Translocations to reestablish populations of the mountain yellow-legged frog

Authors of this repository

Roland A. Knapp (roland.knapp(at)ucsb.edu)

Mark Q. Wilber (mqwilber(at)gmail.com)

Overview of contents

This repository is organized as a reproducible research compendium, and describes frog translocations to reestablish populations of the endangered mountain yellow-legged frog. It contains data on frog survival following translocations conducted during the period 2006-2020, R code to identify predictors of survival and estimate population viability, a notebook to document translocation-related analyses, and a manuscript (submitted). Throughout this repository, frog populations are referenced only by 5-digit unique site identifiers. No site names or x-y coordinates are provided to protect these sensitive populations to the maximum extent possible.

This repository contains the following directories and files:

• code/ directory: Rmd and qmd files to create and analyze the project datasets, and create figures.
• data/ directory: Raw and cleaned data, and map data/layers.
• doc/ directory: Manuscript and notebook files.
• out/ directory: Output files, including files related to the viability analyses.

Notebooks

A notebook describing dataset creation and analysis is available in the doc/notebook directory. Link is to a README file that describes how to view the notebook directly from GitHub.

Reproducing this analysis

Instructions

1. Install the package manager anaconda or miniconda (https://docs.continuum.io/anaconda/install/).
2. Build the conda environment specified in the environmental.yml to install most of the R packages needed to run the analysis. This can be done on the command line using the command
   • conda env create -f environment.yml.
   • See link for details about conda enviroments.
3. Activate the environment in the terminal
   • conda activate r_env_translocation
4. NOTE: You don't have to use the conda environment and can instead use your native R build. Just ensure you have the packages installed that are listed in the environment.yml file.
   • For Linux, we have found that to install the R package devtools you are often prompted to install additional software outside of R. Linux typically tells you what additional packages you need to successfully install devtools in any error message you might get when installing this R package.

Running the Makefile

1. First, run make install_packages to ensure that you have the necessary packages installed in your R environment.
2. To run all of the analyses, type make all in the command line.
3. To run only the translocation analysis, execute make trans_analysis in the command line.
4. To run only the viability analysis, execute make viability_analysis in the command line.
5. To clean your directory of extraneous files create during these runs, execute make clean in the command line.

Compiling journal-formatted PDF documents

1. Render translocation.qmd to latex format.
2. From the doc/manuscript/ subdirectory, run python convert_qmd_to_pnas_latex.py in the command line.
3. To compile the journal-formatted PDFs, run the following in the command line:
   • pdflatex translocation_pnas.tex, bibtex translocation_pnas, pdflatex translocation_pnas.tex, pdflatex translocation_pnas.tex
   • pdflatex translocation_pnas_SI.tex, bibtex translocation_pnas_SI, pdflatex translocation_pnas_SI.tex, pdflatex translocation_pnas_SI.tex
4. If the files fail to compile due to missing latex packages, install packages and rerun the code. In Linux/Ubuntu, packages can be installed using tlmgr install <package_name>.

Contact

Roland Knapp, Research Biologist, University of California Sierra Nevada Aquatic Research Laboratory, Mammoth Lakes, CA 93546 USA; rolandknapp(at)ucsb.edu, https://mountainlakesresearch.com/roland-knapp/