DOI: 10.5061/dryad.0vt4b8h6c
title: House finch leg color changes with infection

description: In numerous animals, dramatic coloration (e.g., bright red or yellow)
 often indicates potential fitness, but it is less clear whether subtle
 coloration in the same individuals (e.g., grey or brown) could also encode
 such signals. To determine if subtle coloration could indicate health in a
 bird species with colorful feathers, house finches (Haemorhous mexicanus),
 we used spectrometry to objectively quantify leg brightness and saturation
 before, six days after, and 13 days after captive individuals were
 inoculated with a naturally-occurring bacterial pathogen, Mycoplasma
 gallisepticum. We found that legs became less bright six days after
 infection (near the typical peak of infection), then more bright and less
 saturated at 13 days (entering the typical recovery period). These results
 suggest that subtle colors could reliably indicate current infection
 status, and therefore survival potential.
description: # House finch leg color changes with infection
 [https://doi.org/10.5061/dryad.0vt4b8h6c](https://doi.org/10.5061/dryad.0vt4b8h6c) Herein are the data and code used for formatting, analyzing, and creating figures for house finch leg color data per the associated manuscript. All formatting, analysis, and figure creation was conducted using the opensource R and R Studio software suite. ## Description of the data and file structure The data and their associated code are contained within a single folder. The main folder contains the following: * "Raw_data" -- a subfolder, which in turn contains 3 subfolders (see sub-bullets below) * "Reflectance Data 11_29 Pre" -- a secondary subfolder with 45 .txt files. Each file contains the band number for its associated bird, followed by "Reflection", the recording number for the individual bird, and a unique identifier. * "Reflectance Data 12_06 DPI6" -- as above, with the addition of an "Extra measurements" subfolder * "Reflectance Data 12_13 DPI13" -- as above * "Exp02_pre_sm_pegged.csv" -- a .csv file with the average reflectance (per 3 repeated measurements) observed at each wavelength (1-nm bins) between 300–700 nm for house finches (*Haemorhous mexicanus*) prior to inoculation with *Mycoplasma gallisepticum*. * "X" is a unique column id, "wl" is wavelength, and the remaining column headers are individual birds * "Exp02_dpi6_sm_pegged.csv" -- as above, but 6 days post-inoculation * "Exp02_dpi13_sm_pegged.csv" -- as above, but 13 days post-inoculation * "Exp02_VOI_pegged.csv" -- a .csv file where the first column is bird id (unlabeled), followed by B1 (brightness, summed reflectance of all recorded light), S2 (saturation, the max reflectance over the minimum reflectance), H1 (hue, peak wavelength), bird_num (the unique band id for a bird), and DPI (days post-inoculation). * "Tillman_PathLoadResults.xlsx" -- an Excel spreadsheet containing 3 sheets. The first two sheets ("PathLoadResults" and "PathLoadResults_minus2birds") show the pathogen load (Path_load*) and total eye score (Tot_eyescore) pre- and post-infection for individual birds (denoted by Band_ID). These two sheets also show the results of paired two sample t-tests with all birds ("PathLoadResults") and without ("PathLoadResults_minus2birds") two birds that showed path. load prior to inoculation. Lastly, Sheet1 is the same data as that in PathLoadResults, but in long format for later data analysis. * "HOFI_leg_brightness.html" and "HOFI_leg_brightness.Rmd" -- These are R Markdown files created to simplify and make transparent how the data were formatted, how the analyses were conducted, and how the figures were created. These files also contain a data index within the "Analysis" section. The .html file can be opened in an internet browser, where all code (and its output) will be visible. The .Rmd file works with R Studio to show the code, which can then be changed. ## Sharing/Access information These data should be publicly available via the open access Journal of Avian Biology: * 10.1111/jav.03187 ## Code/Software * R (version 4.3.2) * R packages: * pavo (version 2.9.0) * tidyverse (version 2.0.0) * ggpubr (version 0.6.0) * psych (version 2.3.9) * lme4 (version 1.1-35.1) * lmerTest (version 3.1-3) * emmeans (version 1.8.9) * nlme (version 3.1-163) * car (version 3.1-2) * MuMIn (version 1.47.5) * gridGraphics (version 0.5-1) * readxl (version 1.4.3) * R studio (version 2023.09.1 +494)