Csik-etal-Functional-Ecology

This repository contains the code and data for reproducing Csik et al. in prep (to be submitted to Functional Ecology): "TITLE HERE" (URL HERE)

The DOI for this code and data repository is managed through Dryad with DOI number NUMBER HERE (LINK HERE).

Title:

Authors: Samantha R. Csik, Bartholomew P. DiFiore, Krista Kraskura, Emily A. Hardison, Joseph S. Curtis, Erika J. Eliason, Christopher L. Jerde, Adrian C. Stier

Abstract:

Repository Structure

Csik-etal-Functional-Ecology
  |_ code
  |_ data
    |_ correlations
      |_ outputs
    |_ foraging
      |_ outputs
      |_ raw
    |_ heart_rate
      |_ inventory_files
      |_ outputs
      |_ raw
    |_ metabolism
      |_ outputs
    |_ metadata
  |_ figures
    |_ main_text
    |_ other
    |_ supplemental
  |_ media

Software

These analyses were performed in R (version 3.6.3).

Code

Code is meant to be run in the order designated by the file name numbers (e.g. 0_libraries.R should be run first, 15_in_text_summary_stats.Rmd should be run last). The only exception to this is the FR_JAGS series (number 11) -- only 11c_FR_JAGS_plotting.R needs to be run (both 11a_FR_JAGS_functions.R and 11b_FR_JAGS_model.R are sourced into this file and do not need to be opened separately to run analyses).

At the start of each script and RMarkdown file, you will find a brief summary of the analyses to follow, an outline of code chunks/subsections, any required packages, and required data (along with their file paths for ease of locating).

Data

The following three files are the primary data used for all analyses. Their metadata are detailed below:

* data/heart_rate/outputs/processed_heart_rates.csv

• date: date/time of data point collection
• temp: acclimation temperature
• lobster_id: unique lobster identifier
• hr: heart rate (beats min^-1)
• QI: Quality index score ranging from 0 (good) to 3 (poor); NOTE: these data have been visually assessed for quality and therefore any hr with a QI = 1-3 was determined to still be an accurate measure.

* data/metabolism/metabolic_traits.csv

• temp: acclimation temperature
• ID: unique lobster identifier
• BW: body weight of lobster (g)
• SMR: standard metabolic rate (mg O₂ kg^-1 min^-1), calculated as the 15th percentile MO₂ measurement
• MMR: maximum metabolic rate (mg O₂ kg^-1 min^-1), calculated as the fastest rate of linear O₂ decline over a 60s inverval
• AAS: absolute aerobic scope (mg O₂ kg^-1 min^-1); calculated as MMR-SMR
• FAS: factorial aerobic scope (unitless); calculated as MMR/SMR

* data/metabolism/epoc.csv

• temp: acclimation temperature
• ID : unique lobster identifier
• spar : the smoothing level applied to the recovery profile (see function smooth.spline parameters)
• EPOC_full : total EPOC (i.e. recovery costs; mg O₂ kg^-1); represents the integrated area under the smoothed line at a particular spar
• end_EPOC_min : total recovery time (min); the time it takes for for the oxygen consumption rate (MO₂; the smoothed line) to reach SMR
• SMR : standard metabolic rate (mg O₂ kg^-1 min^-1), calculated as the 15th percentile MO₂ measurement
• SMR_integrated_full : cost of SMR (area integrated from SMR to 0 mg O₂ kg^-1 min^-1)
• SMR_threshold : the value used to calculate EPOC; here, we consider an individual recovered when oxygen consumption rates fall within 20% of SMR
• EPOC_1hr : EPOC from the start of the measurement (i.e. MMR) until 1 hr post exercise (up to EPOC_5hr; units = mg O₂ kg^-1)
• MO2_1hr : oxygen consumption rate (mg O₂ min^-1) at 1 hour post exercise (i.e. MMR; up to MO2_5hr)
• end_EPOC_mmr : recovery time (min) to reach 50% of MMR
• EPOC_mmr : EPOC at 50% of MMR
• MO2_mmr : the oxygen consumption rate at 50% of MMR
• MMR : maximum metabolic rate (mg O₂ kg^-1 min^-1), calculated as the fastest rate of linear O₂ decline over a 60s inverval

* data/foraging/raw/foraging_assay_data.csv

• date: date the foraging asssay began on (each assay ran for 24h)
• trial: trial number; feeding assays were replicated three times per lobster at each of the five prey densities
• lobster_id: unique lobster identifier
• Initial: number of mussels available at the start of the feeding assay
• Killed: number of mussels consumed by the end of the feeding assay
• temp: acclimation temperature

Figures

• /main_text: contains pdf versions of Figures 1, 2, 3, 4, & 5 found in the main text of the manuscript
• /supplementary: contains pdf version of Figures S1, S2, S3, & S4 found in the supplementary text
• /other: contains plots of raw heart rate data (bpm & ecgs) used for manual data quality assessments

Media

Experimental photos used in this README.

Curious about what some of our experimental trials look like?