{"action":"created","comment":{"url":"https://api.github.com/repos/biocore/scikit-bio/pulls/comments/36523243","id":36523243,"diff_hunk":"@@ -0,0 +1,170 @@\n+# ----------------------------------------------------------------------------\n+# Copyright (c) 2013--, scikit-bio development team.\n+#\n+# Distributed under the terms of the Modified BSD License.\n+#\n+# The full license is in the file COPYING.txt, distributed with this software.\n+# ----------------------------------------------------------------------------\n+\n+from __future__ import absolute_import, division, print_function\n+\n+from skbio.util._decorator import experimental\n+\n+\n+@experimental(as_of=\"0.4.0-dev\")\n+def unweighted_unifrac(u_counts, v_counts, otu_ids, tree):\n+    \"\"\" Compute unweighted unifrac\n+\n+    Parameters\n+    ----------\n+    u_counts, v_counts: list, np.array\n+        Vectors of counts of OTUs for two samples. Must be equal length.\n+    otu_ids: list, np.array\n+        Vector of OTU ids corresponding to tip names in ``tree``. Must be the\n+        same length as ``u_counts`` and ``v_counts``.\n+    tree: skbio.TreeNode\n+        Tree relating the OTUs in otu_ids. The set of tip names in the tree can\n+        be a superset of ``otu_ids``, but not a subset.\n+\n+    Returns\n+    -------\n+    float\n+        The unweighted unifrac distance between the two samples.\n+\n+    Raises\n+    ------\n+    ValueError\n+        If ``u_counts``, ``v_counts``, and ``otu_ids`` are not all of equal\n+        length.\n+    MissingNodeError\n+        If an OTU id is provided that does not correspond to a tip in the\n+        tree.\n+\n+    See Also\n+    --------\n+    weighted_unifrac\n+\n+    Notes\n+    -----\n+    Unweighted unifrac was originally described in [1]_. A discussion of\n+    unweighted (qualitative) versus weighted (quantitiative) diversity metrics\n+    is presented in [2]_.\n+\n+    References\n+    ----------\n+    .. [1] Lozupone, C. & Knight, R. UniFrac: a new phylogenetic method for\n+       comparing microbial communities. Appl. Environ. Microbiol. 71, 8228-8235\n+       (2005).\n+\n+    .. [2] Lozupone, C. A., Hamady, M., Kelley, S. T. & Knight, R. Quantitative\n+       and qualitative beta diversity measures lead to different insights into\n+       factors that structure microbial communities. Appl. Environ. Microbiol.\n+       73, 1576-1585 (2007).\n+\n+    \"\"\"\n+    if len(u_counts) != len(v_counts) != len(otu_ids):\n+        raise ValueError(\"Input vectors u_counts, v_counts, and otu_ids must\"\n+                         \" be of equal length.\")\n+    u_observed_otus = {o: c for o, c in zip(otu_ids, u_counts) if c >= 1}\n+    v_observed_otus = {o: c for o, c in zip(otu_ids, v_counts) if c >= 1}\n+    observed_nodes1 = set(tree.observed_node_counts(u_observed_otus))\n+    observed_nodes2 = set(tree.observed_node_counts(v_observed_otus))\n+    observed_branch_length = sum(\n+        o.length for o in observed_nodes1 | observed_nodes2\n+        if o.length is not None)\n+    if observed_branch_length == 0:\n+        # boundary case where both communities have no members\n+        return 0.0\n+    shared_branch_length = sum(\n+        o.length for o in observed_nodes1 & observed_nodes2\n+        if o.length is not None)\n+    unique_branch_length = observed_branch_length - shared_branch_length\n+    unweighted_unifrac = unique_branch_length / observed_branch_length\n+    return unweighted_unifrac\n+\n+\n+@experimental(as_of=\"0.4.0-dev\")\n+def weighted_unifrac(u_counts, v_counts, otu_ids, tree, normalized=False):\n+    \"\"\" Compute weighted unifrac with or without branch length normalization\n+\n+    Parameters\n+    ----------\n+    u_counts, v_counts: list, np.array\n+        Vectors of counts of OTUs for two samples. Must be equal length.