Systematic Maps are, according to the Environmental Evidence Journal, “overviews of the quantity and quality of evidence in relation to a broad (open) question of policy or management relevance.” In simple terms, this means that documents are categorized according to the type, location, and publication information available for each work within a particular topic. Systematic maps are often used for environmental research, where it is particularly important to track the location of study sites. The spatial nature of a systematic map, particularly for environmental research, means that academics often use some kind of geographic map to analyze and present their information. Understanding the academic community’s familiarity with the R programming language, we built a webapp using R Shiny that could automate certain parts of creating a systematic map for environmental research.
Forestr is an online platform for interactive visualisations of forest plots.
In evidence synthesis it is relatively easy to find published literature on a given topic, and to record what the search string was used in which database, how many records were found, how many were used or not used and why. It is much more difficult to be systematic in searching and recording grey literature.
metadat is an R package that collates and acts as a repository for meta-analytic data across diverse research fields (e.g., psychology, education, ecology, evolution). These data can be used freely for meta-analytic training to demonstrate concepts and complex analyses, re-analysis, and updating past meta-analyses. Meta-analysts from any field can contribute data and/or examples of data use.
This function dynamically generates an analysis report (in html, pdf, or docx format) based on a model object. The report includes information about the model that was fitted, the distribution of the observed outcomes, the estimate of the average outcome based on the fitted model, tests and statistics that are informative about potential (residual) heterogeneity in the outcomes, checks for outliers and/or influential studies, and tests for funnel plot asymmetry. A forest plot and a funnel plot are also provided. References for all methods/analysis steps are also added to the report and cited appropriately. Additional functionality for reports based on meta-regression models will be incorporated soon. The function is already part of the ‘devel’ version of the metafor package.
Evidence synthesis (ES) is the process of identifying, collating and synthesising primary scientific research (such as articles and reports) for the purposes of providing reliable, transparent summaries. The goal of this project is to collect, integrate and expand the universe of available functions for ES projects in R, via our proposed metaverse package. Like tidyverse, metaverse is envisioned as a collector package that makes it straightforward to install a set of functions – currently located in separate packages – for a common purpose.
Paperweight, driven by a combination of natural language processing (NLP) algorithms. In the evidence synthesis process, the first steps typically require reviewers to manually build a database of articles and journals they want to summarize. This process entails an exhaustive search of Google Scholar using manually chosen keywords. This approach is vulnerable to bias since the reviewer might be more likely to find certain articles or journals in their review over other ones, depending on the selected search keywords. Tackling this problem, Paperweight seeks to remove the need for a reviewer to manually choose keywords to form their search queries.
Full-text PDFs are almost always the most reliable source of information from academic articles. Even though several resources allow for the extraction of data from full-text documents, most of the time the information is incomplete, inaccurate, or not available. PDFs were created to look great, not to extract data from. So, when you try to copy/paste from PDF you often get unexpected results. In this first version the project allows users to easily copy text from a PDF and attempts to automatically identify the references.
Citations downloaded from bibliographic databases and other resources, such as Google Scholar, are often missing certain details like abstracts or volume/page details that are important for a variety of reasons, such as screening in systematic reviews or locating full text documents. This functionality is intended to be used for filling in missing information from a set of citation files, including abstracts.
Automation tools are speeding up the conduct of evidence synthesis. However, the uptake of these tools amongst reviewers are slow. Potential barriers to use are; 1) the tools often operate in isolation, 2) reviewers need to manipulate their citation data into a specific format to use the tool, and 3) different tools require different levels of programming or computing expertise.
robvis is an R package that allows users to quickly visualise risk-of-bias assessments performed as part of a systematic review. It allows users to created weighted bar-plots of the distribution of risk-of-bias judgements within each bias domain, in addition to “traffic light” plots of the specific domain-level judgements for each study. The resulting figures are formatted according the risk-of-bias assessment tool use to perform the assessments (currently supported tools are ROB-2, ROBINS-I and QUADAS-2). An associated Shiny app provides a user-friendly interface for the tool.
The ROSES forms were developed to improve the standards of evidence synthesis reporting and the transparency of the methods used for reviews and maps. The website (www.roses-reporting.com) aims to help adoption of the ROSES forms as well as improve the barrier to entry on using the ROSES forms in the least obtrusive way possible. In this project we’ve been working to improve the user experience, increasing efficiency and helping reviewers get the most out of the forms and website. We will be releasing the new version of the ROSES website shortly.
