Folks call me Richie. My research focuses on applying quantitative ecology to invasive species. Currently, I am developing population models to inform Invasive carp management and developing methods for applying occupancy models to environmental DNA (eDNA).
Broadly, I am a research ecologist who studies the interactions between people and their environment. Specifically, I have studied:
- Terrestrial invasive plant species (undergraduate jobs and internships);
- Mosquito/dengue disease dynamics (my MS research);
- Population-level and interspecific effects of pesticides (my PhD research);
- The spatial impacts of wind energy and white-nose syndrome on bat population dynamics (my post-doc project); and
- The distribution and dynamics of aquatic invasive species and the application of this knowledge to their control (my current position).
Or, as a friend once said, "you model things dying".
Along the way, I have picked up skills in ecological, mathematical ecology, computation biology, and high-throughput computing. Although my skill set and research interests may appear to be broad, they have an underlying theme of studying population-level effects and distribution and then applying these finding to resource management.
Professional Experience
Adjunct graduate faculty at University of Wisconsin-La Crosse, Texas Tech, and South Dakota State
EPA Star Graduate Fellow 2010-2013
USGS contractor 2013-2014
Education and Certifications
Texas Tech University (Env. Tox., Math minor), PhD 2013
Texas Tech University (Env. Tox.), MS 2009
University of Wisconsin-Stevens Point (Wildlife and Biology, Chem. minor), BS 2007
Science and Products
Modeling to inform bighead and silver carp management
Modeling Overview at UMESC
Using Jupyter Notebooks to tell data stories and create reproducible workflows
Whole Wildlife Toxicology Catalog
Flocks of a feather dock together: Using Docker and HTCondor to link high-throughput computing across the USGS
Hunting Invasive Species with HTCondor: High Throughput Computing for Big Data and Next Generation Sequencing
BioLake bioclimatic variables based on ERA5-Land lake temperature estimates 1991-2020
Dataset from the Upper Mississippi River Restoration Program (1993-2019) to reconstruct missing data by comparing interpolation techniques
Data Release for Validation of portable eDNA detection kit for Asian carps
Bat demographic look up tables for BatTool R package
Field observation of current velocities (2019) along the Chincoteague Living Shoreline, Virginia
Use of an artificial stream to monitor avoidancebehavior of larval sea lamprey in response to TFM and Niclosamide
Summary of 2019 Environmental Toxicology and Chemistry articles: Data and Code
Assessment of carbon dioxide piscicide treatments: Data
Ethanol and sodium acetate as a preservation method to delay degradation of environmental DNA: Data
Indiana Bat Project data
Assessing the suitability of YY males and ZZ females as an invasive species population control method across life histories
Efficacy of hydrogen peroxide to reduce Gyrodactylus species infestation density on four fish species
Incorporating metapopulation dynamics to inform invasive species management: Evaluating bighead and silver carp control strategies in the Illinois River
BioLake: A first assessment of lake temperature-derived bioclimatic predictors for aquatic invasive species
Targeted metabolomics characterizes metabolite occurrence and variability in stable freshwater mussel populations
MetaIPM: Placing integral projection models into a metapopulation framework
Reconstructing missing data by comparing interpolation techniques: Applications for long-term water quality data
Obtaining and applying public data for training students in technical statistical writing: Case studies with data from U.S. Geological Survey and general ecological literature
Using integral projection models to explore management strategies for silver carp (Hypophthalmichthys molitrix)
Efficacy of florfenicol and oxytetracycline administered in feed to control cisco mortality associated with Aeromonas salmonicida infections
Analysis of per capita contributions from a spatial model provides strategies for controlling spread of invasive carp
Validation of a portable eDNA detection kit for invasive carps
Simulations for assessing the suitability of YY-males as a control method across life histories
Monosex control within integrated pest management
SEIcarP
Application of the SEICarP Model to the Illinois River
Example application of MetaIPM to the Illinois River
Indiana mussel metabolomics data analysis
Calculations of BioLake climate data
Interpolating missing water quality data
Coregonid
Analysis of Grass Carp eDNA Data
BatTool R package
High-throughput calculations of climatch scores
Science and Products
- Science
Modeling to inform bighead and silver carp management
Bighead carp (Hypophthalmichthys nobilis) and silver carp (Hypophthalmichthys molitrix) are invasive carp species within the Mississippi River basin. In the early-1970s these species escaped from ponds where people introduced them to control algae (ICRCC). Invasive carp cause ecological and economic damage by outcompeting native species and disrupting native food webs. Stopping the spread of these...Modeling Overview at UMESC
Models seek to describe the natural world around us and how we interact with the world. For example, physical models might help Upper Midwest Environmental Sciences Center (UMESC) visitors understand landscapes, such as the Mississippi River or topology and water flow.Using Jupyter Notebooks to tell data stories and create reproducible workflows
Increasingly, USGS scientists seek to share and collaborate while working on data and code. Furthermore, these scientists often require advanced computing resources. Jupyter Notebooks are one such tool for creating these workflows. The files are interactive, code “notebooks” which allow users to combine code and text in one document, enabling scientists to share the stories held within their data...Whole Wildlife Toxicology Catalog
Developed in 2008, the Whole Wildlife Toxicology Catalog is a portal to wildlife toxicology-oriented websites and databases. The catalog attempts to compile and provide access to website containing information that should be of value to scientists, regulators, natural resource managers, students and other members of the public. The catalog is updated annually. Please contact Barnett Rattner if you...Flocks of a feather dock together: Using Docker and HTCondor to link high-throughput computing across the USGS
