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comparison rcve.xml @ 0:7740956d197b draft default tip

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Imported from capsule None
author devteam
date Tue, 01 Apr 2014 10:52:35 -0400
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-1:000000000000 0:7740956d197b
1 <tool id="rcve1" name="Compute RCVE" version="1.0.0">
2 <description> </description>
3 <requirements>
4 <requirement type="package" version="2.11.0">R</requirement>
5 <requirement type="package" version="1.7.1">numpy</requirement>
6 <requirement type="package" version="1.0.3">rpy</requirement>
7 </requirements>
8 <command interpreter="python">
9 rcve.py
10 $input1
11 $response_col
12 $predictor_cols
13 $out_file1
14 1>/dev/null
15 </command>
16 <inputs>
17 <param format="tabular" name="input1" type="data" label="Select data" help="Dataset missing? See TIP below."/>
18 <param name="response_col" label="Response column (Y)" type="data_column" data_ref="input1" />
19 <param name="predictor_cols" label="Predictor columns (X)" type="data_column" data_ref="input1" multiple="true">
20 <validator type="no_options" message="Please select at least one column."/>
21 </param>
22 </inputs>
23 <outputs>
24 <data format="input" name="out_file1" metadata_source="input1" />
25 </outputs>
26 <requirements>
27 <requirement type="python-module">rpy</requirement>
28 </requirements>
29 <tests>
30 <!-- Test data with vlid values -->
31 <test>
32 <param name="input1" value="reg_inp.tab"/>
33 <param name="response_col" value="1"/>
34 <param name="predictor_cols" value="2,3,4"/>
35 <output name="out_file1" file="rcve_out.dat"/>
36 </test>
37
38 </tests>
39 <help>
40
41 .. class:: infomark
42
43 **TIP:** If your data is not TAB delimited, use *Edit Datasets-&gt;Convert characters*
44
45 -----
46
47 .. class:: infomark
48
49 **What it does**
50
51 This tool computes the RCVE (Relative Contribution to Variance) for all possible variable subsets using the following formula:
52
53 **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)**,
54 which denotes the case where the 'i'th predictor is dropped.
55
56
57 In general,
58 **RCVE(X+) = [R-sq (full: {X,X+}) - R-sq(reduced: {X})] / R-sq (full: {X,X+})**,
59 where,
60
61 - {X,X+} denotes the set of all predictors,
62 - X+ is the set of predictors for which we compute RCVE (and therefore drop from the full model to obtain a reduced one),
63 - {X} is the set of the predictors that are left in the reduced model after excluding {X+}
64
65
66 The 4 columns in the output are described below:
67
68 - Column 1 (Model): denotes the variables present in the model ({X})
69 - Column 2 (R-sq): denotes the R-squared value corresponding to the model in Column 1
70 - 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.
71 - 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.
72
73
74 </help>
75 </tool>