{"data":{"site":{"siteMetadata":{"courseId":"metaanalysis"}},"markdownRemark":{"htmlAst":{"type":"root","children":[{"type":"element","tagName":"exercise","properties":{"id":"1","title":"Preface & Disclaimer"},"children":[{"type":"text","value":"\n"},{"type":"element","tagName":"p","properties":{},"children":[{"type":"text","value":"I am continuously improving and updating this resource, please get in touch if you have some great suggestions, resources or feedback."}]},{"type":"text","value":"\n"},{"type":"element","tagName":"h1","properties":{},"children":[{"type":"text","value":"About this course"}]},{"type":"text","value":"\n"},{"type":"element","tagName":"p","properties":{},"children":[{"type":"text","value":"Hi and welcome, I am "},{"type":"element","tagName":"strong","properties":{},"children":[{"type":"element","tagName":"a","properties":{"href":"https://www.ljmu.ac.uk/about-us/staff-profiles/faculty-of-science/school-of-biological-and-environmental-sciences/susanne-zajitschek"},"children":[{"type":"text","value":"Susi Zajitschek"}]},{"type":"text","value":", a Senior Lecturer in Animal Behaviour at Liverpool John Moores University"}]},{"type":"text","value":". This course is meant mainly as a primer for students who would like to know more about meta-analysis. I will give you an overview on what meta-analyses are and on why they are useful. I have included hands-on exercises and step-by-step examples on how to conduct meta-analyses. "}]},{"type":"text","value":"\n"},{"type":"element","tagName":"p","properties":{},"children":[{"type":"text","value":"All the actual statistical analyses are performed in the "},{"type":"element","tagName":"a","properties":{"href":"https://www.r-project.org/about.html"},"children":[{"type":"text","value":"software R"}]},{"type":"text","value":", and you will have the opportunity to run R software scripts right here, on this website, without the need to install software on your computer."}]},{"type":"text","value":"\n"},{"type":"element","tagName":"p","properties":{},"children":[{"type":"element","tagName":"img","properties":{"src":"https://github.com/SusZaj/metaanalysis/blob/master/images/pushpin.svg?raw=true"},"children":[]},{"type":"text","value":" Please note, if you plan on actually doing a meta-analysis yourself, beyond just going through this exercise, you will have to download R or "},{"type":"element","tagName":"a","properties":{"href":"https://rstudio.com/products/rstudio/download/"},"children":[{"type":"text","value":"R studio"}]},{"type":"text","value":", if you haven’t already. "}]},{"type":"text","value":"\n"},{"type":"element","tagName":"h1","properties":{},"children":[{"type":"text","value":"How to use this resource"}]},{"type":"text","value":"\n"},{"type":"element","tagName":"p","properties":{},"children":[{"type":"text","value":"We are going through the separate steps involved in a meta-analysis, from getting started and framing a question, to performing literature searches, to extracting information from your selected papers, data manipulation and preparation, and the actual meta-analysis."}]},{"type":"text","value":"\n"},{"type":"element","tagName":"p","properties":{},"children":[{"type":"text","value":"You will also have the opportunity to perform steps directly in R, without having to open it locally. This will look like this grey block below. Just click on the “Run Code” button and see what happens.\n(You may need some patience first time you run a  code block - or sometimes it may fail to connect, so just re-run)."}]},{"type":"text","value":"\n"},{"type":"element","tagName":"codeblock","properties":{"id":"intro_1"},"children":[{"type":"text","value":"\nWrite your name where the dotted line is!\n"}]},{"type":"text","value":"\n"},{"type":"element","tagName":"p","properties":{},"children":[{"type":"text","value":"You can also use the “Show hints”, “Show solution” and “Reset” tabs. Don’t worry about doing in anything “wrong” - you will not be breaking these code blocks! You can also use these blocks to calculate whatever else you think of - try for example writing “1+1”, and run it again! (For advanced R users - you can’t import your own datasets, but of course could add them manually!)"