Repository for an R Markdown (Rmd) Template for Automating U.S. Fish and Wildlife Service Weir Data Series Reports

Author: James K. Boersma
Point of Contact: James Boersma ([email protected])
Repository Type: R Markdown template
Year of Origin: 2025
Version: 1.0.0
DOI: Not available

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Suggested Citation

Boersma JK. 2025.
Repository for an R Markdown template for automating U.S. Fish and Wildlife Service Weir Data Series Reports.
U.S. Fish and Wildlife Service, Kenai Field Office software release. Soldotna, Alaska.

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Author ORCID

• James K. Boersma: 0009-0000-6098-1160

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Overview

This repository provides a reproducible R Markdown template for automating U.S. Fish and Wildlife Service (USFWS) Data Series Reports for weir monitoring projects. The template automates:

• Estimation of missing fish passage
• Stratified age-sex-length (ASL) composition summaries
• Integration of formatted maps, tables, and figures

The output is a Microsoft Word document styled using a USFWS-compliant .docx template.
Users should customize the Rmd, bib, functions, Map, and Code directories to fit their specific project needs.

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Repository Contents

File/Folder	Description
README.md	This file.
LICENSE.md	Generic USFWS license.
DISCLAIMER.md	Standard USFWS disclaimer.
.csl	Citation style files for formatting references.
template.docx	Word template for formatting USFWS Data Series Reports.
Data-series-template.docx	Example compiled output.
Data series template.rmd	Main R Markdown file. Users should edit this.
Code/	R scripts for missing passage and ASL estimation.
Data/	Tidy CSVs containing raw passage and ASL data.
functions/	R helper functions for plots, tables, maps, and text. Customizable.
images/	Static images, logos, or photos.
Map/	Shapefiles for adding spatial detail to maps.
Output/	Generated outputs (e.g., CSV summaries).
Python313/	Python tools for reference updates and .docx post-processing.
renv.lock, renv/	Reproducible R environment using renv.
references.bib	BibTeX reference file. Users should edit this.
updated_refs.py	Python script to retrieve citations from DOIs.
temp_docx/	Temporary .docx folder for header/footer/alt text updates.

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Data Format Notes

ASL Data (Data/ folder):

• Date: Julian date of sampling
• Age: European-style format (e.g., 2.1 means total age = 2 + 1 + 1 = 4)
• Sex: M = Male, F = Female
• MEFL: Mid-eye to fork length (mm)
• Species: Common salmon names; DV = Dolly Varden
• Vial, Tag_No, Tag_col: Genetic/tag metadata (not used in current template)

Passage Data:

• Date: Julian date of complete time series (observed and missing)
• Species columns: Common names for salmon, DV (Dolly Varden), Unk (unidentified)
• M_ prefix columns: Indicates missing/partial days
  • NA: full count
  • 0: no fish counted
  • >0: partial count

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Standard Operating Procedure

1. Run the missing passage estimation script to prepare passage data and ensure ASL weighting is accurate.
2. Run the ASL analysis script to generate composition summaries.
3. Update the .bib file and R Markdown content.
4. Knit the Data series template.rmd to produce the .docx report.
5. Run the Python post-processing script to insert alt text, headers, and footers into the final Word file.

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Background Knowledge

Using this template assumes familiarity with:

• Markdown and LaTeX (for formatting)
• R and R Markdown (for automation and reproducibility)
• Python (for DOI lookups and Word post-processing)

To reproduce the computing environment, run:

renv::restore()