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Rename the package into MultiScaleTreeGraph
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‎.github/workflows/CI.yml‎

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- run: |
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julia --project=docs -e '
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using Documenter: DocMeta, doctest
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using MTG
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DocMeta.setdocmeta!(MTG, :DocTestSetup, :(using MTG); recursive=true)
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doctest(MTG)'
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using MultiScaleTreeGraph
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DocMeta.setdocmeta!(MultiScaleTreeGraph, :DocTestSetup, :(using MultiScaleTreeGraph); recursive=true)
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doctest(MultiScaleTreeGraph)'
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- run: julia --project=docs docs/make.jl
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

‎CITATION.bib‎

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@misc{MTG.jl,
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@misc{MultiScaleTreeGraph.jl,
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author = {remi.vezy <VEZY@users.noreply.github.com> and contributors},
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title = {MTG.jl},
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url = {https://github.com/VEZY/MTG.jl},
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title = {MultiScaleTreeGraph.jl},
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url = {https://github.com/VEZY/MultiScaleTreeGraph.jl},
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version = {v0.1.0},
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year = {2021},
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month = {5}

‎Project.toml‎

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name = "MTG"
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name = "MultiScaleTreeGraph"
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uuid = "dd4a991b-8a45-4075-bede-262ee62d5583"
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authors = ["remi.vezy <[email protected]> and contributors"]
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version = "0.1.0"

‎README.md‎

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# MTG
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# MultiScaleTreeGraph
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[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://VEZY.github.io/MTG.jl/stable)
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[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://VEZY.github.io/MTG.jl/dev)
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[![Build Status](https://github.com/VEZY/MTG.jl/workflows/CI/badge.svg)](https://github.com/VEZY/MTG.jl/actions)
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[![Coverage](https://codecov.io/gh/VEZY/MTG.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/VEZY/MTG.jl)
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[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://VEZY.github.io/MultiScaleTreeGraph.jl/stable)
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[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://VEZY.github.io/MultiScaleTreeGraph.jl/dev)
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[![Build Status](https://github.com/VEZY/MultiScaleTreeGraph.jl/workflows/CI/badge.svg)](https://github.com/VEZY/MultiScaleTreeGraph.jl/actions)
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[![Coverage](https://codecov.io/gh/VEZY/MultiScaleTreeGraph.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/VEZY/MultiScaleTreeGraph.jl)
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[![Code Style: Blue](https://img.shields.io/badge/code%20style-blue-4495d1.svg)](https://github.com/invenia/BlueStyle)
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[![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor's%20Guide-blueviolet)](https://github.com/SciML/ColPrac)
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The goal of MTG.jl is to read, write, analyse and plot MTG (Multi-scale Tree Graph) files. These files describe the plant topology (*i.e.* structure) along with some attributes for each node (*e.g.* geometry, colors, state...).
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The goal of MultiScaleTreeGraph.jl is to read, write, analyse and plot MTG (Multi-scale Tree Graph) files. These files describe the plant topology (*i.e.* structure) along with some attributes for each node (*e.g.* geometry, colors, state...).
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> The package is under intensive development and is in a very early version. The functions may heavily change from one version to another until a more stable version is released.
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## 1. Installation
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You can install the development version of MTG.jl from [GitHub](https://github.com/) using Pkg:
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You can install the development version of MultiScaleTreeGraph.jl from [GitHub](https://github.com/) using Pkg:
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```julia
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using Pkg
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Pkg.add(url="https://github.com/VEZY/MTG.jl", rev="master")
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Pkg.add(url="https://github.com/VEZY/MultiScaleTreeGraph.jl", rev="master")
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```
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## 2. Example
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Read a simple MTG file:
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```julia
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using MTG
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using MultiScaleTreeGraph
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file = download("https://raw.githubusercontent.com/VEZY/XploRer/master/inst/extdata/simple_plant.mtg");
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plot(mtg)
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```
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You can learn more about MTG.jl in the [documentation of the package](https://vezy.github.io/MTG.jl/dev/).
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You can learn more about MultiScaleTreeGraph.jl in the [documentation of the package](https://vezy.github.io/MultiScaleTreeGraph.jl/dev/).
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## 3. Roadmap
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‎docs/Manifest.toml‎

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[[Logging]]
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uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
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[[MTG]]
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[[MultiScaleTreeGraph]]
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deps = ["AbstractTrees", "DataFrames", "DelimitedFiles", "Graphs", "MetaGraphsNext", "MutableNamedTuples", "OrderedCollections", "Printf", "RecipesBase", "SHA", "XLSX"]
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path = ".."
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uuid = "dd4a991b-8a45-4075-bede-262ee62d5583"

‎docs/Project.toml‎

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[deps]
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Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
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MTG = "dd4a991b-8a45-4075-bede-262ee62d5583"
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MultiScaleTreeGraph = "dd4a991b-8a45-4075-bede-262ee62d5583"
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PlotlyJS = "f0f68f2c-4968-5e81-91da-67840de0976a"
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Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"

