PABU_diet README

Files for the analysis of Painted Bunting (PABU) diet data (food abundance, foraging, metabarcoding) on Little Saint Simons, Island (LSSI), Georgia from the 2023 field season.

Directory structure:

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data-raw

• feather_meta.csv
  • csv file that contains metadata for feather samples collected

• food_abun

  • 2023_food_abundance_metadata.csv

    • csv file that contains the metadata associated with food abundance surveys

  • 2023_food_abundance_samples_weights_total.csv

    • csv file that contains the taxa classification ans weights of all arthropod/seed/berry food abundance surveys

  • 2023_plant_biomass.csv

    • csv file that contains the dry vegetation weight of the plants sampled during food abundance surveys

• foraging

  • behavioral_observations1.csv
    • csv file that contains a list of all timed foraging behavior throughout the study site

• metabarcoding

  • COI folder (arthropod)

    • AMPtk_COI.final.txt

      • txt tile with OTU data from the fecal samples

    • AMPtk_COI.mapping_file.txt

      • txt file with metadata to understand what amplicons were analyzed

    • AMPtk_COI.qiime.taxonomy.cleaned.txt

      • txt file with taxonomy information for the fecal samples

  • ITS folder (plant)

    • AMPtk_ITS.final.txt

      • txt tile with OTU data from the fecal samples

    • AMPtk_ITS.mapping_file.txt

      • txt file with metadata to understand what amplicons were analyzed

    • AMPtk_ITS.qiime.taxonomy.cleaned.txt

      • txt file with taxonomy information for the fecal samples

  • ggbc_cells.csv

    • csv file with names and metadata of plates sent to the GGBC

  • SampleTemplate_ggbc.csv

    • csv file with names of plate cells sent to the GGBC

data

• figures

  • food_abun

  • food_use

• food_abun

  • cleaned_food_abun_data.rds

    • rds file

  • food_abun.rds

    • rds file

• foraging

  • behav_obs.rds

    • rds file

  • foraging_clean.rds

    • rds file

• glms_real

  • berry_use.rds

    • rds file

  • grass.rds

    • rds file

  • lep_use.rds

    • rds file

  • other_insect_use.rds

    • rds file

  • seed_use.rds

    • rds file

  • spider_use.rds

    • rds file

• metabarcoding

  • COI folder (animal)

  • ITS folder (plant)

  • glm folder

• tables

  • arthro_otu.docx

    • docx file

  • arthro.docx

    • docx file

  • plant_otu.docx

    • docx file

  • plant.docx

    • docx file

R_scripts

• 01_food_abun.R

  • R script to clean food abundance data collected from PABU food sampling surveys.

• 02_food_abun_figures.R

  • R script to attempt to make figures from food abundance data.

• 03_foraging_obs.R

  • R script to clean PABU foraging observation data and filter for foraging.

• 04_foraging_figures.R

  • R script to attempt to make figures from foraging data.

• 05_metabarcoding_analysis_COI.R

  • R script to analyze bioinformatic output from DNA metabarcoding for COI (animals).

• 06_metabarcoding_analysis_ITS.R

  • R script to analyze bioinformatic output from DNA metabarcoding for ITS (plants).

• 07_metabarcoding_figures.R

  • R script to attempt to make figures from metabarcoding data.

• 08_metabarcoding_analysis_COI_more.R

  • R script to further analyze bioinformatic output from DNA metabarcoding for COI (animals).

• 09_metabarcoding_combined_analysis.R

  • R script for combined analysis bioinformatic output from DNA metabarcoding for COI and ITS.

• 10_diet_glms.R

  • R script that includes generalized linear models (GLMs) for cleaned diet data.

• 11_diet_lm_resids.R

  • R script for linear models with residuals for diet data.

• 12_glm_diet_figures.R

  • R script for figures for diet data resulting from glms.

• 13_species_tables.R

  • R script for tables of species level diet data.

• 14_glm_noU.R

  • R script that includes generalized linear models (GLMs) for cleaned diet data without unknown sex birds.

• 15_feathers_diet.R

  • R script that compiles diet and feather data which was sent to Dan.