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ecopath_matlab-pkg

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Matlab implementation of the Ecopath food web mass-balance algorithm

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- .gitignore
- aggregate.m
- aggregatehist.m
- .gitignore
- cellstr2.m
- .gitignore
- ConsoleProgressBar.m
- license.txt
- test_ProgressBar.m
- .gitignore
- cprintf.m
- cprintf.png
- license.txt
- - addpedigree.m
  - calcstanza.m
  - combinegroups.m
  - createensemble.m
  - displaybasic.m
  - ecopath.m
  - ecopathmodel.m
  - graph.m
  - networkindices.m
  - sort.m
  - sortbytrophic.m
  - subpedigreevalues.m
  - unitconvert.m
- - calcclusteredparams.m
  - calcstanza.m
  - displayecopath.m
  - ecopath2graph.m
  - ecopathinputcheck.m
  - ecopathinputinfo.m
  - ecopathlite.m
  - eweunitconvert.m
  - rpath2ewein.m
  - sortewein.m
- - README.md
  - setup.py
- .gitignore
- ecopathmodel2rpath.m
- editstanzacalcs.m
- eiixml2ecopathmodel.m
- ewef2ecopathmodel.m
- mdb2ecopathmodel.m
- networkindices.m
- rpath2ecopathmodel.m
- trophiclevel.m
- - gen37_diet.csv
  - gen37_model.csv
- - REco_diet.csv
  - REco_Flatfish1.csv
  - REco_Flatfish2.csv
  - REco_model.csv
  - REco_pedigree.csv
  - REco_Roundfish1.csv
  - REco_Roundfish2.csv
  - REco_stanza_groups.csv
  - REco_stanzas.csv
- - REco_diet.csv
  - REco_Flatfish1.csv
  - REco_Flatfish2.csv
  - REco_model.csv
  - REco_pedigree.csv
  - REco_Roundfish1.csv
  - REco_Roundfish2.csv
  - REco_stanza_groups.csv
  - REco_stanzas.csv
- - tb_diet.csv
  - tb_model.csv
  - tb_stanza_groups.csv
  - tb_stanzas.csv
- Generic_37.EwEmdb
- rpath_example.R
- Tampa_Bay.EwEmdb
- ecopathmodel_overview.html
- ecopathmodel_overview.png
- ecopathmodel_overview_01.png
- ecopathmodel_overview_02.png
- ecopathmodel_overview_03.png
- ecopathmodel_overview_04.png
- pedigree.png
- .gitignore
- legendflex.m
- .gitignore
- license.txt
- readtext.m
- .gitignore
- regexpfound.m
- .gitignore
- getpos.m
- setgetposexamples.m
- setpos.m
- - wraptext_documentation.html
- .gitignore
- license.txt
- wraptext.m
- wraptext_documentation.m
.gitignore
ecopathmodel_overview.m
fexinfo.txt
license.txt
matlabEcopathLogo.png
matlabEcopathLogo_white.png
paper.bib
paper.md
README.md

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[![status](http://joss.theoj.org/papers/10.21105/joss.00064/status.svg)](http://joss.theoj.org/papers/10.21105/joss.00064)
[![DOI](https://zenodo.org/badge/66112224.svg)](https://zenodo.org/badge/latestdoi/66112224)
[![View ecopath_matlab: A Matlab implementation of Ecopath on File Exchange](https://www.mathworks.com/matlabcentral/images/matlab-file-exchange.svg)](https://www.mathworks.com/matlabcentral/fileexchange/40082-ecopath_matlab-a-matlab-implementation-of-ecopath)

<img src="./matlabEcopathLogo.png" width="100">

**Author: Kelly Kearney**

This package provides a Matlab-based implementation of the Ecopath algorithm (part of the popular fisheries ecosystem modeling tool [Ecopath with Ecosim](http://www.ecopath.org)), as well as a few functions for further analysis and visualization of an Ecopath-style food web.

This software is intended for people already familiar with the Ecopath concept who wish to perform that particular calculation, as well as related analysis of food web properties, outside of the GUI environment provided by the original EwE software.  It assumes a basic working knowledge of Matlab.

If you use this code in your research, please cite as follows:

K. A. Kearney, “ecopath_matlab: A Matlab-based implementation of the Ecopath food web algorithm,” Journal of Open Source Software, vol. 2, no. 9, 2017.

## Getting Started

### Prerequisites

This software requires [Matlab R2015b](http://www.mathworks.com/products/matlab/) or later (everything except the graph method should be functional in R2014b or later).  It also requires the [Statistics and Machine Learning Toolbox](http://www.mathworks.com/products/statistics/).

No OS limitations beyond those required for Matlab itself.

At present, this package is not compatible with Octave (v4.0.3).
  
### Downloading

Git users can clone directly:

`git clone git@github.com:kakearney/ecopath_matlab-pkg`

Alternatively, you may download a zipped version of the source code via the _Clone or Download_ > _Download zip_ button above, or from the [ecopath_matlab](http://www.mathworks.com/matlabcentral/fileexchange/40082-ecopathlite-m--a-matlab-implementation-of-ecopath "FEX ecopath_matlab") entry on the MatlabCentral File Exchange.  The File Exchange entry is updated daily from this repository.