}]},{"type":"text","value":"\n"},{"type":"element","tagName":"p","properties":{},"children":[{"type":"text","value":"Each section may contain links to online resources, such as this "},{"type":"element","tagName":"a","properties":{"href":"https://scholar.google.com/"},"children":[{"type":"text","value":"link to google scholar"}]},{"type":"text","value":", questions to answer (including feedback on getting it right or wrong), and tasks to do on your own - as indicated by this laptop icon  "},{"type":"element","tagName":"img","properties":{"src":"https://github.com/SusZaj/metaanalysis/blob/master/images/computertaskicon.svg?raw=true"},"children":[]},{"type":"text","value":". If we think we have a particularly useful note or resource, you will see this pushpin  "},{"type":"element","tagName":"img","properties":{"src":"https://github.com/SusZaj/metaanalysis/blob/master/images/pushpin.svg?raw=true"},"children":[]},{"type":"text","value":".\n"},{"type":"element","tagName":"br","properties":{},"children":[]}]},{"type":"text","value":"\n"},{"type":"element","tagName":"p","properties":{},"children":[{"type":"text","value":"Please note, this is meant as a quick primer to give you some overview of how a meta-analysis is done. Perhaps it will be a student project, but perhaps it may serve as a starting point for you if you’re planning on doing your own, publishable and solid meta-analysis. If that’s the case, we highly recommend to check out some of the additional resources that are out there. Our resource here is only a starting point, and also does not cover the full range of R packages that are available for meta-analyses."}]},{"type":"text","value":"\n"},{"type":"element","tagName":"p","properties":{},"children":[{"type":"text","value":"We are here are focussing on the “metafor” package. For a small collection of freely available resources (that may be using other R packages) please see Chapter 5."}]},{"type":"text","value":"\n"}]},{"type":"text","value":"\n"},{"type":"element","tagName":"exercise","properties":{"id":"2","title":"Introduction"},"children":[{"type":"text","value":"\n"},{"type":"element","tagName":"h1","properties":{},"children":[{"type":"text","value":"WHAT IS A META-ANALYSIS and WHY TO META-ANALYSE?"}]},{"type":"text","value":"\n"},{"type":"element","tagName":"h2","properties":{},"children":[{"type":"text","value":"A short side-trip to the roots of knowledge"}]},{"type":"text","value":"\n"},{"type":"element","tagName":"p","properties":{},"children":[{"type":"text","value":"Humans strive to understand the world. The organized framework to do this is science, more specifically the "},{"type":"element","tagName":"em","properties":{},"children":[{"type":"element","tagName":"a","properties":{"href":"https://en.wikipedia.org/wiki/Scientific_method"},"children":[{"type":"text","value":"scientific method"}]}]},{"type":"text","value":". Science is cumulative in nature. This means that studies and experiments build upon the findings of previous studies and experiments. New scientific insights might be gained by a more or less progressive accumulation of knowledge about a specific question, adding on to existing knowledge. Or, according to "},{"type":"element","tagName":"a","properties":{"href":"https://en.wikipedia.org/wiki/Thomas_Kuhn"},"children":[{"type":"text","value":"Thomas Kuhn"}]},{"type":"text","value":", real progression in science might require "},{"type":"element","tagName":"a","properties":{"href":"https://en.wikipedia.org/wiki/Paradigm_shift"},"children":[{"type":"text","value":"paradigm shifts"}]},{"type":"text","value":" that throw old theories over board and make way for new better theories. These shifts in how we explain the world depend themselves on the accumulation of results, which did not fit the old established theories, but which turned out to be not due to error of any kind (for example methodological mistakes or human error in performing studies)."}]},{"type":"text","value":"\n"},{"type":"element","tagName":"h2","properties":{},"children":[{"type":"text","value":"What makes a successful scientific theory?"}]},{"type":"text","value":"\n"},{"type":"element","tagName":"p","properties":{},"children":[{"type":"text","value":"We are talking about empirical research here, meaning results from studies and experiments that are based on observations. But what is the criterion that scientists use to accept a scientific theory as the currently most successful theory to explain observed phenomena?"