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comparison tools/regVariation/rcve.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="rcve1" name="Compute RCVE" version="1.0.0">
2 <description> </description>
3 <command interpreter="python">
4 rcve.py
5 $input1
6 $response_col
7 $predictor_cols
8 $out_file1
9 1>/dev/null
10 </command>
11 <inputs>
12 <param format="tabular" name="input1" type="data" label="Select data" help="Dataset missing? See TIP below."/>
13 <param name="response_col" label="Response column (Y)" type="data_column" data_ref="input1" />
14 <param name="predictor_cols" label="Predictor columns (X)" type="data_column" data_ref="input1" multiple="true">
15 <validator type="no_options" message="Please select at least one column."/>
16 </param>
17 </inputs>
18 <outputs>
19 <data format="input" name="out_file1" metadata_source="input1" />
20 </outputs>
21 <requirements>
22 <requirement type="python-module">rpy</requirement>
23 </requirements>
24 <tests>
25 <!-- Test data with vlid values -->
26 <test>
27 <param name="input1" value="reg_inp.tab"/>
28 <param name="response_col" value="1"/>
29 <param name="predictor_cols" value="2,3,4"/>
30 <output name="out_file1" file="rcve_out.dat"/>
31 </test>
32
33 </tests>
34 <help>
35
36 .. class:: infomark
37
38 **TIP:** If your data is not TAB delimited, use *Edit Datasets-&gt;Convert characters*
39
40 -----
41
42 .. class:: infomark
43
44 **What it does**
45
46 This tool computes the RCVE (Relative Contribution to Variance) for all possible variable subsets using the following formula:
47
48 **RCVE(i) = [R-sq (full: 1,2,..,i..,p-1) - R-sq(without i: 1,2,...,p-1)] / R-sq (full: 1,2,..,i..,p-1)**,
49 which denotes the case where the 'i'th predictor is dropped.
50
51
52 In general,
53 **RCVE(X+) = [R-sq (full: {X,X+}) - R-sq(reduced: {X})] / R-sq (full: {X,X+})**,
54 where,
55
56 - {X,X+} denotes the set of all predictors,
57 - X+ is the set of predictors for which we compute RCVE (and therefore drop from the full model to obtain a reduced one),
58 - {X} is the set of the predictors that are left in the reduced model after excluding {X+}
59
60
61 The 4 columns in the output are described below:
62
63 - Column 1 (Model): denotes the variables present in the model ({X})
64 - Column 2 (R-sq): denotes the R-squared value corresponding to the model in Column 1
65 - Column 3 (RCVE_Terms): denotes the variable/s for which RCVE is computed ({X+}). These are the variables that are absent in the reduced model in Column 1. A '-' in this column indicates that the model in Column 1 is the Full model.
66 - Column 4 (RCVE): denotes the RCVE value corresponding to the variable/s in Column 3. A '-' in this column indicates that the model in Column 1 is the Full model.
67
68
69 </help>
70 </tool>