> fieldEco.phy.vstMat <- GenomicRanges::assay(fieldEco.phy.rld) # Extract transformed OTU table
Error: 'assay' is not an exported object from 'namespace:GenomicRanges'

I guess you're following some script, and the script is written for a different version of software than the one you are using, or the script is wrong. So provide more information, including the source of the commands you write above, and the output of the command

sessionInfo()

executed on your computer after the error occurs.