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| Offset 186, 15 lines modified | Offset 186, 15 lines modified |
| 186 | <p>Note:·names·present·in·only·one·of·the·two·trees·will·count·as | 186 | <p>Note:·names·present·in·only·one·of·the·two·trees·will·count·as |
| 187 | mismatches:·if·you·don’t·want·this·behavior,·strip·out·the·non-matching | 187 | mismatches:·if·you·don’t·want·this·behavior,·strip·out·the·non-matching |
| 188 | tips·first.</p> | 188 | tips·first.</p> |
| 189 | </dd></dl> | 189 | </dd></dl> |
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| 190 | <dl·class="py·method"> | 190 | <dl·class="py·method"> |
| 191 | <dt·id="cogent3.core.tree.PhyloNode.compare_by_tip_distances"> | 191 | <dt·id="cogent3.core.tree.PhyloNode.compare_by_tip_distances"> |
| 192 | <code·class="sig-name·descname">compare_by_tip_distances</code><span·class="sig-paren">(</span><em·class="sig-param">other</em>,·<em·class="sig-param">sample=None</em>,·<em·class="sig-param">dist_f=<function·distance_from_r></em>,·<em·class="sig-param">shuffle_f=<bound·method·Random.shuffle·of·<random.Random·object·at·0x8ef5ab8>></em><span·class="sig-paren">)</span><a·class="headerlink"·href="#cogent3.core.tree.PhyloNode.compare_by_tip_distances"·title="Permalink·to·this·definition">¶</a></dt> | 192 | <code·class="sig-name·descname">compare_by_tip_distances</code><span·class="sig-paren">(</span><em·class="sig-param">other</em>,·<em·class="sig-param">sample=None</em>,·<em·class="sig-param">dist_f=<function·distance_from_r></em>,·<em·class="sig-param">shuffle_f=<bound·method·Random.shuffle·of·<random.Random·object·at·0x99772b8>></em><span·class="sig-paren">)</span><a·class="headerlink"·href="#cogent3.core.tree.PhyloNode.compare_by_tip_distances"·title="Permalink·to·this·definition">¶</a></dt> |
| 193 | <dd><p>Compares·self·to·other·using·tip-to-tip·distance·matrices.</p> | 193 | <dd><p>Compares·self·to·other·using·tip-to-tip·distance·matrices.</p> |
| 194 | <p>Value·returned·is·dist_f(m1,·m2)·for·the·two·matrices.·Default·is | 194 | <p>Value·returned·is·dist_f(m1,·m2)·for·the·two·matrices.·Default·is |
| 195 | to·use·the·Pearson·correlation·coefficient,·with·+1·giving·a·distance | 195 | to·use·the·Pearson·correlation·coefficient,·with·+1·giving·a·distance |
| 196 | of·0·and·-1·giving·a·distance·of·+1·(the·madimum·possible·value). | 196 | of·0·and·-1·giving·a·distance·of·+1·(the·madimum·possible·value). |
| 197 | Depending·on·the·application,·you·might·instead·want·to·use | 197 | Depending·on·the·application,·you·might·instead·want·to·use |
| 198 | distance_from_r_squared,·which·counts·correlations·of·both·+1·and·-1 | 198 | distance_from_r_squared,·which·counts·correlations·of·both·+1·and·-1 |
| 199 | as·identical·(0·distance).</p> | 199 | as·identical·(0·distance).</p> |