+ 
+
+Content not found. Please use links in the navbar.
+
+ 
+
Main repository:
[](https://cran.r-project.org/package=dartR)
diff --git a/_pkgdown.yml b/_pkgdown.yml
new file mode 100644
index 00000000..10327515
--- /dev/null
+++ b/_pkgdown.yml
@@ -0,0 +1,5 @@
+url: https://green-striped-gecko.github.io/dartR/
+template:
+ bootstrap: 5
+ bootswatch: quartz
+
diff --git a/code_of_conduct.md b/code_of_conduct.md
new file mode 100644
index 00000000..d33878e1
--- /dev/null
+++ b/code_of_conduct.md
@@ -0,0 +1,134 @@
+
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+ and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+ community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+ any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+ without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+ professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+[INSERT CONTACT METHOD].
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
+[https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations
+
diff --git a/codemeta.json b/codemeta.json
new file mode 100644
index 00000000..0843d1a2
--- /dev/null
+++ b/codemeta.json
@@ -0,0 +1,1031 @@
+{
+ "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
+ "@type": "SoftwareSourceCode",
+ "identifier": "dartR",
+ "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, once SNP or related fragment presence/absence data from any source is imported into a genlight object many of the functions can be used. Functions are available for input and output of SNP and silicodart data, for reporting on and filtering on various criteria (e.g. CallRate, Heterozygosity, Reproducibility, maximum allele frequency). Advanced filtering is based on Linkage Disequilibrium and HWE (Hardy-Weinberg equilibrium). Other functions are available for visualization after PCoA (Principle Coordinate Analysis), or to facilitate transfer of data between genlight/genind objects and newhybrids, related, phylip, structure, faststructure packages.",
+ "name": "dartR: Importing and Analysing SNP and Silicodart Data Generated by\n Genome-Wide Restriction Fragment Analysis",
+ "codeRepository": "https://github.com/green-striped-gecko/dartR",
+ "license": "https://spdx.org/licenses/GPL-3.0",
+ "version": "2.3",
+ "programmingLanguage": {
+ "@type": "ComputerLanguage",
+ "name": "R",
+ "url": "https://r-project.org"
+ },
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+ "@type": "Organization",
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+ "url": "https://cran.r-project.org"
+ },
+ "author": [
+ {
+ "@type": "Person",
+ "givenName": "Bernd",
+ "familyName": "Gruber",
+ "email": "bernd.gruber@canberra.edu.au"
+ },
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+ "@type": "Person",
+ "givenName": "Arthur",
+ "familyName": "Georges",
+ "email": "georges@aerg.edu.au"
+ },
+ {
+ "@type": "Person",
+ "givenName": "Jose L.",
+ "familyName": "Mijangos",
+ "email": "Luis.MijangosAraujo@canberra.edu.au"
+ },
+ {
+ "@type": "Person",
+ "givenName": "Carlo",
+ "familyName": "Pacioni",
+ "email": "carlo.pacioni@delwp.vic.gov.au"
+ }
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+ "@type": "Person",
+ "givenName": "Peter J.",
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+ "familyName": "Berry",
+ "email": "oliver.berry@csiro.au"
+ },
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+ "givenName": "Lindsay V.",
+ "familyName": "Clark",
+ "email": "lvclark@illinois.edu"
+ },
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+ "givenName": "Floriaan",
+ "familyName": "Devloo-Delva",
+ "email": "Floriaan.Devloo-Delva@csiro.au"
+ },
+ {
+ "@type": "Person",
+ "givenName": "Eric",
+ "familyName": "Archer",
+ "email": "eric.archer@noaa.gov"
+ }
+ ],
+ "maintainer": [
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+ "datePublished": "2018",
+ "author": [
+ {
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+}
diff --git a/doc/dartRTutorials.R b/doc/dartRTutorials.R
deleted file mode 100644
index 8b137891..00000000
--- a/doc/dartRTutorials.R
+++ /dev/null
@@ -1 +0,0 @@
-
diff --git a/doc/dartRTutorials.Rmd b/doc/dartRTutorials.Rmd
deleted file mode 100644
index 96e97e48..00000000
--- a/doc/dartRTutorials.Rmd
+++ /dev/null
@@ -1,15 +0,0 @@
----
-title: "dartR Tutorials"
