12,300, rank #3,840 |  |
| Other channels, past year | – | r2u 510, conda-forge 3,234 |  |
| Reverse dependencies | – | 0 direct, 0 indirect |  |
| Suggested by | – | 2 |  |
| Repository | – | 47 stars, 3 open issues |  |
| Last commit | – | 8 Sep 2026 |  |
| Task views | – | [Anomaly Detection](/topics/cran/AnomalyDetection.md) |  |

Downloads, reverse dependencies and repository activity describe pcadapt today, not 3.0. They are on the [4.4.1 page](/cran/pcadapt/v/4.4.1.md).

## Sources

| Part | 3.0 | 4.4.1 |
| --- | --- | --- |
| Release history | CRAN package versions, 28 Oct 2026 | CRAN package versions, 28 Oct 2026 |
| Advisories | osv-advisories 1.0.0, R version 4.6.1 (2026-06-24), 28 Oct 2026 | osv-advisories 1.0.0, R version 4.6.1 (2026-06-24), 28 Oct 2026 |
| CRAN checks | CRAN check results, Kept only for the current release | CRAN check results, 28 Oct 2026 |
| Tests, documentation, code | rpkg-analyzer 0.5.2, 5 Oct 2026 | rpkg-analyzer 0.5.2, 5 Oct 2026 |
| Coverage | covr, Not measured for this release | covr 3.6.5 on R 4.6.1, run on 4.4.1 |
| Use | CRAN downloads, reverse dependencies, repository, Not shown for this release | – |
| Downloads | – | conda-forge, 30 Sep 2026 |
| Reverse dependencies | – | CRAN package metadata, 28 Oct 2026 |
| Repository | – | github.com/bcm-uga/pcadapt, 28 Oct 2026 |
| Task views | – | CRAN Task Views, 28 Oct 2026 |

Daily data releases are kept on GitHub, so the data behind this record can be fetched again from v2026-10-28 (merged 23:10 UTC). Values not kept for a release say so and are never filled in from another release.

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R Observatory is independent of the R Project, CRAN and Bioconductor. The same page for people is at /cran/pcadapt/compare/3.0...4.4.1?view=record, and every address is listed at /llms.txt.