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| 2 | ·a04c854946527c80ff014af3c64a4515·1895936·python·optional·python3-cogent3_2023.2.12a1+dfsg-2+deb12u1_amd64.deb | 2 | ·a04c854946527c80ff014af3c64a4515·1895936·python·optional·python3-cogent3_2023.2.12a1+dfsg-2+deb12u1_amd64.deb |
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| 1 | -rw-r--r--···0········0········0········4·2023-10-29·20:45:00.000000·debian-binary | 1 | -rw-r--r--···0········0········0········4·2023-10-29·20:45:00.000000·debian-binary |
| 2 | -rw-r--r--···0········0········0····10360·2023-10-29·20:45:00.000000·control.tar.xz | 2 | -rw-r--r--···0········0········0····10360·2023-10-29·20:45:00.000000·control.tar.xz |
| 3 | -rw-r--r--···0········0········0···7229 | 3 | -rw-r--r--···0········0········0···722956·2023-10-29·20:45:00.000000·data.tar.xz |
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| 287 | <p>Note:·names·present·in·only·one·of·the·two·trees·will·count·as | 287 | <p>Note:·names·present·in·only·one·of·the·two·trees·will·count·as |
| 288 | mismatches:·if·you·don’t·want·this·behavior,·strip·out·the·non-matching | 288 | mismatches:·if·you·don’t·want·this·behavior,·strip·out·the·non-matching |
| 289 | tips·first.</p> | 289 | tips·first.</p> |
| 290 | </dd></dl> | 290 | </dd></dl> |
| 291 | <dl·class="py·method"> | 291 | <dl·class="py·method"> |
| 292 | <dt·class="sig·sig-object·py"·id="cogent3.core.tree.PhyloNode.compare_by_tip_distances"> | 292 | <dt·class="sig·sig-object·py"·id="cogent3.core.tree.PhyloNode.compare_by_tip_distances"> |
| 293 | <span·class="sig-name·descname"><span·class="pre">compare_by_tip_distances</span></span><span·class="sig-paren">(</span><em·class="sig-param"><span·class="n"><span·class="pre">other</span></span></em>,·<em·class="sig-param"><span·class="n"><span·class="pre">sample=None</span></span></em>,·<em·class="sig-param"><span·class="n"><span·class="pre">dist_f=<function</span>·<span·class="pre">distance_from_r></span></span></em>,·<em·class="sig-param"><span·class="n"><span·class="pre">shuffle_f=<bound</span>·<span·class="pre">method</span>·<span·class="pre">Random.shuffle</span>·<span·class="pre">of</span>·<span·class="pre"><random.Random</span>·<span·class="pre">object</span>·<span·class="pre">at</span>·<span·class="pre">0x2 | 293 | <span·class="sig-name·descname"><span·class="pre">compare_by_tip_distances</span></span><span·class="sig-paren">(</span><em·class="sig-param"><span·class="n"><span·class="pre">other</span></span></em>,·<em·class="sig-param"><span·class="n"><span·class="pre">sample=None</span></span></em>,·<em·class="sig-param"><span·class="n"><span·class="pre">dist_f=<function</span>·<span·class="pre">distance_from_r></span></span></em>,·<em·class="sig-param"><span·class="n"><span·class="pre">shuffle_f=<bound</span>·<span·class="pre">method</span>·<span·class="pre">Random.shuffle</span>·<span·class="pre">of</span>·<span·class="pre"><random.Random</span>·<span·class="pre">object</span>·<span·class="pre">at</span>·<span·class="pre">0x2276690>></span></span></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> |
| 294 | <dd><p>Compares·self·to·other·using·tip-to-tip·distance·matrices.</p> | 294 | <dd><p>Compares·self·to·other·using·tip-to-tip·distance·matrices.</p> |
| 295 | <p>Value·returned·is·dist_f(m1,·m2)·for·the·two·matrices.·Default·is | 295 | <p>Value·returned·is·dist_f(m1,·m2)·for·the·two·matrices.·Default·is |
| 296 | to·use·the·Pearson·correlation·coefficient,·with·+1·giving·a·distance | 296 | to·use·the·Pearson·correlation·coefficient,·with·+1·giving·a·distance |
| 297 | of·0·and·-1·giving·a·distance·of·+1·(the·madimum·possible·value). | 297 | of·0·and·-1·giving·a·distance·of·+1·(the·madimum·possible·value). |
