https://github.com/tguillerme/inapp
Inapplicable GUI algorithm
https://github.com/tguillerme/inapp
Last synced: 3 months ago
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Inapplicable GUI algorithm
- Host: GitHub
- URL: https://github.com/tguillerme/inapp
- Owner: TGuillerme
- Created: 2017-03-13T14:46:59.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2024-01-17T14:04:23.000Z (over 1 year ago)
- Last Synced: 2025-01-13T08:47:07.451Z (5 months ago)
- Language: HTML
- Size: 19.8 MB
- Stars: 4
- Watchers: 5
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
- Support: support/Data/MartinTree.tre
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README
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**Inapp**: ancestral reconstruction and step counting for discrete characters with inapplicable data.
Check out the [presentation](https://figshare.com/articles/Guillerme_Evolution2017_pdf/5140222).
This package allows to run the algorithm described in [this paper](https://dx.doi.org/10.1093/sysbio/syy083/5238046).
You can either directly run the package on your web browser (Graphical User Interface mode!), or install it in `R` as a proper package (or both!).
The `C` implementation of the algorithm is available in [morphylib](https://github.com/mbrazeau/morphylib/) and the algorithm is implemented in the '[TreeSearch](https://github.com/ms609/TreeSearch/)' `R` package.
## Running Inapp online
Super easy! Simply click on the following link:
[https://tguillerme.shinyapps.io/inapp/](https://tguillerme.shinyapps.io/inapp/)
## Running Inapp locally on your web browser
Not hard! In `R`, simply copy/paste the following:
```r
if(!require(devtools)) install.packages("devtools")
if(!require(shiny)) install.packages("shiny")
runGitHub("Inapp", "TGuillerme")
```
## Running Inapp in your R console
Not much more complicated! In `R`, copy/paste the following:
```r
## Installing the App:
if(!require(devtools)) install.packages("devtools")
devtools::install_github("TGuillerme/Inapp")
## Running the App:
Inapp::runInapp()
```
Check out the package [vignette](https://tguillerme.github.io/inapp.html) for (many) more details on the GUI possibilities.
Authors
-------
[Thomas Guillerme](http://tguillerme.github.io), [Martin Brazeau](http://www.imperial.ac.uk/people/m.brazeau), [Martin Smith](https://community.dur.ac.uk/martin.smith/)
Citations
-------
If you are using this package, please cite both the published description of this algorithm:
* Brazeau MD, Guillerme T, Smith MR. (**2019**) An algorithm for morphological phylogenetic analysis with inapplicable data. *Systematic Biology* 68(4): 619--631. [doi:10.1093/sysbio/syy083](https://dx.doi.org/10.1093/sysbio/syy083/5238046)
###### [BibTeX](https://academic.oup.com/Citation/Download?resourceId=5238046&resourceType=3&citationFormat=2), [RIS](https://academic.oup.com/Citation/Download?resourceId=5238046&resourceType=3&citationFormat=0), [EndNote](https://academic.oup.com/Citation/Download?resourceId=5238046&resourceType=3&citationFormat=1), [more...](https://academic.oup.com/sysbio/article/68/4/619/5238046#)
And the DOI of this package:
* Guillerme T, Brazeau MD, Smith MR. (**2018**). Inapp: Reconstruction of Inapplicable Discrete Characters on Phylogenetic Trees. *Zenodo*. [doi:10.5281/zenodo.1484656](http://doi.org/10.5281/zenodo.1484656)
###### [BibTeX](https://zenodo.org/record/1484656/export/hx), [CSL](https://zenodo.org/record/1484656/export/csl), [DataCite](https://zenodo.org/record/1484656/export/dcite3), [Dublin core](https://zenodo.org/record/1484656/export/xd), [Mendeley](https://www.mendeley.com/import/?url=https://zenodo.org/record/1484656), [more...](https://zenodo.org/record/1484656/#.XTpLtlBS8W8)