dartRverse	dartR.base	dartR.data	dartR
cran
main
beta
dev

	dartR.captive	dartR.popgen	dartR.sexlinked	dartR.sim	dartR.spatial
cran
main
beta
dev

Publication:

Zenodo:

dartRverse aims to support the installation of packages of the dartRverse. Currently there are two core packages that need to be installed to use dartR:

• dartR.base
• dartR.data

Additional packages are

• dartR.sim (functions to simulate SNP data)
• dartR.spatial (spatial analysis)
• dartR.popgen (popgen analysis)
• dartR.captive (relatedness and captive breeding)
• dartR.sexlinked (identification of sex linked SNPs)

dartR is a collaboration between the University of Canberra, CSIRO and Diversity Arrays Technology, and is supported with funding from the ACT Priority Investment Program, CSIRO and the University of Canberra.

dartRverse is on CRAN, so to install it, simply type:

install.packages("dartRverse")

This installs dartRverse, which is used to handle and install the additional packages

library(dartRverse)
#> **********************************************
#> **** Welcome to dartRverse [Version 0.93] ****
#> **********************************************
#> ── Core dartRverse packages ────────────────────────────────────── dartRverse ──
#> ✔ dartR.base 0.95      ✔ dartR.data 1.0.8
#> ── Installed dartRverse packages   ─────────────────────────────── dartRverse ──
#> ✔ dartR.captive   0.89     ✔ dartR.sim       0.88
#> ✔ dartR.popgen    0.88     ✔ dartR.spatial   0.88
#> ✔ dartR.sexlinked 0.96

will tell you, which packages are installed and also which other dartRverse packages are missing. As a minimum you need to install dartR.base [which in turn will install dartR.data] to use dartR. All packages are on CRAN, so you can simply type:

install.packages("dartR.base")

to install the core packages of the dartRverse. The core packages are handling the basic import and export functions, reporting, filtering and some basic analysis (e.g PCoA).

In case you want to install the complete suit of packages (bring some time with you), we recommend to use the code printed with the command:

dartRverse_install("all")
#> 
#> To install all packages from the dartRverse, please empty your workspace, restart R and run the following commands (you can copy the commands from here):
#> 
#> #########################################
#> # bioconductor package:
#> install.packages('BiocManager')
#> BiocManager::install('SNPRelate')
#> # core packages:
#> library(dartRverse)
#> dartRverse_install('dartR.base', rep='CRAN')
#> #installs also dartR.data
#> # additional packages:
#> dartRverse_install('dartR.popgen', rep='CRAN')
#> dartRverse_install('dartR.captive', rep='CRAN')
#> dartRverse_install('dartR.sim', rep='CRAN')
#> dartRverse_install('dartR.spatial', rep='CRAN')
#> dartRverse_install('dartR.sexlinked', rep='CRAN')
#> #########################################
#> 
#> In case you want to install the latest version from Github, please use the following commands:
#> [You can change the branch to 'beta' or 'dev' to get the latest changes and fixes.]
#> 
#> dartRverse_install('dartR.popgen', rep='Github', branch='main')
#> dartRverse_install('dartR.captive', rep='Github', branch='main')
#> dartRverse_install('dartR.sim', rep='Github', branch='main')
#> dartRverse_install('dartR.spatial', rep='Github', branch='main')
#> dartRverse_install('dartR.sexlinked', rep='Github', branch='main')

To make sure there are no packages already in your current R session, we recommend to clear you workspace, restart R and copy the code printed above into your restarted R console.

In case you want to intall a specific package say dartR.popgen you can either use the CRAN version typing:

install.packages("dartR.popgen")

or use the dartRverse_install function, specifying the package and the repository. In case you want to use github versions, you can also specify the branch:

#installs the dev branch from github
dartRverse_install("dartR.popgen", repository = "github", branch = "dev")

On github there are three branches you might want to choose: main, beta and dev

• main: is the same version as on CRAN [so same as using install.packages()]
• beta: is the next version to be released on CRAN. It is tested and should be stable
• dev: is the development version. It is not tested and might not work properly. So use it on your on risk, or if we announce a bug fix or new feature that you want to test.