}]},{"type":"text","value":"\n"},{"type":"element","tagName":"ul","properties":{},"children":[{"type":"text","value":"\n"},{"type":"element","tagName":"li","properties":{},"children":[{"type":"text","value":"A successful scientific theory should give a good explanation and make accurate predictions"}]},{"type":"text","value":"\n"},{"type":"element","tagName":"li","properties":{},"children":[{"type":"text","value":"This should be the case in a wide range of circumstances, i.e. it shouldn’t be hyper-sensitive to natural variation in traits that are not the direct focus of the studies"}]},{"type":"text","value":"\n"}]},{"type":"text","value":"\n"},{"type":"element","tagName":"p","properties":{},"children":[{"type":"text","value":"Different scientific disciplines will have different criteria for how we define "},{"type":"element","tagName":"em","properties":{},"children":[{"type":"text","value":"good explanation"}]},{"type":"text","value":", "},{"type":"element","tagName":"em","properties":{},"children":[{"type":"text","value":"accurate prediction"}]},{"type":"text","value":", "},{"type":"element","tagName":"em","properties":{},"children":[{"type":"text","value":"sensitive"}]},{"type":"text","value":", and "},{"type":"element","tagName":"em","properties":{},"children":[{"type":"text","value":"natural variation"}]},{"type":"text","value":" that I used above.\nThis self-guided course is mainly focussed on research in biological sciences. My own research involves the study of animal behaviour, which often has a high level of noise in the data, especially when compared to some studies in physics or geology (if interested, read up on the colloquial terms of soft and hard sciences, e.g. "},{"type":"element","tagName":"a","properties":{"href":"https://en.wikipedia.org/wiki/Hard_and_soft_science"},"children":[{"type":"text","value":"here"}]},{"type":"text","value":"). "}]},{"type":"text","value":"\n"},{"type":"element","tagName":"h1","properties":{},"children":[{"type":"text","value":"Meta-analysis can help"}]},{"type":"text","value":"\n"},{"type":"element","tagName":"p","properties":{},"children":[{"type":"text","value":"We established that science works cumulatively. To gain support for specific hypothesis, we do not want to rely on the outcome of single studies. We can try to combine the knowledge gained in multiple studies which tested specific traits of interest. This can be achieved while still taking into account that studies differ in their quality and their size, for example, lending different levels of weights to their results. "}]},{"type":"text","value":"\n"},{"type":"element","tagName":"p","properties":{},"children":[{"type":"text","value":"This combination of multiple test results can be achieved by qualitatively summarising previous work on a specific subject. Classically, this was done in a literature review, for example at the beginning of a graduate or postgraduate degree. While this type of review has still its merit (especially if it is done "},{"type":"element","tagName":"strong","properties":{},"children":[{"type":"element","tagName":"em","properties":{},"children":[{"type":"text","value":"systematically"}]}]},{"type":"text","value":"), we want to introduce you here to the meta-analytical approach (which strictly speaking is a "},{"type":"element","tagName":"strong","properties":{},"children":[{"type":"text","value":"quantitative systematic review"}]},{"type":"text","value":"), which can provide a quantitative summary and test of specific research questions (the Greek prefix "},{"type":"element","tagName":"em","properties":{},"children":[{"type":"text","value":"meta"}]},{"type":"text","value":" (μετά, “after” or “beyond”) means "},{"type":"element","tagName":"em","properties":{},"children":[{"type":"text","value":"more comprehensive"}]},{"type":"text","value":")."}]},{"type":"text","value":"\n"}]},{"type":"text","value":"\n"},{"type":"element","tagName":"exercise","properties":{"id":"3","title":"Overview: the structure of a meta-analysis and some examples"},"children":[{"type":"text","value":"\n"},{"type":"element","tagName":"h1","properties":{},"children":[{"type":"text","value":"Overview"}]},{"type":"text","value":"\n"},{"type":"element","tagName":"p","properties":{},"children":[{"type":"text","value":"This is meant as a first step to get you started.  Here’s an overview of the workflow:"}]},{"type":"text","value":"\n"},{"type":"element","tagName":"p","properties":{},"children":[{"type":"element","tagName":"img","properties":{"src":"https://github.com/SusZaj/metaanalysis/blob/master/images/overview2.png?raw=true"},"children":[]},{"type":"text","value":"\n"},{"type":"element","tagName":"br","properties":{},"children":[]},{"type":"text","value":"\n"},{"type":"element","tagName":"br","properties":{},"children":[]},{"type":"text","value":"\nAs just mentioned, all of these steps have to be described and laid out in a protocol. "}]},{"type":"text","value":"\n"},{"type":"element","tagName":"p","properties":{},"children":[{"type":"text","value":"Protocols are necessary to minimize any bias that we might introduce - either knowingly, but most often unknowingly - into the decisions that have to be taken at each meta-analysis step. Bias might already be present in how the research question we want to tackle is phrased. Furthermore, bias can originate in the specific way we search for literature, both in where we search (for example, which databases we use, or whether we only include published results), and how we search (for example our choice of search terms)."