Import the population structure in R as a data frame and then use the `strata()` function to add the data frame (see
https://rdrr.io/cran/adegenet/man/strata-methods.html for details).
For example, if you have VCF file called "population.vcf" and your populations structure file is called "population-data.txt" and it's comma-delimited, you can use:
vcf <- vcfR::read.vcfR("population.vcf")
gid <- vcfR::vcfR2genlight(vcf)
# if you want a genind object (8X larger memory footprint), you can use vcfR::vcfR2genind(vcf, return.alleles = TRUE)
population_strata <- read.csv("population-data.txt", header = TRUE)
strata(gid) <- population_strata # this will set the strata based on the column names of your stratifications