dartR
Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis
Description
Functions are provided that facilitate the import and analysis of 'SNP' (single nucleotide polymorphism) and 'silicodart' (presence/absence) data. The main focus is on data generated by 'DarT' (Diversity Arrays Technology), however, data from other sequencing platforms can be used once 'SNP' or related fragment presence/absence data from any source is imported. Genetic datasets are stored in a derived 'genlight' format (package 'adegenet'), that allows for a very compact storage of data and metadata. Functions are available for importing and exporting of 'SNP' and 'silicodart' data, for reporting on and filtering on various criteria (e.g. 'CallRate', heterozygosity, reproducibility, maximum allele frequency). Additional functions are available for visualization (e.g. Principle Coordinate Analysis) and creating a spatial representation using maps. 'dartR' supports also the analysis of 3rd party software package such as 'newhybrid', 'structure', 'NeEstimator' and 'blast'. Since version 2.0.3 we also implemented simulation functions, that allow to forward simulate 'SNP' dynamics under different population and evolutionary dynamics. Comprehensive tutorials and support can be found at our 'github' repository: github.com/green-striped-gecko/dartR/. If you want to cite 'dartR', you find the information by typing citation('dartR') in the console.
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| 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 | NOTE |
| r-devel-linux-x86_64-fedora-gcc | NOTE |
| r-devel-macos-arm64 | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | NOTE |
| r-oldrel-macos-x86_64 | NOTE |
| r-oldrel-windows-x86_64 | NOTE |
| 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 details (5 non-OK)
dependencies in R code
Namespace in Imports field not imported from: ‘foreach’ All declared Imports should be used.
dependencies in R code
Namespace in Imports field not imported from: ‘foreach’ All declared Imports should be used.
installed package size
installed size is 6.4Mb
sub-directories of 1Mb or more:
R 2.0Mb
help 2.6Mb
installed package size
installed size is 6.3Mb
sub-directories of 1Mb or more:
R 2.0Mb
help 2.6Mb
installed package size
installed size is 6.0Mb
sub-directories of 1Mb or more:
R 1.7Mb
help 2.6Mb
Check History
NOTE 9 OK · 5 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026
dependencies in R code
Namespace in Imports field not imported from: ‘foreach’ All declared Imports should be used.
dependencies in R code
Namespace in Imports field not imported from: ‘foreach’ All declared Imports should be used.
installed package size
installed size is 6.4Mb
sub-directories of 1Mb or more:
R 2.0Mb
help 2.6Mb
installed package size
installed size is 6.3Mb
sub-directories of 1Mb or more:
R 2.0Mb
help 2.6Mb
installed package size
installed size is 6.0Mb
sub-directories of 1Mb or more:
R 1.7Mb
help 2.6Mb