\n+    otu_ids: list, np.array\n+        Vector of OTU ids corresponding to tip names in ``tree``. Must be the\n+        same length as ``u_counts`` and ``v_counts``.\n+    tree: skbio.TreeNode\n+        Tree relating the OTUs in otu_ids. The set of tip names in the tree can\n+        be a superset of ``otu_ids``, but not a subset.\n+    normalized: boolean, optional\n+        If ``True``, apply branch length normalization. Resulting distances\n+        will then be in the range ``[0, 1]``.\n+\n+    Returns\n+    -------\n+    float\n+        The weighted unifrac distance between the two samples.\n+\n+    Raises\n+    ------\n+    ValueError\n+        If ``u_counts``, ``v_counts``, and ``otu_ids`` are not all equal in\n+        length.\n+    MissingNodeError\n+        If an OTU id is provided that does not correspond to a tip in the\n+        tree.\n+\n+    See Also\n+    --------\n+    unweighted_unifrac\n+\n+    Notes\n+    -----\n+    Unweighted unifrac was originally described in [1]_, which includes a\n+    discussion of unweighted (qualitative) versus weighted (quantitiative)\n+    diversity metrics.\n+\n+    References\n+    ----------\n+    .. [1] Lozupone, C. A., Hamady, M., Kelley, S. T. & Knight, R. Quantitative\n+       and qualitative beta diversity measures lead to different insights into\n+       factors that structure microbial communities. Appl. Environ. Microbiol.\n+       73, 1576–1585 (2007).\n+\n+    \"\"\"\n+    u_observed_otus = {o: c for o, c in zip(otu_ids, u_counts) if c >= 1}\n+    u_total_count = sum(u_counts)\n+    v_observed_otus = {o: c for o, c in zip(otu_ids, v_counts) if c >= 1}\n+    v_total_count = sum(v_counts)\n+    if u_total_count == 0 and v_total_count == 0:\n+        # boundary case where both communities have no members\n+        return 0.0\n+    u_observed_nodes = tree.observed_node_counts(u_observed_otus)\n+    v_observed_nodes = tree.observed_node_counts(v_observed_otus)\n+    weighted_unifrac = 0\n+    D = 0\n+    for o in set(u_observed_nodes) | set(v_observed_nodes):\n+        # handle the case of o.length is None\n+        b = o.length or 0\n+        u_branch_weight = _sample_branch_weight(\n+            u_observed_nodes[o], u_total_count)\n+        v_branch_weight = _sample_branch_weight(\n+            v_observed_nodes[o], v_total_count)\n+        branch_weight = abs(u_branch_weight - v_branch_weight)\n+        weighted_unifrac += b * branch_weight\n+        if o.is_tip() and normalized:\n+            d = o.accumulate_to_ancestor(tree.root())\n+            normed_weight = u_branch_weight + v_branch_weight\n+            D += (d * normed_weight)\n+    if normalized:\n+        return weighted_unifrac / D\n+    else:\n+        return weighted_unifrac\n+\n+\n+def _sample_branch_weight(observed_nodes, total_count):\n+    if total_count == 0:\n+        return 0","path":"skbio/diversity/beta/_unifrac.py","position":168,"original_position":168,"commit_id":"538347e1bf6c1aac649bb43d4f0567f44614cc82","original_commit_id":"538347e1bf6c1aac649bb43d4f0567f44614cc82","user":{"login":"mortonjt","id":4184797,"avatar_url":"https://avatars.githubusercontent.com/u/4184797?v=3","gravatar_id":"","url":"https://api.github.com/users/mortonjt","html_url":"https://github.com/mortonjt","followers_url":"https://api.github.com/users/mortonjt/followers","following_url":"https://api.github.com/users/mortonjt/following{/other_user}","gists_url":"https://api.github.com/users/mortonjt/gists{/gist_id}","starred_url":"https://api.github.com/users/mortonjt/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mortonjt/subscriptions","organizations_url":"https://api.github.com/users/mortonjt/orgs","repos_url":"https://api.github.com/users/mortonjt/repos","events_url":"https://api.github.com/users/mortonjt/events{/privacy}","received_events_url":"https://api.github.com/users/mortonjt/received_events","type":"User","site_admin":false},"body":"I'm just curious.  