Software

occStan is an R package (R Core Team 2021) providing a collection of occpuancy Bayesian models written in the Stan language as called through RStan (Stan Development Team 2021). 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 and occupancy

Matching climate envelopes of allows people to examine how potential invasive species may match habitats. The Australian government created Climatch to do allow for these comparisons. However, this webpage does not allow for readily scripting climate matching. Hence, the authors created climatchR, an R package (R Core Team 2020) implementing the climatch method in R. This was created to allow auto

The National Streamflow Statistics (NSS) Application is an online computer application that provides a simple method for applying regional flood-peak streamflow estimates and low flow frequency/duration streamflow estimates.

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 patches.

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 code is t

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 shocking data, a

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.