{"id":562,"date":"2018-04-09T08:30:00","date_gmt":"2018-04-09T12:30:00","guid":{"rendered":"http:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/?p=562"},"modified":"2018-04-08T14:27:29","modified_gmt":"2018-04-08T18:27:29","slug":"causal-inference-in-ecology-introduction-to-the-series","status":"publish","type":"post","link":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/blog\/2018\/04\/09\/causal-inference-in-ecology-introduction-to-the-series\/","title":{"rendered":"Causal inference in ecology &#8211; Introduction to the series"},"content":{"rendered":"<p>If you\u2019ve been following posts here since the first of the year, you know that I\u2019ve been writing about how I keep myself organized. Today I\u2019m starting a completely different series in which I begin to collect my thoughts on how we can make judgments about the cause (or causes) of ecological phenomena<sup><a id=\"ffn1\" class=\"footnote\" href=\"#fn1\">1<\/a><\/sup> and the circumstances under which judgments are possible. Before I start, I need to offer a few disclaimers.<\/p>\n<ul>\n<li>Any evolutionary biologist or ecologist who knows me and my work knows that it\u2019s not uncommon for my ideas to represent a minority opinion. (Think pollen discounting for those of you who know my work on the evolution of plant mating systems.) I make no claim that anything I write here is broadly representative of what my fellow evolutionary biologists and ecologists think, only that it\u2019s what I think. Please challenge me on anything you think I\u2019ve got wrong, because I\u2019m sure there will be things I get wrong, and the easiest way for me to discover those errors is for someone else to point them out.<\/li>\n<li>I had a minor in Philosophy as an undergraduate and there is an <em><strong>enormous<\/strong><\/em> literature on causality in the philosophy of science. I\u2019ll be using a very crude understanding of \u201ccause.\u201d I don\u2019t think it is wildly misleading, but I\u2019m certain it wouldn\u2019t stand up to serious scrutiny.<sup><a id=\"ffn2\" class=\"footnote\" href=\"#fn2\">2<\/a><\/sup><\/li>\n<li>I\u2019ll be thinking about causal inference in the specific context of trying to infer causes from observational data using statistics rather than from inferring causes controlled experiments.<sup><a id=\"ffn3\" class=\"footnote\" href=\"#fn3\">3<\/a><\/sup> I\u2019ll be using an approach developed in the 1970s by Donald Rubin, the <a href=\"https:\/\/en.wikipedia.org\/wiki\/Rubin_causal_model\">Rubin Causal Model<\/a>.<sup><a id=\"ffn4\" class=\"footnote\" href=\"#fn4\">4<\/a><\/sup><\/li>\n<li>There is a <em><strong>very<\/strong><\/em> large literature on causal inference in the social sciences. I\u2019ll be drawing heavily on Imbens and Rubin, <em><a href=\"https:\/\/www.amazon.com\/Causal-Inference-Statistics-Biomedical-Sciences\/dp\/0521885884\">Causal Inference for Statistics, Social and Biomedical Sciences: An Introduction<\/a><\/em>,<sup><a id=\"ffn5\" class=\"footnote\" href=\"#fn5\">5<\/a><\/sup> but there\u2019s an enormous amount of material there that I won\u2019t attempt to cover. I am also pretty new to the concepts associated with the Rubin causal model, so it\u2019s entirely possible that I\u2019ll misrepresent or misinterpret a point that the real experts got right. In other words, if something I say doesn\u2019t make any sense, it\u2019s more likely I got it wrong than that Imbens and Rubin got it wrong.<\/li>\n<\/ul>\n<p>Although I will be thinking about causal inference in the context of observational data and statistics, I don\u2019t plan to write much (if at all) about the problems with P-values, Bayes factors, credible\/confidence intervals overlapping 0 (or not), and the like. If you\u2019d like to know the concerns I have about them, here are links to old posts on those issues.<\/p>\n<ul>\n<li><a href=\"http:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/blog\/2016\/08\/31\/inference-from-noisy-data-with-small-samples\/\">Inference from noisy data with small samples<\/a><\/li>\n<li><a href=\"http:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/blog\/2016\/09\/09\/being-bayesian-wont-save-you\/\">Being Bayesian won\u2019t save you<\/a><\/li>\n<li><a href=\"http:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/blog\/2016\/09\/19\/even-an-informative-prior-doesnt-help-much\/\">Even an informative prior doesn\u2019t help much<\/a><\/li>\n<li><a href=\"http:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/blog\/2016\/09\/23\/noisy-data-and-small-samples-are-a-bad-combination\/\">Noisy data and small samples are a bad combination<\/a><\/li>\n<\/ul>\n<ol id=\"footnotes\">\n<li id=\"fn1\">I\u2019m calling the post \u201cCausal inference in ecology\u201d only because \u201cCausal inference in ecology, evolutionary biology, and population genetics\u201d would be too long. <a href=\"#ffn1\">&#x21a9;<\/a><\/li>\n<li id=\"fn2\">There\u2019s a good chance that a moderately competent undergraduate Philosophy major would find it woefully inadequate. <a href=\"#ffn2\">&#x21a9;<\/a><\/li>\n<li id=\"fn3\">To be more precise, we don\u2019t infer causes from controlled experiments. Rather, we have pre-existing hypotheses about possible causes, and we use controlled experiments to test those hypotheses. <a href=\"#ffn3\">&#x21a9;<\/a><\/li>\n<li id=\"fn4\">In my relatively limited reading on the subject, I\u2019ve most often seen it referred to as the Rubin causal model, but it is sometimes referred to as the Neyman causal model. <a href=\"#ffn4\">&#x21a9;<\/a><\/li>\n<li id=\"fn5\">Reminder: If you click on that link, it will take you to Amazon.com. I use that link simply because it\u2019s convenient. You can buy the book, if you\u2019re so inclined, from many other outlets. I am not an Amazon affiliate, and I will not receive any compensation if you decide to buy the book regardless of whether you buy it at Amazon or elsewhere. By the way, Chapter 23 in Gelman and Hill\u2019s book, <em><a href=\"https:\/\/www.amazon.com\/Jennifer-Regression-Multilevel-Hierarchical-Paperback\/dp\/B004QP1B0S\/ref=sr_1_2?s=books&amp;ie=UTF8&amp;qid=1523210705&amp;sr=1-2&amp;keywords=gelman+and+hill&amp;dpID=41n%252B6JnSZdL&amp;preST=_SY291_BO1,204,203,200_QL40_&amp;dpSrc=srch\">Data Analysis Using Regression and Multilevel\/Hierarchical Models<\/a><\/em> has an excellent overview of the Rubin causal model. <a href=\"#ffn5\">&#x21a9;<\/a><\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"<p>If you\u2019ve been following posts here since the first of the year, you know that I\u2019ve been writing about how I keep myself organized. Today I\u2019m starting a completely different&#8230; <a class=\"read-more-button\" href=\"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/blog\/2018\/04\/09\/causal-inference-in-ecology-introduction-to-the-series\/\">Read more &gt;<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[10],"tags":[],"class_list":["post-562","post","type-post","status-publish","format-standard","hentry","category-statistics"],"_links":{"self":[{"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/wp-json\/wp\/v2\/posts\/562","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/wp-json\/wp\/v2\/comments?post=562"}],"version-history":[{"count":0,"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/wp-json\/wp\/v2\/posts\/562\/revisions"}],"wp:attachment":[{"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/wp-json\/wp\/v2\/media?parent=562"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/wp-json\/wp\/v2\/categories?post=562"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/wp-json\/wp\/v2\/tags?post=562"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}