‎docs/make.jl‎

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using MTG
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using MultiScaleTreeGraph
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using Documenter
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using Plots
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DocMeta.setdocmeta!(MTG, :DocTestSetup, :(using MTG); recursive = true)
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DocMeta.setdocmeta!(MultiScaleTreeGraph, :DocTestSetup, :(using MultiScaleTreeGraph); recursive = true)
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makedocs(;
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modules = [MTG],
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modules = [MultiScaleTreeGraph],
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authors = "remi.vezy <[email protected]> and contributors",
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repo = "https://github.com/VEZY/MTG.jl/blob/{commit}{path}#{line}",
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sitename = "MTG.jl",
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repo = "https://github.com/VEZY/MultiScaleTreeGraph.jl/blob/{commit}{path}#{line}",
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sitename = "MultiScaleTreeGraph.jl",
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format = Documenter.HTML(;
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prettyurls = get(ENV, "CI", "false") == "true",
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canonical = "https://VEZY.github.io/MTG.jl",
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canonical = "https://VEZY.github.io/MultiScaleTreeGraph.jl",
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assets = String[],
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),
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pages = [
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)
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deploydocs(;
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repo = "github.com/VEZY/MTG.jl",
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repo = "github.com/VEZY/MultiScaleTreeGraph.jl",
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)

‎docs/src/api.md‎

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# MTG.jl functions
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# MultiScaleTreeGraph.jl functions
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Here is a list of all exported functions from MTG.jl. For more details, click on the link and you'll be directed to the function help.
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Here is a list of all exported functions from MultiScaleTreeGraph.jl. For more details, click on the link and you'll be directed to the function help.
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```@index
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```
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```@autodocs
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Modules = [MTG]
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Modules = [MultiScaleTreeGraph]
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```

‎docs/src/get_started.md‎

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## 1. Installation
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You can install the development version of MTG.jl from [GitHub](https://github.com/) using Pkg:
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You can install the development version of MultiScaleTreeGraph.jl from [GitHub](https://github.com/) using Pkg:
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```julia
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using Pkg
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Pkg.add(url="https://github.com/VEZY/MTG.jl", rev="master")
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Pkg.add(url="https://github.com/VEZY/MultiScaleTreeGraph.jl", rev="master")
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```
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## 2. Example
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```@setup usepkg
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using MTG
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file = joinpath(dirname(dirname(pathof(MTG))),"test","files","simple_plant.mtg")
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using MultiScaleTreeGraph
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file = joinpath(dirname(dirname(pathof(MultiScaleTreeGraph))),"test","files","simple_plant.mtg")
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mtg = read_mtg(file)
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transform!(mtg, :Length => (x -> isnothing(x) ? nothing : x * 100.) => :length_mm)
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```
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Read a simple MTG file:
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```@example usepkg
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using MTG
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using MultiScaleTreeGraph
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file = joinpath(dirname(dirname(pathof(MTG))),"test","files","simple_plant.mtg")
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file = joinpath(dirname(dirname(pathof(MultiScaleTreeGraph))),"test","files","simple_plant.mtg")
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mtg = read_mtg(file)
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```
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‎docs/src/index.md‎

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```@meta
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CurrentModule = MTG
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CurrentModule = MultiScaleTreeGraph
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```
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# MTG.jl
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# MultiScaleTreeGraph.jl
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[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://VEZY.github.io/MTG.jl/stable)
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[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://VEZY.github.io/MTG.jl/dev)
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[![Build Status](https://github.com/VEZY/MTG.jl/workflows/CI/badge.svg)](https://github.com/VEZY/MTG.jl/actions)
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[![Coverage](https://codecov.io/gh/VEZY/MTG.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/VEZY/MTG.jl)
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[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://VEZY.github.io/MultiScaleTreeGraph.jl/stable)
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[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://VEZY.github.io/MultiScaleTreeGraph.jl/dev)
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[![Build Status](https://github.com/VEZY/MultiScaleTreeGraph.jl/workflows/CI/badge.svg)](https://github.com/VEZY/MultiScaleTreeGraph.jl/actions)
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[![Coverage](https://codecov.io/gh/VEZY/MultiScaleTreeGraph.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/VEZY/MultiScaleTreeGraph.jl)
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[![Code Style: Blue](https://img.shields.io/badge/code%20style-blue-4495d1.svg)](https://github.com/invenia/BlueStyle)
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[![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor's%20Guide-blueviolet)](https://github.com/SciML/ColPrac)
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Documentation for [MTG.jl](https://github.com/VEZY/MTG.jl).
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Documentation for [MultiScaleTreeGraph.jl](https://github.com/VEZY/MultiScaleTreeGraph.jl).
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## Overview
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The goal of MTG.jl is to read, write, analyse and plot MTG (Multi-scale Tree Graph) files.
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The goal of MultiScaleTreeGraph.jl is to read, write, analyse and plot MTG (Multi-scale Tree Graph) files.
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The Multi-Scale Tree Graph, or MTG, is a data structure used to encode a plant to describe its topology (*i.e.* structure) and any attributes (*e.g.* geometry, colours, state...). It was developed in the [AMAP lab](https://amap.cirad.fr/) in the 90's to cope with the need of a generic yet scalable structure for plant topology and traits measurement, analysis and modelling.
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The format is described in details in the original paper from Godin et al. (1997).
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The MTG format helps describe the plant at different scales at the same time. For example we can describe a plant at the scale of the organ (e.g. leaf, internode), the scale of a growth unit, the scale of the axis, the crown or even at the whole plant.
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You can find out hw to use the package on the [Getting started](@ref) section.
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You can find out how to use the package on the [Getting started](@ref) section.
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## References
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Godin, C., et Y. Caraglio. 1998. « A Multiscale Model of Plant Topological Structures ». Journal of Theoretical Biology 191 (1): 1‑46. https://doi.org/10.1006/jtbi.1997.0561.

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