Mercurial > repos > iuc > rpy_statistics_collection
comparison cca.xml @ 0:ffcdde989859 draft
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| author | iuc |
|---|---|
| date | Tue, 29 Jul 2014 06:30:45 -0400 |
| parents | |
| children | 2e7bc1bb2dbe |
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| -1:000000000000 | 0:ffcdde989859 |
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| 1 <tool id="cca1" name="Canonical Correlation Analysis" version="1.1.0"> | |
| 2 <description> </description> | |
| 3 <expand macro="requirements" /> | |
| 4 <macros> | |
| 5 <import>statistic_tools_macros.xml</import> | |
| 6 </macros> | |
| 7 <command interpreter="python"> | |
| 8 cca.py | |
| 9 $input1 | |
| 10 $x_cols | |
| 11 $y_cols | |
| 12 $x_scale | |
| 13 $y_scale | |
| 14 $std_scores | |
| 15 $out_file1 | |
| 16 $out_file2 | |
| 17 </command> | |
| 18 <inputs> | |
| 19 <param format="tabular" name="input1" type="data" label="Select data" help="Dataset missing? See TIP below."/> | |
| 20 <param name="x_cols" label="Select columns containing X variables " type="data_column" data_ref="input1" numerical="True" multiple="true" > | |
| 21 <validator type="no_options" message="Please select at least one column."/> | |
| 22 </param> | |
| 23 <param name="y_cols" label="Select columns containing Y variables " type="data_column" data_ref="input1" numerical="True" multiple="true" > | |
| 24 <validator type="no_options" message="Please select at least one column."/> | |
| 25 </param> | |
| 26 <param name="x_scale" type="select" label="Type of Scaling for X variables" help="Can be used to center and/or scale variables"> | |
| 27 <option value="none" selected="true">None</option> | |
| 28 <option value="center">Center only</option> | |
| 29 <option value="scale">Scale only</option> | |
| 30 <option value="both">Center and Scale</option> | |
| 31 </param> | |
| 32 <param name="y_scale" type="select" label="Type of Scaling for Y variables" help="Can be used to center and/or scale variables"> | |
| 33 <option value="none" selected="true">None</option> | |
| 34 <option value="center">Center only</option> | |
| 35 <option value="scale">Scale only</option> | |
| 36 <option value="both">Center and Scale</option> | |
| 37 </param> | |
| 38 <param name="std_scores" type="select" label="Report standardized scores?" help="Selecting 'Yes' will rescale scores (and coefficients) to produce scores of unit variance"> | |
| 39 <option value="no" selected="true">No</option> | |
| 40 <option value="yes">Yes</option> | |
| 41 </param> | |
| 42 </inputs> | |
| 43 <outputs> | |
| 44 <data format="input" name="out_file1" metadata_source="input1" /> | |
| 45 <data format="pdf" name="out_file2" /> | |
| 46 </outputs> | |
| 47 <tests> | |
| 48 <test> | |
| 49 <param name="input1" value="iris.tabular"/> | |
| 50 <param name="x_cols" value="3,4"/> | |
| 51 <param name="y_cols" value="1,2"/> | |
| 52 <param name="x_scale" value="both"/> | |
| 53 <param name="y_scale" value="scale"/> | |
| 54 <param name="std_scores" value="yes"/> | |
| 55 <output name="out_file1" file="cca_out1.tabular"/> | |
| 56 <output name="out_file2" file="cca_out2.pdf"/> | |
| 57 </test> | |
| 58 </tests> | |
| 59 <help> | |
| 60 | |
| 61 | |
| 62 .. class:: infomark | |
| 63 | |
| 64 **TIP:** If your data is not TAB delimited, use *Edit Datasets->Convert characters* | |
| 65 | |
| 66 ----- | |
| 67 | |
| 68 .. class:: infomark | |
| 69 | |
| 70 **What it does** | |
| 71 | |
| 72 This tool uses functions from 'yacca' library from R statistical package to perform Canonical Correlation Analysis (CCA) on the input data. | |
| 73 It outputs two files, one containing the summary statistics of the performed CCA, and the other containing helioplots, which display structural loadings of X and Y variables on different canonical components. | |
| 74 | |
| 75 *Carter T. Butts (2009). yacca: Yet Another Canonical Correlation Analysis Package. R package version 1.1.* | |
| 76 | |
| 77 ----- | |
| 78 | |
| 79 .. class:: warningmark | |
| 80 | |
| 81 **Note** | |
| 82 | |
| 83 - This tool currently treats all predictor and response variables as continuous numeric variables. Running the tool on categorical variables might result in incorrect results. | |
| 84 | |
| 85 - Rows containing non-numeric (or missing) data in any of the chosen columns will be skipped from the analysis. | |
| 86 | |
| 87 - The summary statistics in the output are described below: | |
| 88 | |
| 89 - correlation: Canonical correlation between the canonical variates (i.e. transformed variables) | |
| 90 - F-statistic: F-value obtained from F Test for Canonical Correlations Using Rao's Approximation | |
| 91 - p-value: denotes significance of canonical correlations | |
| 92 - Coefficients: represent the coefficients of X and Y variables on each canonical variate | |
| 93 - Loadings: represent the correlations between the original variables in each set and their respective canonical variates | |
| 94 - CrossLoadings: represent the correlations between the original variables in each set and the opposite canonical variates | |
| 95 | |
| 96 </help> | |
| 97 </tool> |