This repository contains scripts used in the analysis of Wang et al. 2021 Late Quaternary dynamics of Arctic biota from ancient environmental genomics. https://doi.org/10.1038/s41586-021-04016-x
| Script | used in which section of the paper | function |
|---|---|---|
| bam_header_subset.R | Supplementary Information section 9.2.4 | to subset headers of bam file to include only reference headers appeared in the alignments |
| Plant_normalization.R | Supplementary Information section 9.5.2 | plant reads normalisation |
| paleoDistributionModel.R | Supplementary Information section 12.2 | ancient human distribution niche modelling |
| ExtractAndMapModels.R | Supplementary Information section 12.2 | mapping human niche modelling results to each eDNA site |
| get_consensus.py | Supplementary Information section 14.1.2 | to creat a consensus sequence from the multiple sequence alignment |
| fix_vcf.R | Supplementary Information section 14.1.2 | to fix the deletions/missing data represented by *s in the vcf files |
| Animal_spatiotenporal_modelling.R | Supplementary Information section 13.3 | to model covariates of animal eDNA presence/absence |
| INLA_ST_functions.R | Supplementary Information section 13.3 | functions used in Animal_spatiotenporal_modelling.R |
| spde-book-functions.R | Supplementary Information section 13.3 | functions used in Animal_spatiotenporal_modelling.R |