}]},{"type":"text","value":"\n"},{"type":"element","tagName":"p","properties":{},"children":[{"type":"text","value":"The following diagram (Figure 1 from Nakagawa et al. 2017)]("},{"type":"element","tagName":"a","properties":{"href":"https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-017-0357-7"},"children":[{"type":"text","value":"https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-017-0357-7"}]},{"type":"text","value":") shows a more in depth overview over steps and quality control that are part of a well-conducted meta-analysis. The questions on the right hand side need to be answered in your final product to provide reproducibility, the flow chart on the left details the methods and options that have to be considered for each step. "}]},{"type":"text","value":"\n"},{"type":"element","tagName":"p","properties":{},"children":[{"type":"element","tagName":"img","properties":{"src":"https://github.com/SusZaj/metaanalysis/blob/master/images/Nakagawa_etal_Fig1.gif?raw=true"},"children":[]},{"type":"text","value":"\n"},{"type":"element","tagName":"br","properties":{},"children":[]},{"type":"text","value":"\n"},{"type":"element","tagName":"br","properties":{},"children":[]}]},{"type":"text","value":"\n"},{"type":"element","tagName":"h2","properties":{},"children":[{"type":"text","value":"Some examples"}]},{"type":"text","value":"\n"},{"type":"element","tagName":"p","properties":{},"children":[{"type":"text","value":"If you haven’t looked at many meta-analyses yet, you can have a glance and see what questions were asked and how the results are presented in the examples below. Especially the first in the list (Macartney et al. 2019) is a very good example, with protocols, data, and R code published and made freely available (see "},{"type":"element","tagName":"em","properties":{},"children":[{"type":"text","value":"Data & R Code"}]},{"type":"text","value":" below). In fact, we’ll use a subset of their data in our guided example in the data analysis parts in Chapter 3:"}]},{"type":"text","value":"\n"},{"type":"element","tagName":"ul","properties":{},"children":[{"type":"text","value":"\n"},{"type":"element","tagName":"li","properties":{},"children":[{"type":"text","value":"\n"},{"type":"element","tagName":"p","properties":{},"children":[{"type":"element","tagName":"a","properties":{"href":"http://www.bonduriansky.net/Macartney_et_a_2019_Biological_Reviews.pdf"},"children":[{"type":"text","value":"Effects of nutrient limitation on sperm and seminal fluid: a systematic review and meta‐analysis (Macartney et al. 2019)"}]},{"type":"text","value":" "},{"type":"element","tagName":"a","properties":{"href":"https://osf.io/aqw8u/"},"children":[{"type":"text","value":"Data & R code on osf.io"}]},{"type":"element","tagName":"br","properties":{},"children":[]},{"type":"text","value":"\n"},{"type":"element","tagName":"em","properties":{},"children":[{"type":"text","value":"Macartney, E.L., Crean, A.J., Nakagawa, S. and Bonduriansky, R. 2019. Effects of nutrient limitation on sperm and seminal fluid: a systematic review and meta-analysis. Biological Reviews 94:1722-1739"}]}]},{"type":"text","value":"\n"}]},{"type":"text","value":"\n"},{"type":"element","tagName":"li","properties":{},"children":[{"type":"text","value":"\n"},{"type":"element","tagName":"p","properties":{},"children":[{"type":"element","tagName":"a","properties":{"href":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3972767/"},"children":[{"type":"text","value":"The repeatability of behaviour: a meta-analysis (Bell et al. 2009)"}]},{"type":"text","value":"."},{"type":"element","tagName":"br","properties":{},"children":[]},{"type":"text","value":"\n"},{"type":"element","tagName":"em","properties":{},"children":[{"type":"text","value":"Bell, A. M., Hankison, S. J., & Laskowski, K. L. (2009). The repeatability of behaviour: a meta-analysis. Animal behaviour, 77(4), 771–783. "},{"type":"element","tagName":"a","properties":{"href":"https://doi.org/10.1016/j.anbehav.2008.12.022"},"children":[{"type":"text","value":"https://doi.org/10.1016/j.anbehav.2008.12.022"}]}]}]},{"type":"text","value":"\n"}]},{"type":"text","value":"\n"},{"type":"element","tagName":"li","properties":{},"children":[{"type":"text","value":"\n"},{"type":"element","tagName":"p","properties":{},"children":[{"type":"element","tagName":"a","properties":{"href":"https://royalsocietypublishing.org/doi/10.1098/rspb.2017.2823"},"children":[{"type":"text","value":"Meta-analysis reveals weak associations between intrinsic state and personality (Niemelä & Dingemanse 2018)"}]},{"type":"text","value":"."