Date of last update: 2025-08-01

Repository contents

Bd_colouration_project/
├── data/
│    └── Bd_coloration_metadata.csv -> Final dataset used for statistical analysis
| analyses, including frog and Bd infection information.
│    └── Black_RGB_KC.csv -> RGB reflectance values (mean and sd) of the black ROIs
| for Kaw and Cacao populations.
│ └── Black_RGB_M.csv -> RGB reflectance values (mean and sd) of the black ROIs for
| Mataroni population.
│ └── Black_RGB_N.csv -> RGB reflectance values (mean and sd) of the black ROIs for
| Nouragues population.
│ └── Black_RGB_PF.csv -> RGB reflectance values (mean and sd) of the black ROIs for
| Petit Matoury and Mont Fortuné populations.
│ └── Yellow_RGB_KC.csv -> RGB reflectance values (mean and sd) of the yellow ROIs
| for Kaw and Cacao populations.
│ └── Yellow_RGB_M.csv -> RGB reflectance values (mean and sd) of the yellow ROIs
| for Mataroni population.
│ └── Yellow_RGB_N.csv -> RGB reflectance values (mean and sd) of the yellow ROIs
| for Nouragues population.
│ └── Yellow_RGB_PF.csv -> RGB reflectance values (mean and sd) of the yellow ROIs
| for Kaw and Cacao populations.
├── scripts/
└── Effects_Bd_coloration.R -> R script to reproduce analyses

Description of "Bd_coloration_metadata.csv"

This CSV file contains the information regarding the Dendrobates tinctorius individuals sampled in 2023, their measurements, and the ddPCR results (Bd infection status and infection loads).

• Site: Name of the population
• Sample_ID: Unique ID for each D. tinctorius individual sampled
• Target: Specific DNA sequence being amplified and detected (pathogen Bd)
• Supermix: Premixed reaction buffer used in ddPCR containing all necessary reagents (excluding dUTP) for probe-based amplification
• DyeName: Fluorescent dye linked to a probe, identifying which target is measured (FAM for Bd)
• Concentration_1/2/3: Number of target DNA copies per microliter of reaction, based on
• the proportion of positive to total droplets for each ddPCR run
• Accepted_1/2/3: Total number of droplets successfully generated and analyzed from
• a sample that passed quality control thresholds for each ddPCR run
• Positive_1/2/3: Number of droplets containing detectable levels of the target DNA
• (showing a fluorescence signal above threshold) for each ddPCR run
• Negative_1/2/3: Number of droplets that do not contain the target DNA and show no
• detectable fluorescence for each ddPCR run
• freq:Number of times that a ddPCR was run for each sample
• Infected:Outcome of ddPCR regarding Bd infection (final decision)
• Bd.load_co: Number of Bd DNA copies detected per μl of each swab sample
• Sex: Sex of the individual (Female, Male, or Juvenile)
• Weight: Weight of the frog (in grams)
• SVL: Snout-vent length of the frog (in cm)

Note: any NA cells represent not applicable data (e.g., NA for juveniles' sex).

Description of "Effects_Bd_coloration.R"

R code for reproducing the analyses and visualizations presented in the article, including statistical tests and figure generation.

R version 4.4.2 (2024-10-31 ucrt)
Platform: x86_64-w64-mingw32 (64-bit)
Running under: Windows 11

Data maniuplation and organization

library(tidyverse) # 2.0.0
library(dplyr) #1.1.4
library(stringr) # 1.5.2
library(purrr) # 1.1.0
library(magrittr) # 2.0.4
library(here) # 1.0.2

Visualization

library(ggplot2) # 4.0.0
library(ggpubr) # 0.6.1
library(ggrepel) # 0.9.6
library(colorspace) # 2.1-1

Statistical modeling and inference

library(MuMIn) # 1.48.11
library(car) # 3.1-3
library(effects) # 4.2-4
library(Matrix) # 1.7-1
library(lme4) # 1.1-37
library(lmerTest) # 3.1-3
library(DHARMa) # 0.4.7
library(MASS) # 7.3-65
library(ggeffects) # 2.3.1
library(emmeans) # 1.11.2-8
library(smatr) # 3.4-8

Circular data analysis (Hue analysis)

library(bpnreg) # 2.0.3
library(circular) # 0.5-2
library(signal) # 1.8-1