Things to consider

• topic

• audience

• reputation or impact factor

• cost; open access (OA) journals can be $3000+ per article

Look over the journal’s “scope”

For example, Can J Fish Aquat Sci

• Do you read articles in this journal?

• Do people you know publish in this journal?

• Are the articles you cite published in this journal?

• What is known about the editorial process?

• Is the editorial office friendly & helpful?

• Is the review process transparent & timely

• Are the reviews collegial & helpful?

• Frequency with which the average article in a journal has been cited in a particular year or period

• IF’s can be used to approximate the prestige of journals

• Many people, including search & tenure committees, pay close attention to journal IF’s

Number of citations in year t divided by total publications during the previous two years

\[ \text{IF}_t = \frac{citations_t}{pubs_{t-1} + pubs_{t-2}} \]

Web of Science

• Use Web of Science to find a journal of interest

• Enter the name of the journal and its impact factor here

Guidelines list important details about

• article type & length

• section names & requirements

• formatting of references, tables & figures

• for example, Can J Fish Aquat Sci

Page charges vary widely among journals; options include

• OA (anyone can access) = higher flat rate

• journal subscribers = lower flat rate (+ color figures)

• membership (eg, PeerJ)

• some are free (eg, Can J Fish Aquat Sci)

• Navigate to the website for the journal you chose earlier to find its impact factor

• Find the publication cost(s) and enter it here

2 reasons for (good) cover letters:

1. publishing is a business—will your article make them money?

2. editors are busy—can you follow directions?

Dear Sirs,

I am sending you our manuscript entitled “Patterns in fish size across lakes”. We would like to have the manuscript considered for publication in your journal.

Please let me know of your decision at your earliest convenience.

Sincerely yours,
Lance Manion, PhD

• Similar articles previously published by the target journal

• Relevant works by you or co-authors that are previously published or under consideration by other journals

• Any prior discussions with editor(s)

• Technical specialties required to evaluate your paper

• Potential reviewers and their contact information

• Reviewers to exclude

• include any graduate degrees in the editor’s name

• if the editor’s name is unknown, use the relevant title (eg,“Managing Editor”, “Editor-in-Chief”)

• Never use “Sirs”, “Mrs.” or “Miss”

• Don’t use too much jargon or include too many acronyms

• Don’t over-sell your findings or their significance (eg, avoid “novel” or “ground-breaking”)

• Don’t name drop

• Don’t drone on and on (aim for a one-page letter)

Up-Goer Five Text Editor restricts you to the 1000 most commonly used words

Describing a rocket via XKCD

• Use the Up-Goer Five Text Editor to write a 4-5 sentence description of your research interests

• When finished, click the “PERMA-LINK” button and copy/paste the URL into GitHub Discussion - https://github.com/course-fish521-2023/assistance/discussions/5

The increasingly important online side of journals allows authors to include additional info in supplementary material

• methods (data & code)

• results (tables & figures)

• Including the information necessary to reproduce analyses & results aids in the review process

• It also helps your future self and others understand what was done

We are witnessing an increasing number of examples where the original analysis cannot be reproduced

• For example, a group of Amgen scientists could only confirm the results in 6 out of 53 cancer studies (Begley & Ellis 2012)

According to the National Science Foundation:

The calculation of quantitative scientific results by independent researchers using the original data and methods

Reproducibility can be further broken down

• empirical (eg, sample IDs, sampling gear, instrument settings)

• statistical (eg, which statistical tests, what model parameters)

• computational (eg, code, software, hardware)

“A standard and easily recognizable way for organizing the digital materials of a project to enable others to inspect, reproduce, and extend the research.”

1. Project organization should follow the conventions of the scientific community

   • The community might be a lab group
   • The convention(s) support tool building

1. Project organization should follow the conventions of the scientific community

2. Maintain a clear separation of data, methods and output

   • Separate data from code
   • Separate cleaning, analysis & output code

|-code
  |-01_data-ingest.R
  |-02_data-cleaning.R
  |-03_data-QAQC.R
  |-04_model-fitting.R
  |-05_create-figures.R
|-data
  |-skagit_steelhead-escapement.csv
  |-skagit_river-flow.csv

1. Project organization should follow the conventions of the scientific community

2. Maintain a clear separation of data, methods and output

3. Specify the computational environment

   • Which software/package(s) and what version(s)?
   • Ranges from simple text description to self-contained environments

• Increased efficiency, simplified file management and streamlined workflows

• Increased visibility and scientific impact

• Ability to return later and understand the process

Organize your compendium so another person knows what to expect from the plain meaning of the file and directory names

1. Licensing

   • Who can (re)use the work?
   • Are there restrictions?
   • Many depositories require Creative Commons licenses

1. Licensing

2. Version control

   • Facilitates private collaboration among colleagues on the project
   • Allows for distribution and maintenance of the compendium in the future

1. Licensing

2. Version control

3. Persistence

   • Consider the “life span” of the analysis
   • A Digital Object Identifier (DOI) is more permanent than a URL

1. Licensing

2. Version control

3. Persistence

4. Metadata

   • Publishing data with a DOI requires a description of the data themselves
   • Who, what, where, when, how

1. Licensing

2. Version control

3. Persistence

4. Metadata

5. Location

   • GitHub is very common
   • Zenodo, Figshare are alternatives

One could always create a structure from scratch

Alternatively, consider some existing tools

• Jeff Hollister’s {manuscriptPackage}

• Carl Boettiger’s {template}

• Ben Marwick’s {rrtools}