| 298 | Depending·on·the·application,·you·might·instead·want·to·use | 298 | Depending·on·the·application,·you·might·instead·want·to·use |
| 299 | distance_from_r_squared,·which·counts·correlations·of·both·+1·and·-1 | 299 | distance_from_r_squared,·which·counts·correlations·of·both·+1·and·-1 |
| 300 | as·identical·(0·distance).</p> | 300 | as·identical·(0·distance).</p> |
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| 144 | ············differ. | 144 | ············differ. |
| 145 | ············Other·is·expected·to·be·a·tree·object·compatible·with·PhyloNode. | 145 | ············Other·is·expected·to·be·a·tree·object·compatible·with·PhyloNode. |
| 146 | ············Note:·names·present·in·only·one·of·the·two·trees·will·count·as | 146 | ············Note:·names·present·in·only·one·of·the·two·trees·will·count·as |
| 147 | ············mismatches:·if·you·donât·want·this·behavior,·strip·out·the·non- | 147 | ············mismatches:·if·you·donât·want·this·behavior,·strip·out·the·non- |
| 148 | ············matching·tips·first. | 148 | ············matching·tips·first. |
| 149 | ········compare_by_tip_distances(other,·sample=None,·dist_f=<function | 149 | ········compare_by_tip_distances(other,·sample=None,·dist_f=<function |
| 150 | ········distance_from_r>,·shuffle_f=<bound·method·Random.shuffle·of | 150 | ········distance_from_r>,·shuffle_f=<bound·method·Random.shuffle·of |
| 151 | ········<random.Random·object·at·0x2 | 151 | ········<random.Random·object·at·0x2276690>>)¶ |
| 152 | ············Compares·self·to·other·using·tip-to-tip·distance·matrices. | 152 | ············Compares·self·to·other·using·tip-to-tip·distance·matrices. |
| 153 | ············Value·returned·is·dist_f(m1,·m2)·for·the·two·matrices.·Default·is | 153 | ············Value·returned·is·dist_f(m1,·m2)·for·the·two·matrices.·Default·is |
| 154 | ············to·use·the·Pearson·correlation·coefficient,·with·+1·giving·a | 154 | ············to·use·the·Pearson·correlation·coefficient,·with·+1·giving·a |
| 155 | ············distance·of·0·and·-1·giving·a·distance·of·+1·(the·madimum·possible | 155 | ············distance·of·0·and·-1·giving·a·distance·of·+1·(the·madimum·possible |
| 156 | ············value).·Depending·on·the·application,·you·might·instead·want·to·use | 156 | ············value).·Depending·on·the·application,·you·might·instead·want·to·use |
| 157 | ············distance_from_r_squared,·which·counts·correlations·of·both·+1·and·- | 157 | ············distance_from_r_squared,·which·counts·correlations·of·both·+1·and·- |
| 158 | ············1·as·identical·(0·distance). | 158 | ············1·as·identical·(0·distance). |
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| 1629 | ········"compare_by_nam":·38, | 1629 | ········"compare_by_nam":·38, |
| 1630 | ········"compare_by_subset":·38, | 1630 | ········"compare_by_subset":·38, |
| 1631 | ········"exclude_absent_taxa":·38, | 1631 | ········"exclude_absent_taxa":·38, |
| 1632 | ········"compare_by_tip_dist":·38, | 1632 | ········"compare_by_tip_dist":·38, |
| 1633 | ········"dist_f":·38, | 1633 | ········"dist_f":·38, |
| 1634 | ········"distance_from_r":·38, | 1634 | ········"distance_from_r":·38, |
| 1635 | ········"shuffle_f":·38, | 1635 | ········"shuffle_f":·38, |
| 1636 | ········"0x2 | 1636 | ········"0x2276690":·38, |
| 1637 | ········"m1":·38, | 1637 | ········"m1":·38, |
| 1638 | ········"m2":·38, | 1638 | ········"m2":·38, |
| 1639 | ········"pearson":·[38,·80], | 1639 | ········"pearson":·[38,·80], |
| 1640 | ········"correl":·[38,·80,·102], | 1640 | ········"correl":·[38,·80,·102], |
| 1641 | ········"coeffici":·38, | 1641 | ········"coeffici":·38, |
| 1642 | ········"madimum":·38, | 1642 | ········"madimum":·38, |
| 1643 | ········"applic":·[38,·49,·66,·124], | 1643 | ········"applic":·[38,·49,·66,·124], |