Defining a good search strategy for systematic reviews can be a particularly challenging task. Some of the problems encountered are: when asking two people for a strategy they will get totally different outputs, the number of hits is prohibitively high, there are missing relevant references because a specific keyword was omitted, few means of validating search strategies exist, it is difficult to adapt the strategy for other databases, errors may be introduced when adapting strategies between databases, etc.
This project provides an easy-to-use template for web visualisations of environmental evidence maps. Thalloo is a combination of map components and a Jekyll theme that enable quick, simple, and customisable deployment of a web-based tool to display evidence maps. The framework has the following features: i) Visual clustering and display of categorical data. Given a display category (e.g. crop, commodity), and a custom colour palette, points are displayed on a map. Depending on the zoom level and extent, points are clustered dynamically for best display. Any cluster can be selected to see the full metadata about the evidence points it contains; ii) Filtering. Data can be filtered by property in real time, using multiple filters within a property, and using multiple properties to filter; iii) Slicing of dimensionality. Given continuous data (e.g. publication year, time, or an effect size), the map allows real time ‘slicing’ of the dataset along one or many dimensions; iv) Abstract and funding logos. Provide attribution to your funders and partner institutions by including their logos at the top of your map view.
DiscussionsLimitations and biases of commercial bibliographic databases | Proposed Academic Paper
Reliable evidence synthesis requires access to a comprehensive, unbiased body of literature that can be searched for relevant information. Systematic reviewers typically search multiple (upwards of 10) bibliographic databases to identify sets of search results that might yield relevant results. Access to these databases is often restrictively expensive, hampering efforts to synthesise evidence by smaller organisations and groups from low- and middle- income countries, for example. When reviewers export references from these databases they must typically do so in small batches (this supposedly stops people from replicating commercial databases for profit): for Web of Science this must be done in batches of 500, which can add considerable time to a review with 20,000 search results or more! Finally, databases such as Web of Science exacerbate publication bias by selecting journals and publishers that are perceived to be of ‘high impact’, for example using citation indices. So, these resources may be expensive, hard to use, and offer a biased selection of evidence. In order to facilitate evidence synthesis and to reduce bias in how information is indexed and found, we call for the production of an Open Source, Open Access on-stop-shop database that catalogues all known academic research. Since tables of contents are freely available online, technology exists that can produce such an important and useful tool.
Future of research synthesis - Utopia or dystopia? | Proposed Academic Paper
The number of publications has been increasing exponentially, and as a result, so has the research field of evidence synthesis. Consequently, there is now a need to maintain the quality, currency and credibility of evidence synthesis approaches. Within this commentary, we aim to provide a vision for evidence synthesis as a fundamental tool for generating and guiding decision-making. This paper will be aimed at all stakeholders, including researchers, institutions, and the broader general community.
R for Evidence Synthesis | Proposed Academic Paper
R is a widely-used, open source programming language and statistical environment. Users are able to contribute add-ons to R functionality in a standardised way by developing new software ‘packages’. However, identifying which packages are most useful for a specific task can be challenging, particularly for evidence synthesis (ES) projects which typically include a number of discrete tasks, many using packages that may have been designed for other purposes. Consequently, a valuable tool for future researchers (and hackathons) would be a ‘map’ of available software packages, showing how those packages apply to ES. This would help guide new users through effective workflows, as well as identifying parts of the evidence synthesis process that are currently well supported in R, or conversely, in need of further software development. This project is currently in the data collection phase, wherein participants systematically search for R packages of potential value to ES projects and catalogue their findings in a structured way. The intended output is an academic article describing our findings, linked to a live database of R packages, the functions they contain, and the specific ES tasks that they each solve.
Making primary research synthesis ready | Proposed Academic Paper
Evidence synthesis relies on primary research that is reliable, transparent, and where key information is readily accessible and useful for broader synthesis. We propose a succinct list of ideal attributes that primary research articles should report as standard so that they are more likely to be found and included in evidence syntheses. We discuss how implementing these changes to primary research reporting might be incentivised for authors, peer reviewers, editors, journals, and institutions such changes and this broad across medicine, environment, ecology, and social science disciplines.