rehh
Searching for Footprints of Selection using 'Extended Haplotype Homozygosity' Based Tests
Description
Population genetic data such as 'Single Nucleotide Polymorphisms' (SNPs) is often used to identify genomic regions that have been under recent natural or artificial selection and might provide clues about the molecular mechanisms of adaptation. One approach, the concept of an 'Extended Haplotype Homozygosity' (EHH), introduced by (Sabeti 2002) <doi:10.1038/nature01140>, has given rise to several statistics designed for whole genome scans. The package provides functions to compute three of these, namely: 'iHS' (Voight 2006) <doi:10.1371/journal.pbio.0040072> for detecting positive or 'Darwinian' selection within a single population as well as 'Rsb' (Tang 2007) <doi:10.1371/journal.pbio.0050171> and 'XP-EHH' (Sabeti 2007) <doi:10.1038/nature06250>, targeted at differential selection between two populations. Various plotting functions are included to facilitate visualization and interpretation of these statistics.
Downloads
718
Last 30 days
4602nd
2K
Last 90 days
13.7K
Last year
Trend: +17.3% (30d vs prior 30d)
25
Last 30 days
117
Last 90 days
413
Last year
Trend: -39% (30d vs prior 30d)
5
Last 7 days
15
Last 30 days
1
All-time
autoCRAN-only: this name is served only by autoCRAN, so the count is exact.
CRAN Check Status
Show all 13 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check History
OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 8, 2026
ERROR 12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Jun 7, 2026
re-building of vignette outputs
Error(s) in re-building vignettes:
...
--- re-building ‘examples.Rmd’ using rmarkdown
--- finished re-building ‘examples.Rmd’
--- re-building ‘rehh.Rmd’ using rmarkdown
Warning in file("", "w+b") :
cannot open file '/tmp/RtmpjxpTVL/Rf1c50a26669c
...[truncated]...
~~~~~~~~~~
Error: processing vignette 'rehh.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘rehh.Rmd’
SUMMARY: processing the following file failed:
‘rehh.Rmd’
Error: Vignette re-building failed.
Execution halted
OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE May 11, 2026
WARNING 12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE May 10, 2026
PDF version of manual
LaTeX errors when creating PDF version. This typically indicates Rd problems. LaTeX errors found:
OK 14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026
Code
Structure
Lines of code
17,042
Files
149
Compiled share
14.2%
Has compiled src
Yes
Language breakdown
API
Exported functions
25
Internal functions
21
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.40
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Return-value doc rate
72%
\dontrun example ratio
0%
Roxygen coverage
100%
Has pkgdown
No
NEWS present
Yes
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
2.10
System requirements
–
C++ standard
–
License
GPL (>= 2)
License flags
SPDX valid, OSI approved
History
Versions
19
First release
2012-03-05
Latest release
2026-01-30
Avg cadence
115 days
Cold removal rate
100%
Dep drift
2
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/cran-code-metrics.