### Installation

The following folders need to be added to you Matlab Path (via `pathtool`, `addpath`, etc.):

```
ecopath_matlab-pkg/ConsoleProgressBar
ecopath_matlab-pkg/aggregate
ecopath_matlab-pkg/cellstr2 
ecopath_matlab-pkg/cprintf
ecopath_matlab-pkg/ecopath_matlab
ecopath_matlab-pkg/legendflex
ecopath_matlab-pkg/readtext
ecopath_matlab-pkg/regexpfound
ecopath_matlab-pkg/setgetpos_V1.2
ecopath_matlab-pkg/wraptext
```

## Package Contents

### The `ecopathmodel` class

This package centers around a custom Matlab class, `ecopathmodel`.  The properties of an `ecopathmodel` object hold the typical input parameters associated with a single ecosystem food web; the methods provide functions to calculate Ecopath mass balance.

Constructor Summary

*  `ecopathmodel`:	Create an ecopathmodel object

Property Summary

*  `dc`:	Table of diet composition data 
*  `df`:	Table of detritus fates 
*  `discard`:	Table of fisheries discards 
*  `discardFate`:	Table of discard fates 
*  `fleet`:	Names corresponding to each fishing gear/fleet in the model 
*  `groupdata`:	Table of group-related parameters 
*  `landing`:	Table of fisheries landings 
*  `name`:	Names corresponding to each group in the model 
*  `ngear`:	Number of fishing gears/fleets in model 
*  `ngroup`:	Number of groups (living and detrital) in model 
*  `nlive`:	Number of living groups (non-detrital) in model 
*  `pedigree`:	Table of pedigree values applied to parameters 
*  `stanza`:	Names corresponding to each multi-stanza set 
*  `stanzadata`:	Table of multi-stanza-set-related parameters

Method Summary

*  `addpedigree`:	Add entries to the pedigree table 
*  `calcstanza`:	Calculate B and Q/B values for multi-stanza Ecopath groups 
*  `checkstanza`:	Fill in (or validate) B, QB, and BA values for stanzas 
*  `combinegroups`:	Combine groups and/or fleets in an ecopathmodel object 
*  `createensemble`:	Build an ensemble of Ecopath model parameters 
*  `displaybasic`:	Prints ecopath results to screen 
*  `ecopath`:	Rewrite of Ecopath algorithms 
*  `getpedigreevals`:	Extract values corresponding to pedigree entries 
*  `graph`:	Convert ecopathmodel object to a diagraph object 
*  `networkindices`:	Calculate ecological network indices 
*  `sort`:	Sort groups and fleets in an ecopathmodel object 
*  `sortbytrophic`:	Sort ecopathmodel object groups by trophic level 
*  `stanzaindices`:	Extract indices of stanza groups, in order of age 
*  `subpedigreevalues`:	Replace values in ecopathmodel based on pedigree 
*  `unitconvert`:	Convert units of parameter values

### Additional functions

A few additional functions are provided alonside the `ecopathmodel` class, including functions for import and export of data, as well as a few helper functions that are called by the `ecopathmodel` class methods but can also be called independently by users:

* `ecopathmodel2rpath`: Print ecopathmodel data to comma-delimited files
* `editstanzacalcs`: Replicate multi-stanza calculations from Ecopath
* `eiixml2ecopathmodel`: Create ecopathmodel object from EwE6 .eiixml file
* `mdb2ecopathmodel`: Create ecopathmodel object from EwE6 data file
* `networkindices`: Calculate network indices for a food web
* `rpath2ecopathmodel`: Create ecopathmodel object from Rpath data files
* `trophiclevel`: Estimates trophic level of food web members

## Usage

Documentation for each function and method in this package is provided via standard Matlab function headers, accessed in Matlab via the `help` command.  The reference page for the `ecopathmodel` class (including links to descriptions of all properties and methods) can be accessed by typing the following in the Matlab Command Window:

```matlab
doc ecopathmodel
```

For an overview of the class, along with several examples of usage, please see the overview document: `ecopathmodel_overview.m`.  A published version of this file can be found in [html/ecopathmodel_overview.html](https://rawgit.com/kakearney/ecopath_matlab-pkg/master/html/ecopathmodel_overview.html).

If you use this code in a scientific publication, please cite using the Journal of Open Source Software documentation paper (see JOSS badge link above).

## Contributions

Community contributions to this package are welcome!

To report bugs, please submit an issue [here](https://github.com/kakearney/ecopath_matlab-pkg/issues), and include:

- your operating system
- your version of Matlab and all relevant toolboxes (type `ver` at the Matlab command line to get this info)
- code/data to reproduce the error or buggy behavior, and the full text of any error messages received

Please also feel free to submit enhancement requests, or to send pull requests for bug fixes or new features.

I do monitor the MatlabCentral FileExchange entry for any issues raised in the comments, but would prefer to track issues here on GitHub.

### A note on versions

I maintain tagged versions of this software for citation purposes only.  Actual improvements to the code are made continuously as issues arise, and are not labeled with version numbers.  My numbering system is, roughly:

- 0.x: ecopathlite.m in its infancy, tailored to my Ph.D. thesis work.
- 1.x: The mostly-stable ecopathlite.m code suite (available on GitHub as [ecopathlite-pkg](https://github.com/kakearney/ecopathlite-pkg)).  I plan to keep that code around for back-compatibility and previous citation purposes, but am no longer making any updates to it.
- 2.x: Rewrite of ecopathlite.m and its companion functions with an object-oriented approach; reorganized, fully-documented, and now intended for full use by others.

I began syncing the GitHub repository and the MatlabCentral File Exchange (FEX) entry in May 2015; the FEX labels that entry as "1.3". Version numbers on the FEX prior to that point were automatically assigned by MatlabCentral, and do not match up to the tagged versions in the GitHub repo.  Please only use the GitHub tagged release numbers, and not the FEX numbers, if you need to reference a particular release.  As noted above, the preferred method of citation for this code is to cite its companion documentation paper (see JOSS badge above).