Software

MetaIPM is a Python package (Python Software Foundation 2020) that models meta-population dynamics and continuous growth rates via an integral projection model (IPM) for species living in distinct habitat patches. The package stems from a model that compares invasive carp population control strategies. The package supports differing sex and any organisms living in distinct habitat...

fishStan is an R package (R Core Team 2020) providing a collection of hierarchical Bayesian models written in the Stan language as called through RStan (Stan Development Team 2020). The package is a USGS software software release. The purpose of the package is to document these models for use in USGS projects and allow easy discrimination. The package assumes the user is familiar with R...

fishstan is an R package for fitting common fisheries models using RStan

This code supports the manuscript "Refinement of eDNA as an early monitoring tool at the landscape-level: Study design considerations". The code fit a three-level occupancy model with two detection assays in the program Stan through R. We programmed this code for a specific project with the USFWS and it will likely not generalize to other situations. The primary purpose of releasing this...

The data set is six separate csv files. Four of which contain the quantity of DNA copy numbers and fluor used to analyze the DNA quantities collected from water samples from four separate portions of the study (adult SL field, adult SL lab, larval SL field, larval SL lab) and need to be in their own csv file. Also included is a csv with adult SL trapping data, a csv for larval SL...

These scripts prepare input files and run a Generalized Random Tessellation Stratified (GRTS) draw to select sampling locations for the Integrated Monarch Monitoring Program in the U.S., Canada, and Mexico.

Provides U.S. Geological Survey developed and published regression equations for estimating streamflow statistics such as mean annual and monthly mean flows, flow-duration percentiles, and peak and low flows.

Provides multiple water use resources, such as categories, source types, use types as well as watershed summary resource, which aggregate selected source time series by watershed location to provide a simple annual and monthly watershed summary; grouped by defined source, use, category, and month to watershed managers.

Provides a geostatistical variogram model for correlating ungaged locations to USGS gages for implemented locations.

Provides core StreamStats functionality, such as watershed delineation, basin characteristics and flow statistics.

Provides network connectivity for spatial datasets, such as stream trace, network path and flow path.

UMESC hosts a web service for the retrieval of LTRM fish catch data using the GeoJSON data format. By using this data service, the public can automate data access to LTRM fisheries data. UMESC has written a series of example Python scripts that illustrate data retrieval and plotting. These example scripts focus on plotting fish catch, but there are limitless geo-spatial, tabular, and...