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TEDIEmanual_t.html
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<!DOCTYPE html>
<html>
<head>
<title></title>
</head>
<body>
</body>
</html>
<!-- this is for the title -->
<head>
<meta charset = 'utf-8'>
<title>TEDIE Manual </title>
</head>
<style>
body {background-color: white}
h2 {color: #3498D8;}
.tsection
{
border: thin #336699 solid;
background-color: white;
padding: 20px;
margin: 20px;
text-align: left;
font-size: 14pt;
}
</style>
<body>
<!-- this is for the content part of the TEDIE manual -->
<h1> TEDIE MANUAL </h1>
<nav>
<ul>
<li><a href = "#TEDIE_matlab">Use TEDIE in MATLAB</a></li>
<li><a href = "#load_data">Load Data for TEDIE</a></li>
<li><a href = "#disc_choice">Choose Discretization Method for TEDIE</a></li>
<li><a href="#result">TEDIE Result in Commend Window</a></li>
<li><a href="#code">TEDIE Source Code</a></li>
</ul>
</nav>
<!-- this is for the body part of the TEDIE manual -->
<h2 id = TEDIE_matlab>Use TEDIE in MATLAB</h2>
<div class = "tsection">
This document explains how two-step discretization evaluation (TEDIE) works with an example data file. <br>
TEDIE is developed under MATLAB2016b. It is also compatible with MATLAB2017a. <br>
<p>We run TEDIE using the <a href = main_example.m>main</a> script. </p>
<img src="ManualImage/MainScript.png" alt = "Main Script Screenshot" style = "width:80%"><br>
</div>
<h2 id = "load_data">Load Data for TEDIE</h2>
<div class = "tsection">
<p>
Background:
<br>
We include an example (also the default) data file, example.mat, dealing with data from an in silico network with 13 nodes.
The .mat file has info for 24 matrices: the original data, and 23 different discretizations of it
(bikmeans2-5, i2-5, kmeans2-5, max25, max50, max75, mean, q2-5, TDT, top25, top75).
Each matrix contains 8 time series on the 13 node network, each with 9 time points, resulting in a 104 by 9 matrix.
If you are using your own data, please make sure that for each of the 8 time series, each variable (node) is in its own row.
The columns correspond to the time points.
</p>
<p>
To run the main_example.m script on MATLAB: open the file in the editor, and click “Run”.
Alternatively, enter the following command in the Command Window: main_example
<br>
When a dialog window will pop up, you can choose your own data (*.mat) file.
Closing the window or hitting “Cancel” will load the default example data into MATLAB workspace.
<br>
<img src="ManualImage/UDload.png" alt = "load user data" style = "width:80%"><br>
or default data is loaded. <br>
<img src = "ManualImage/DDload.png" alt = "load default data" style = "width:80%">
<br>
Another dialog will ask for the number of time series and the number of nodes for each dataset.
The default values correspond with our default example data. Click OK to move on.
<br>
<img src = "ManualImage/input.png" alt = "input data specs" style = "width:25%">
</p>
</div>
<h2 id = "disc_choice">Choose Discretization Method for TEDIE</h2>
<div class = "tsection">
<p>Next, select the discretization of interest in the new dialog, and click “close”. <br>
<img src="ManualImage/DiscretizationChoose.png" alt = "Choose Discretization Window" style = "width: 100%"><br>
</p>
</div>
<h2 id = "result">TEDIE Result in Command Window</h2>
<div class = "tsection">
<p>
The Command Window will display the discretization of choice, and whether it passes qualification step; if passed, then the mean area between the curves will follow. <br>
<img src="ManualImage/s1s2.png" alt = "result that passes qualification and calculate MABC" style = "width: 100%"><br>
Otherwise, it will tell you to choose another discretization method.
<img src="ManualImage/s1.png" alt = "result that fails to pass qualification" style = "width: 100%"><br>
If you are interested in obtaining the qualification and mean area between the curves for all discretizations at once, run <a href = "main_eval_all.m">main_eval_all.m</a>.
The process is same as documented above, but without the discretization selection step.
</p>
</div>
<h2 id = "code">TEDIE Source Code</h2>
<div class = "tsection">
<ul>
<li><a href = "main_example.m"> the file that should run when using TEDIE </a></li>
<li><a href = "prebenchmark.m"> calculate area between two lines </a></li>
<li><a href = "benchmark.m"> the TEDIE main function, including both qualification and mean area between the curves </a></li>
<li><a href = "choosedialog.m"> discretizaztion choosing window </a></li>
<li><a href = "input_dim_dialog.m"> data dimensions dialogue window </a></li>
<li><a href = "GetDiscretizationMethods.m"> function file for discretization selection window </a></li>
<li><a href = "example.mat"> example data file </a></li>
<li>folder <a href = "ManualImage">ManualImage</a>: the images for this HTML file</li>
</ul>
</div>
</html>