Does this scenario ever happen?\r\nIf the user inputs a list with no counts in it, shouldn't that raise an error?","created_at":"2015-08-07T14:23:10Z","updated_at":"2015-08-07T14:23:10Z","html_url":"https://github.com/biocore/scikit-bio/pull/1027#discussion_r36523243","pull_request_url":"https://api.github.com/repos/biocore/scikit-bio/pulls/1027","_links":{"self":{"href":"https://api.github.com/repos/biocore/scikit-bio/pulls/comments/36523243"},"html":{"href":"https://github.com/biocore/scikit-bio/pull/1027#discussion_r36523243"},"pull_request":{"href":"https://api.github.com/repos/biocore/scikit-bio/pulls/1027"}}},"pull_request":{"url":"https://api.github.com/repos/biocore/scikit-bio/pulls/1027","id":41707296,"html_url":"https://github.com/biocore/scikit-bio/pull/1027","diff_url":"https://github.com/biocore/scikit-bio/pull/1027.diff","patch_url":"https://github.com/biocore/scikit-bio/pull/1027.patch","issue_url":"https://api.github.com/repos/biocore/scikit-bio/issues/1027","number":1027,"state":"open","locked":false,"title":"adds phylogenetic diversity metrics","user":{"login":"gregcaporaso","id":192372,"avatar_url":"https://avatars.githubusercontent.com/u/192372?v=3","gravatar_id":"","url":"https://api.github.com/users/gregcaporaso","html_url":"https://github.com/gregcaporaso","followers_url":"https://api.github.com/users/gregcaporaso/followers","following_url":"https://api.github.com/users/gregcaporaso/following{/other_user}","gists_url":"https://api.github.com/users/gregcaporaso/gists{/gist_id}","starred_url":"https://api.github.com/users/gregcaporaso/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gregcaporaso/subscriptions","organizations_url":"https://api.github.com/users/gregcaporaso/orgs","repos_url":"https://api.github.com/users/gregcaporaso/repos","events_url":"https://api.github.com/users/gregcaporaso/events{/privacy}","received_events_url":"https://api.github.com/users/gregcaporaso/received_events","type":"User","site_admin":false},"body":"Adds PD, unweighted unifrac, and weighted unifrac (with and without normalization). \r\n\r\nTo do before merge:\r\n- [ ] interface work (how will this be imported/used)\r\n - [x] add stability decorators\r\n - [ ] should ``normalized=True`` be the default for ``weighted_unifrac``?\r\n - [x] modify ``pw_distances`` to take ``metric`` as the first argument and not have a default \r\n - [x] update ``pw_distances`` to take skbio's distance functions as strings and this should be the preferred/documented way of passing them (similar to SciPy's ``pdist``)\r\n - [x] for PD, ``u`` becomes ``counts`` to match our other alpha diversity metrics\r\n - [x] for *unifrac, ``u`` and ``v`` become ``u_counts`` and ``v_counts``, to match the alpha diversity metrics and SciPy\r\n - [x] ``phylogenetic_diversity`` renamed to ``faith_pd`` and move to ``_base.py``; make it accessible from ``skbio.diversity.alpha``\r\n - [x] ``*unifrac`` should be accessible from ``skbio.diversity.beta``, and ``skbio/diversity/beta/_stats.py`` should be renamed ``skbio/diversity/beta/_unifrac.py``\r\n\r\n- [ ] testing\r\n - [ ] expand unit tests to include direct computation of distance metrics with ``pw_distances``, including referencing the metric both by passing the function and the name (as a string)\r\n - [ ] expand unit tests to use another tree, including:\r\n  - [ ] tree with no branch lengths\r\n  - [ ] tree with duplicated tip names\r\n  - [ ] tree with one node\r\n  - [ ] non-trivial case where tips in tree are superset of ``otu_ids``\r\n - [x] add test with input vector of ``length == 0``\r\n - [ ] add test of vector with negative counts (see ``skbio.diversity.alpha._validate``)\r\n\r\n- [ ] documentation\r\n - [x] add numpy-doc (with [cite](http://aem.asm.org/content/73/5/1576.long))\r\n - [ ] add formulas for metrics\r\n - [x] update ``skbio.diversity.beta`` doctests to use a phylogenetic metric\r\n - [ ] update ``skbio.diversity.alpha`` doctests to use ``faith_pd``\r\n\r\n- [ ] misc\r\n - [x] inline ``_to_pdist_metric``\r\n - [ ] add tree/otu ids ``_validate`` function\r\n - [ ] add ``_validate`` for beta diversity metrics, similar (or the same as ``skbio.diversity.alpha._validate``)\r\n\r\n- [ ] squash commits\r\n- [ ] add ChangeLog note\r\n\r\n\r\n\r\n\r\n\r\n\r\nAddresses #46, #820.\r\n","created_at":"2015-08-05T17:59:14Z","updated_at":"2015-08-07T14:23:10Z","closed_at":null,"merged_at":null,"merge_commit_sha":"e49cc206b96422936de154e4f5a36f11617b4cf1","assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/biocore/scikit-bio/pulls/1027/commits","review_comments_url":"https://api.github.com/repos/biocore/scikit-bio/pulls/1027/comments","review_comment_url":"https://api.github.com/repos/biocore/scikit-bio/pulls/comments{/number}","comments_url":"https://api.github.com/repos/biocore/scikit-bio/issues/1027/comments","statuses_url":"https://api.github.com/repos/biocore/scikit-bio/statuses/538347e1bf6c1aac649bb43d4f0567f44614cc82","head":{"label":"gregcaporaso:issue-46","ref":"issue-46","sha":"538347e1bf6c1aac649bb43d4f0567f44614cc82","user":{"login":"gregcaporaso","id":192372,"avatar_url":"https://avatars.githubusercontent.com/u/192372?v=3","gravatar_id":"","url":"https://api.github.com/users/gregcaporaso","html_url":"https://github.com/gregcaporaso","followers_url":"https://api.github.com/users/gregcaporaso/followers","following_url":"https://api.github.com/users/gregcaporaso/following{/other_user}","gists_url":"https://api.github.com/users/gregcaporaso/gists{/gist_id}","starred_url":"https://api.github.com/users/gregcaporaso/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gregcaporaso/subscriptions","organizations_url":"https://api.github.com/users/gregcaporaso/orgs","repos_url":"https://api.github.com/users/gregcaporaso/repos","events_url":"https://api.github.com/users/gregcaporaso/events{/privacy}","received_events_url":"https://api.github.com/users/gregcaporaso/received_events","type":"User","site_admin":false},"repo":{"id":22703109,"name":"scikit-bio","full_name":"gregcaporaso/scikit-bio","owner":{"login":"gregcaporaso","id":192372,"avatar_url":"https://avatars.githubusercontent.com/u/192372?v=3","gravatar_id":"","url":"https://api.github.com/users/gregcaporaso","html_url":"https://github.com/gregcaporaso","followers_url":"https://api.github.com/users/gregcaporaso/followers","following_url":"https://api.github.com/users/gregcaporaso/following{/other_user}","gists_url":"https://api.github.com/users/gregcaporaso/gists{/gist_id}","starred_url":"https://api.github.com/users/gregcaporaso/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gregcaporaso/subscriptions","organizations_url":"https://api.github.com/users/gregcaporaso/orgs","repos_url":"https://api.github.com/users/gregcaporaso/repos","events_url":"https://api.github.com/users/gregcaporaso/events{/privacy}","received_events_url":"https://api.github.com/users/gregcaporaso/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/gregcaporaso/scikit-bio","description":"Core 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