Flow diagram for journal policy study.

This flow chart illustrates the journal screening process and shows the number of observations excluded and reasons for exclusion at each phase of screening. Data are available at https://osf.io/d2sa3/, in the journal policy study folder [12]. (TIF)</p

The level of methodological detail required depends on the reader.

All readers need an overview of the study design, methods used to answer the research question, and information needed to assess scientific rigor and the risk of bias. These details should always be presented in the methods section of the paper. While fewer readers need the details required to reproduce or reuse the method, these individuals are particularly important because they are most likely to perform follow-up experiments. Very simple methods that can be explained and reproduced easily may be described in the methods section. Protocol repositories or method or protocol journals are better for many methods, as it is difficult to provide the details needed to implement or reuse the method within the methods section.</p

Decision tree for the responsible use of shortcut citations.

This decision tree helps authors to prepare reproducible methods sections by determining when to use shortcut citations and when to share detailed methods through protocol repositories or methods articles.</p

Reasons for citing a resource in the methods section of a paper.

The box plots illustrate the number of times that each type of citation was used, per article, for neuroscience (yellow), biology (blue), and psychiatry (red). The horizontal line within each box shows the median, whereas the top and bottom of the box show the 25th and 75th percentiles. Whiskers represent the furthest datapoint that is within 1.5* the interquartile range from the box. Dots above the whiskers show outliers. Data are available at https://osf.io/d2sa3/, in the methodological citations study folder [12]. (TIF)</p

Age of the youngest, median, and oldest shortcut citations within a paper for each field.

This table shows summary statistics for Fig 3A. IQR, interquartile range. Data are available at https://osf.io/d2sa3/, in the methodological citations study folder [12]. (DOCX)</p

Shortcut citations in example paper 2.

This diagram maps the process of finding methodological details for a neuroscience paper in the fourth quintile of probable + possible shortcut citations in the shortcut citation chains study. The diagram shows the publication year and type of each cited resource and whether the resource was behind a paywall. Text on the diagram provides information, describes problems encountered when searching for details about the cited method.</p

Reasons for citations in the methods section.

Methods sections are often missing essential details. Methodological shortcut citations, in which authors cite previous papers instead of describing the method in detail, may contribute to this problem. This meta-research study used 3 approaches to examine shortcut citation use in neuroscience, biology, and psychiatry. First, we assessed current practices in more than 750 papers. More than 90% of papers used shortcut citations. Other common reasons for using citations in the methods included giving credit or specifying what was used (who or what citation) and providing context or a justification (why citation). Next, we reviewed 15 papers to determine what can happen when readers follow shortcut citations to find methodological details. While shortcut citations can be used effectively, they can also deprive readers of essential methodological details. Problems encountered included difficulty identifying or accessing the cited materials, missing or insufficient descriptions of the cited method, and shortcut citation chains. Third, we examined journal policies. Fewer than one quarter of journals had policies describing how authors should report previously described methods. We propose that methodological shortcut citations should meet 3 criteria; cited resources should provide (1) a detailed description of (2) the method used by the citing authors’, and (3) be open access. Resources that do not meet these criteria should be cited to give credit, but not as shortcut citations. We outline actions that authors and journals can take to use shortcut citations responsibly, while fostering a culture of open and reproducible methods reporting.</div

Methods repositories used in neuroscience, biology, and psychiatry.

Values are n (% of articles). Data are available at https://osf.io/d2sa3/, in the methodological citations study folder [12]. (DOCX)</p

Comparing methods of sharing detailed protocols.

JOVE, Journal of Visualized Experiments; N/A, not applicable; OA, open access. * protocols.io offers a partnership with PLOS ONE where authors can publish a methods article linked to their protocol. (DOCX)</p

Understanding the use of citations in the methods sections, methods supplements, and methods repositories.

(A) The most common reasons why authors cite papers in the methods section are to explain how a method was performed, give credit or specify what was used (who or what), or provide context or a justification (why). These numbers should be regarded as approximations. Small changes in the wording or position of the reference could alter the categorization, as could variations in reader expertise (see limitations). (B) Citations and shortcut citations often appear in the methods section of published papers. In the violin plot on the right, values for probable shortcut citations are shown in darker hues on the left half of each violin, whereas possible shortcut citations are shown in lighter hues on the right side of each violin. Most papers contain both probable and possible shortcut citations. Dashed lines on each half of the violin indicate the 25th, 50th, and 75th percentiles. Median (25th percentile, 75th percentile) for the number of probable shortcut citations per paper were as follows: neuroscience 3 (1, 6); biology 2 (1, 4); psychiatry 3 (1, 5). Median and 25th and 75th percentiles for the number of possible shortcut citations per paper were as follows: neuroscience 2 (1, 4); biology 1 (0, 2); psychiatry 2 (1, 4). (C) Methods are often shared in supplements but are less likely to be deposited on methods repositories. Percentages may not total 100% due to rounding errors. Data are available at https://osf.io/d2sa3/, in the methodological citations study folder [12].</p