September 8, 2020

Guidelines for data on Dryad

 The American Naturalist has begun the process of creating a new editorial board position: 'Data Editors'. Their job will be to help facilitate and check compliance with the journal's open-data policies. We require publication of raw data and metadata on Dryad or equivalent public repositories, and we recommend including code to reproduce analyses. Exceptions can be made, to post the data but embargo public access for a set amount of time to allow authors to publish related papers, but we rarely get these requests.

It has come to our attention recently that compliance with our data policies is ...  not quite as effective as we'd like. This mostly comes down to missing material in the posted data, or unclear metadata. To help authors do a better job of meeting our data publication expectations, I began a committee composed of Bob Montgomerie, Paulinha Lemos, and Rob Knell.  They have produced the following Data Archiving Checklist, listing best-practices which authors may find useful in preparing materials for Dryad or other data archives. You may also find the DRYAD best practices list useful.

Checklist for preparing data to upload to DRYAD or other repository

 

*  assemble all of your data files used to prepare your paper

*  ensure that every observation is a row and every variable is a column

*  if you analyzed means rather than the raw data, also supply a data file with the raw data from which those means were calculated

*  from each file remove variables not analyzed

*  identify each variable (column names) with a short name (no spaces or symbols), preferably <10 characters long. Use an underline (e.g. wing_length) or camel case (e.g., WingLength) to distinguish words if you think that is needed. See the Google R style guide (https://google.github.io/styleguide/Rguide.html) and the Tidyverse style guide (https://style.tidyverse.org/syntax.html#object-names) for more information

*  prepare a README file that lists all of your data and code files with a brief description of the file and a list of all variable names and an explanation of each variable so that someone else could understand what that variable means (including units). See Dryad suggestions here.

*  save the README file as a text (.txt) file and all of the data files as comma-separated variable (.csv) files

*  if your data are in EXCEL spreadsheets you are welcome to submit those as well (to indicate colour coding and provide additional information (formulas etc) but each worksheet of data should also be saved as a separate .csv file.

*  Save each file with a short, meaningful file name (see DRYAD recommendations here), except the README file which should just be called README.txt

*  save all image, audio, and video files in formats recommended by DRYAD (here). You may wish to contact DRYAD or your Editor if the raw data files are too large.

*  upload all of your files to DRYAD or other repository and fill in all of the metadata and information requested by the repository, even if this is not required as it makes your data easier to find and understand

*  from the repository get a URL that can be used by editors and reviewers before your data are made public with a DOI

 

 

last updated 7 September 2020

September 1, 2020

 The Editorial Board of The American Naturalist has completed an evaluation of a paper by Pruitt JN , Howell KA , Gladney SJ , Yang Y , Lichtenstein JLL , Spicer MElise , Echeverri SA, and Pinter-Wollman N . 2017. Behavioral Hypervolumes of Predator Groups and Predator-Predator Interactions Shape Prey Survival Rates and Selection on Prey Behavior . The American Naturalist. 189:254–266

https://www.journals.uchicago.edu/doi/abs/10.1086/663680

A committee of six individuals, including both Associate Editors and outside research community members, were appointed by the Editor, Dan Bolnick, in late February 2020. They delivered their report on this in April 2020. After several rounds of comment by Dr. Pruitt and his co-authors, the committee requested that the Dryad repository be updated. This update has been completed (https://datadryad.org/stash/dataset/doi:10.5061/dryad.8q8p7)  and the committee and this Editor have no further concerns about this paper.

The concern identified by the committee is summarized here:

Inconsistency between sea star sample sizes reported in the paper, and the data provided. The paper reports a sample size of 28 sea stars. But there are only 19 lines of personality data for the sea stars, although in some data files a seastar with ID #20 is listed. In figures reporting sea star behavioral repeatability data, there are either 19 or 20 visible data points (Figs. A2-3, and Fig. A4, respectively), and the statistics reported in the paper seem consistent with a sample size of 19.

Based on communications from Dr. Pinter-Wollman and Dr. Pruitt, it appears that:

1) not all collected individuals were used, hence the difference between 28 collected individuals and the actual sample size in the study. This point is slightly confusing for readers but not significant enough to require publication of a correction, as the Methods do not state that 28 individuals were used.
2) A 20th individual of unknown original provenance, obtained from a laboratory setting, was included in the study but not in the Dryad repository. The committee suggested, and the authors agreed, that this can be fixed by updating the Dryad data repository to include the 20th individual. Note that this entails the addition of a new version of the data file, not a replacement [the original version remains]. From our point of view, the correction statement is sufficient to clarify what was absent in the original data file, and why. The Dryad repository has now been corrected as of August 18 2020. The .csv file in the update has a header that reads:
"Not all 28 sampled sea stars were used for the study. Note the 20th individual used in this study came from a teaching collection."
The Editorial Board remains concerned that the use of one individual of unknown provenance, in a sample of otherwise wild-caught sea stars, is a less than optimal experimental design, as it may inflate trait variance in a study of sea star behavioral variation. The origin of the 20th individual was not made clear in the published manuscript methods, nor was the rationale for its addition explained. However, the concern was deemed relatively minor, by the committee, as we do not have grounds to believe this changed the core results of the paper. We therefore accept the correction to the Dryad repository as sufficient to satisfy the minor concerns raised regarding this paper. Unless other concerns come to light that we are not presently aware of, we consider this paper to be valid and suitable for citing in future work.

Signed,
Daniel Bolnick
Editor-In-Chief, The American Naturalist
September 1, 2020