},{"type":"element","tagName":"br","properties":{},"children":[]},{"type":"text","value":"\n"},{"type":"element","tagName":"em","properties":{},"children":[{"type":"text","value":"Niemelä, P. T., & Dingemanse, N. J. (2018). Meta-analysis reveals weak associations between intrinsic state and personality. Proceedings. Biological sciences, 285(1873), 20172823. "},{"type":"element","tagName":"a","properties":{"href":"https://doi.org/10.1098/rspb.2017.2823"},"children":[{"type":"text","value":"https://doi.org/10.1098/rspb.2017.2823"}]}]}]},{"type":"text","value":"\n"}]},{"type":"text","value":"\n"},{"type":"element","tagName":"li","properties":{},"children":[{"type":"text","value":"\n"},{"type":"element","tagName":"p","properties":{},"children":[{"type":"element","tagName":"a","properties":{"href":"https://bmcevolbiol.biomedcentral.com/articles/10.1186/s12862-016-0768-z"},"children":[{"type":"text","value":"The effect of dietary restriction on reproduction: a meta-analytic perspective (Moatt et al. 2016)"}]},{"type":"text","value":"."},{"type":"element","tagName":"br","properties":{},"children":[]},{"type":"text","value":"\n"},{"type":"element","tagName":"em","properties":{},"children":[{"type":"text","value":"Moatt, J. P., Nakagawa, S., Lagisz, M., & Walling, C. A. (2016). The effect of dietary restriction on reproduction: a meta-analytic perspective. BMC evolutionary biology, 16(1), 199. "},{"type":"element","tagName":"a","properties":{"href":"https://doi.org/10.1186/s12862-016-0768-z"},"children":[{"type":"text","value":"https://doi.org/10.1186/s12862-016-0768-z"}]}]}]},{"type":"text","value":"\n"}]},{"type":"text","value":"\n"}]},{"type":"text","value":"\n"},{"type":"element","tagName":"p","properties":{},"children":[{"type":"element","tagName":"strong","properties":{},"children":[{"type":"text","value":"Meta-analysis and research synthesis: an outlook"}]}]},{"type":"text","value":"\n"},{"type":"element","tagName":"ul","properties":{},"children":[{"type":"text","value":"\n"},{"type":"element","tagName":"li","properties":{},"children":[{"type":"element","tagName":"a","properties":{"href":"https://ecoevorxiv.org/ga2qz/"},"children":[{"type":"text","value":"Research Weaving: Visualizing the Future of Research Synthesis (Nakagawa et al., 2018)"}]},{"type":"element","tagName":"br","properties":{},"children":[]},{"type":"text","value":"\n"},{"type":"element","tagName":"em","properties":{},"children":[{"type":"text","value":"Nakagawa, S., Samarasinghe, G., Haddaway, N.R., Westgate, M.J., O’Dea, R.E., Noble, D.W.A., Lagisz, M., 2019. Research weaving: visualizing the future of research synthesis. Trends Ecol. Evol. 34, 224–238. "},{"type":"element","tagName":"a","properties":{"href":"https://doi.org/10.1016/j.tree.2018.11.007"},"children":[{"type":"text","value":"https://doi.org/10.1016/j.tree.2018.11.007"}]}]}]},{"type":"text","value":"\n"}]},{"type":"text","value":"\n"},{"type":"element","tagName":"p","properties":{},"children":[{"type":"element","tagName":"strong","properties":{},"children":[{"type":"text","value":"A key reference for how to conduct a meta-analysis"}]}]},{"type":"text","value":"\n"},{"type":"element","tagName":"ul","properties":{},"children":[{"type":"text","value":"\n"},{"type":"element","tagName":"li","properties":{},"children":[{"type":"element","tagName":"a","properties":{"href":"https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-017-0357-7"},"children":[{"type":"text","value":"Meta-evaluation of meta-analysis: Ten appraisal questions for biologists (Nakagawa et al. 2017)"}]},{"type":"element","tagName":"br","properties":{},"children":[]},{"type":"text","value":"\n"},{"type":"element","tagName":"em","properties":{},"children":[{"type":"text","value":"Nakagawa, S., Noble, D. W., Senior, A. M., & Lagisz, M. (2017). Meta-evaluation of meta-analysis: ten appraisal questions for biologists. BMC biology, 15(1), 18. "},{"type":"element","tagName":"a","properties":{"href":"https://doi.org/10.1186/s12915-017-0357-7"},"children":[{"type":"text","value":"https://doi.org/10.1186/s12915-017-0357-7"}]}]}]},{"type":"text","value":"\n"}]},{"type":"text","value":"\n"}]}],"data":{"quirksMode":false}},"frontmatter":{"id":1,"title":"Chapter 1: Getting started: Introduction to Meta-Analysis","description":"This chapter will introduce where meta-analysis fits into the scientific method, give some background, and examples.","next":"chapter2","prev":null}}},"pageContext":{"isCreatedByStatefulCreatePages":false,"slug":"/chapter1"}}