This data archive includes R code and data for reproducing the analyses and figures in Lafferty, Metabarcoding is (usually) more cost effective than seining or qPCR for detecting tidewater gobies and other estuarine fishes.   To view the supplementary tables, open the Fig&TableSuppl.docx file. This file also includes the manuscript figures and tables and some explanatory text about how to generate them. To reproduce the figures, open the Fig&TableCode.Rmd in R studio and be sure the needed csv files included in the Dryad repository are in the working directory. The data files include more information than used in the analyses and can be used for other purposes. The code is not software, nor is it intended as an R package, but the code is annotated so others can understand and manipulate it. For each CSV file there is an associated metadata file that defines entries and columns and an information file that contains an abstract and ownership information. One of the data files required to reproduce the analyses (Schmelzle&Kinziger_occupancy.csv) was created from previously published data and was not produced by the author.  Please cite it as: Schmelzle, Molly C., Kinziger, Andrew P. 2015. Data from: Using occupancy modeling to compare environmental DNA to traditional field methods for regional-scale monitoring of an endangered aquatic species. Dryad. 6rs23