READ ME file for data and analyses appearing in: 
"Yearly and seasonal variation in the food of red knot chicks in Alaska"

Roos C. I. Winters, Judith van Bleijswijk, Jan A. van Gils, James A. Johnson, Theunis Piersma, Zachary M. Pohlen,  Wietse Reitsma, Tim Oortwijn 

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The data is analysed using 2 scripts and 7 datafiles (of which 2 (no.6 and no.7) are generated in the scripts) 

Data files include 
1. Roos_data_and_357_358.xlsx
2. Mapping_file_all.xlsx
3. Negative_control_list.xlsx
4. snowmelt.xlsx
5. pitfalls_2022_23_24.xlsx
6. filtered_family_data_long_new.xlsx
7. chicks.xlsx

Scripts include 
1. data_preparation.R 
2. data_analysis.R 

METADATA 1. snowmelt.xlsx
This file contains satellite-derived data on the date at which the tundra at our study site near Nome, Alaska was 50% snowfree. 

Year 				Year 
Snowmelt_DoY 		Day-of-year snowmelt date 

	
METADATA 2. Roos_data_and_357_358.xlsx
This file contains the fractional number of reads per ASV for all faecal samples analysed using DNA barcoding

#OTU_ID									Amplicon sequence variant number
NIOZ398.003.004 - NIOZ358.079.090 		Read count per sample 
identity								Percentage sequence identity between the ASV and its best match in the reference database used for taxonomic assignment.
taxonomy								Full taxonomy (kingdom to species)

METADATA 3. Pitfalls_2022_23_24.xlsx

This file contains information on the identification of arthropod specimens and their biomass, sampled in pitfall traps in Nome, Alaska, in 2022, 2023 and 2024. 

Station				Pitfall trap location
Year 				Year of study
Date				Collection date
Poskey 				Sample name 	
Biomass 			Biomass (mg)
Family 				Arthropod family
plotID 				Subsection of study area 

METADATA 4. Negative_control_list.xlsx

This file contains an overview of all negative extraction controls and no template controls. 

Negative_Controls			Sample name
 
METADATA 5. Mapping_file_all.xlsx

This file contains data on red knots caught and measured near Nome, Alaska in 2019, 2022, 2023 and 2024

Seq_sample_name			Sample ID 
Description 			Type of sample (faecal, negative control, positive control) 
collection_date			Collection date of sample
RingCode				Ring number of individual
Year					Year of study
BroodID					ID number of the brood (all chicks hatched from the same nest)
Age						Lifestage of individual (adult/chick) 
Hatchdate				Hatch date of chick 
PlotID					Area within the study site

METADATA 6. filtered_family_data_long_new.xlsx
This file is created in the script "data_preparation.r"
This file contains the fractional number of reads per family for all faecal samples analysed using DNA barcoding. 

taxonomy 			Arthropod family (Order-Family)
Seq_sample_name		Sample ID 
count				Number of reads
RRA					Relative Read Abundance 

METADATA 7. chicks.xlsx
This file is created in the script "data_analysis.r"
This file contains data on juvenile red knots caught and measured near Nome, Alaska in 2019, 2022, 2023 and 2024, 
combined with the fractional number of reads per family for all faecal samples analysed using DNA barcoding. 

taxonomy 			Arthropod family (Order-Family)
Seq_sample_name		Sample ID 
count				Number of reads
RRA					Relative Read Abundance 
BroodID				ID number of the brood (all chicks hatched from the same nest)
RingCode 			Ring number of individual chick
Year				Year of study
collection_date		Collection date of sample
collection_DoY 		Day-of-year collection date (numerical)
Hatchdate			Hatch date of chick
Hatch_DoY 			Day-of-year hatch date (numerical)
Snowmelt_DoY		Day-of-year snowmelt date (average over study area)
period 				Time of the season (Early, Mid, Late) of sample collection
Age_chick 			Age of chick in days


--- SCRIPTS --- 
1. data_preparation.r 

This script uses data files 1-3 to prepare diet data for downstream analyses. 
Positive and negative controls are analysed to assess background contamination and sequencing noise, 
which are used to determine an identity cutoff for taxonomic assignments. Filtered ASVs are subsequently aggregated to the family level, 
after which the number of families included in the analysis is reduced by applying a cutoff to remove rare families. 

2. data_analysis.r 

This script uses data files 4-7 to link the processed family-level diet data to chick metadata and performs all main statistical analyses 
described in the data analysis section of the manuscript. The script generates model outputs and figures used in the main text and appendix.