-author: "Bernd Gruber, Peter Unmack, Oliver Berry, Luis Mijangos & Arthur Georges"
-date: '`r Sys.Date()`'
-output:
- pdf_document
-vignette: >
- %\VignetteIndexEntry{dartR_Tutorials}
- %\VignetteEngine{knitr::rmarkdown}
- \usepackage[utf8]{inputenc}
----
-
-Tutorials for beginner and developer in dartR can be found on our github pages
-
-* [Tutorials for dartR please click here http://georges.biomatix.org/dartR](http://georges.biomatix.org/dartR)
\ No newline at end of file
diff --git a/doc/dartRTutorials.pdf b/doc/dartRTutorials.pdf
deleted file mode 100644
index 56535582..00000000
Binary files a/doc/dartRTutorials.pdf and /dev/null differ
diff --git a/docs/404.html b/docs/404.html
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index 00000000..bbac6e73
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+
+
+
+
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+
+
+Version 3, 29 June 2007
Copyright © 2007 Free Software Foundation, Inc. <http://fsf.org/>
Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.
+The GNU General Public License is a free, copyleft license for software and other kinds of works.
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+Nothing in this License shall be construed as excluding or limiting any implied license or other defenses to infringement that may otherwise be available to you under applicable patent law.
+If conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot convey a covered work so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not convey it at all. For example, if you agree to terms that obligate you to collect a royalty for further conveying from those to whom you convey the Program, the only way you could satisfy both those terms and this License would be to refrain entirely from conveying the Program.
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+END OF TERMS AND CONDITIONS
+If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms.
+To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the “copyright” line and a pointer to where the full notice is found.
+<one line to give the program's name and a brief idea of what it does.>
+Copyright (C) <year> <name of author>
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program. If not, see <http://www.gnu.org/licenses/>.Also add information on how to contact you by electronic and paper mail.
+If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode:
+<program> Copyright (C) <year> <name of author>
+This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'.
+This is free software, and you are welcome to redistribute it
+under certain conditions; type 'show c' for details.The hypothetical commands show w and show c should show the appropriate parts of the General Public License. Of course, your program’s commands might be different; for a GUI interface, you would use an “about box”.
You should also get your employer (if you work as a programmer) or school, if any, to sign a “copyright disclaimer” for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see <http://www.gnu.org/licenses/>.
+The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read <http://www.gnu.org/philosophy/why-not-lgpl.html>.
+dartRTutorials.RmdTutorials for beginner and developer in dartR can be found on our +github pages
+Bernd Gruber. Author, maintainer. +
+Arthur Georges. Author. +
+Jose L. Mijangos. Author. +
+Carlo Pacioni. Author. +
+Peter J. Unmack. Contributor. +
+Oliver Berry. Contributor. +
+Lindsay V. Clark. Contributor. +
+Floriaan Devloo-Delva. Contributor. +
+Eric Archer. Contributor. +
+Gruber, B, Unmack, PJ, Berry, OF, Georges, A. dartr: An r package to facilitate analysis of SNP data generated from reduced representation genome sequencing. Mol Ecol Resour. 2018; 18: 691-699. https://doi.org/10.1111/1755-0998.12745
+@Article{,
+ author = {Bernd Gruber and Peter J Unmack and Oliver F Berry and Arthur Georges},
+ doi = {10.1111/1755-0998.12745},
+ journal = {Molecular Ecology Resources},
+ keywords = {bioinformatics,next-generation-sequencing, phylogenomics,SNPs, population genomics, R pacakge, RADSeq},
+ pages = {691--699},
+ title = { dartr: An r package to facilitate analysis of SNP data generated from reduced representation genome sequencing},
+ volume = {18},
+ year = {2018},
+}
+