To check which packages are already installed (and which version), simply type:

#takes a while to load all the version numbers....
dartRverse_install()
#> 
#> dartRverse packages:
#> ✔ dartR.base      0.95 | CRAN: 0.65 | Github: 0.88 (main) | 0.88 (beta) | 0.95 (dev)     
#> ✔ dartR.data      1.0.8 | CRAN: 1.0.8 | Github: 1.0.4 (main) | 1.0.8 (beta) | 1.0.8 (dev)
#> ✔ dartR.sim       0.88 | CRAN: 0.70 | Github: 0.70 (main) | 0.89 (beta) | 0.89 (dev)     
#> ✔ dartR.popgen    0.88 | CRAN: 0.32 | Github: 0.32 (main) | 0.88 (beta) | 0.88 (dev)     
#> ✔ dartR.spatial   0.88 | CRAN: 0.78 | Github: 0.78 (main) | 0.89 (beta) | 0.89 (dev)     
#> ✔ dartR.captive   0.89 | CRAN: 0.75 | Github: 0.75 (main) | 0.90 (beta) | 0.90 (dev)     
#> ✔ dartR.sexlinked 0.96 | CRAN: NA | Github: 0.24 (main) | 0.89 (beta) | 0.96 (dev)

The figures in bold are you currently installed versions and the other version numbers are the current versions on CRAN and Github (for the three branches).

dartR provides several functions for handling all the steps involved in genetic data analysis, from reading multiple data input formats to manipulating, filtering, exploring and analysing the data.

We use the prefix ‘gl’ in function names to acknowledge the use of the genlight object from package adegenet as our input format.

In most cases, the following term in the function name indicates a subset of functions.

Similarly, in most cases the first function parameter (input) is the genlight object.

For instance, you might use the code below to generate a report and then filter your data based on the percentage of missing data:

library(dartR.base)
test <- platypus.gl
rep <- gl.report.callrate(test)
test_1 <- gl.filter.callrate(test)

1. Are you a R rookie? If you want to learn R and RStudio without any fuss, have a look at our R-refresher tutorial.

2. Let’s get started by reading your genetic data into dartR; if you have DArT data, follow this tutorial; if not, follow this one.

3. Checking out our data manipulation tutorial is the easiest way to get your feet wet with dartR.

4. This tutorial will provide some pointers on how to filter your data effectively, an important step that depends on making sound threshold assessments.

5. Check out our simulations tutorial to learn more about our simulation model, a powerful tool for illuminating intricate evolutionary and genetic processes.

6. In more advanced topics, check our technical notes on Genetic Distances and their Visualization in Population Genetics and Fixed Difference Analysis.

1. Google groups Q&A forum in support of users can be accessed here.

2. The RStudio community provides a welcoming environment in which to ask any inquiry.

3. Answers to frequently asked topics may usually be found on Stack Overflow.

If you want to help shape the future of dartR, this tutorial is for you.

Please acknowledge dartR if you use it in your study. Copy and paste the following code to the R console to retrieve the citation information:

citation("dartRverse")
#> To cite dartR in publications use:
#> 
#>   Gruber, B, Unmack, PJ, Berry, OF, Georges, A. (2018). dartr: An r
#>   package to facilitate analysis of SNP data generated from reduced
#>   representation genome sequencing. Molecular Ecology Resources 18:
#>   691-699. https://doi.org/10.1111/1755-0998.12745
#> 
#>   Mijangos, J. L., Gruber, B., Berry, O., Pacioni, C., & Georges, A.
#>   (2022). dartR v2: An accessible genetic analysis platform for
#>   conservation, ecology and agriculture. Methods in Ecology and
#>   Evolution, (early access). https://doi.org/10.1111/2041-210X.13918
#> 
#> To see these entries in BibTeX format, use 'print(<citation>,
#> bibtex=TRUE)', 'toBibtex(.)', or set
#> 'options(citation.bibtex.max=999)'.

Check out our articles and our awards.

Have fun working with dartR!

Cheers,

Bernd, Arthur, Luis, Carlo, Diana, Florian & Olly