USGS scientists often face computationally intensive tasks that require high-throughput computing capabilities. Several USGS facilities use HTCondor to run their computational pools but are not necessarily connected to the larger USGS pool. This project demonstrated how to connect HTCondor pools by flocking, or coordinating, within the USGS. In addition to flocking the Upper Midwest EnvironmentalHunting Invasive Species with HTCondor: High Throughput Computing for Big Data and Next Generation Sequencing
Large amounts of data are being generated that require hours, days, or even weeks to analyze using traditional computing resources. Innovative solutions must be implemented to analyze the data in a reasonable timeframe. The program HTCondor (https://research.cs.wisc.edu/htcondor/) takes advantage of the processing capacity of individual desktop computers and dedicated computing resources as a sing - Data
BioLake bioclimatic variables based on ERA5-Land lake temperature estimates 1991-2020
These BioLake raster data provide global estimates (~10.0 x 12.4 km resolution) of twelve bioclimatic variables based on estimated lake temperature. Eleven of these twelve variables (BioLake01 - BioLake11) are estimated for each of three lake strata: lake mix (surface) layer, lake bottom, and total lake water column. These eleven variables correspond to CHELSA (Climatologies at high resolution forDataset from the Upper Mississippi River Restoration Program (1993-2019) to reconstruct missing data by comparing interpolation techniques
The dataset accompanies the scientific article, "Reconstructing missing data by comparing interpolation techniques: applications for long-term water quality data." Missingness is typical in large datasets, but intercomparisons of interpolation methods can alleviate data gaps and common problems associated with missing data. We compared seven popular interpolation methods for predicting missing valData Release for Validation of portable eDNA detection kit for Asian carps
This is the qPCR and loop-mediated isothermal amplification (LAMP) data in support of the article "Validation of a portable eDNA detection kit for invasive carps". There are four types of data contained in five files including: limit of detection analysis for each method (qPCR and LAMP), qPCR analysis and LAMP analysis of eDNA samples collected over time from ponds containing 3 or 33 Grass Carp (CBat demographic look up tables for BatTool R package
Demographic look up tables allow the translation of a population growth rate, which is estimable from count data, to a set of vital rates parameterizing the birth and survival processes of the population. These tables are used in the BatTool R package to produce realistic simulations of population abundance trajectories given a range of population growth rates.Field observation of current velocities (2019) along the Chincoteague Living Shoreline, Virginia
This dataset contains measured current velocity during March 1 to May 2, 2019, at eleven locations along the Chincoteague Living Shoreline, Virginia.Use of an artificial stream to monitor avoidancebehavior of larval sea lamprey in response to TFM and Niclosamide
AEH-18-Baybar-01_compiled_for_R: CSV file with column headers; Trial Date (date the individual trial took place), Location of SL (where they ended up in the system at the end of trial), Total SL Mort (how many dead SL were found in this location), Total SL (how many SL were found in this location), Treatment type (Control, TFM, or Nic), Mainstream chemical (chem that was in mainstream), Side ChannSummary of 2019 Environmental Toxicology and Chemistry articles: Data and Code
Statistical inferences play a critical role in ecotoxicology. Historically, Null Hypothesis Significance Testing (NHST) has been the dominant method for inference in ecotoxicology. As a brief and informal definition of the NHST approach, researchers compare (or test) an experimental treatment or observation against a hypothesis of no relationship or effect (the null hypothesis) using the collectedAssessment of carbon dioxide piscicide treatments: Data
Spreadsheets include data that was used to evaluate the efficacy of dry ice administered under-ice as a tool for reducing the overwinter survival of invasive carps. There are 10 CSV associated with this studyEthanol and sodium acetate as a preservation method to delay degradation of environmental DNA: Data
This data contains environmental DNA (eDNA) sample assay results that were collected from water samples taken from a tank housing Asian carp and placed either on ice or at room temperature. At both treatment temperatures, water samples were left untreated or were treated with an ethanol and sodium acetate solution (EtOH-NaAc). This was done to evaluate an ethanol and sodium acetate solution to maiIndiana Bat Project data
Our model is a full-annual-cycle population model {hostetler2015full} that tracks groups of bat surviving through four seasons: breeding season/summer, fall migration, non-breeding/winter, and spring migration. Our state variables are groups of bats that use a specific maternity colony/breeding site and hibernaculum/non-breeding site. Bats are also accounted for by life stages (juveniles/first-yea - Publications
Filter Total Items: 73
Assessing the suitability of YY males and ZZ females as an invasive species population control method across life histories
Natural resource managers use tools to control invasive species. In theory, stocking YY males or ZZ females would allow managers to skew sex ratios until populations collapse. In combination with other suppression methods, such as removal, this approach could be incorporated into Integrated Pest Management plans. For example, fishery managers have stocked YY males to control isolated non-native brAuthorsRichard A. Erickson, Hannah Mann Thompson, Stacie A. Kageyama, Grace M. Andriacchi, Aaron R. Cupp, Reynaldo Patiño, Jon AmbergEfficacy of hydrogen peroxide to reduce Gyrodactylus species infestation density on four fish species
ObjectiveThe ability to effectively treat parasitic infestations of fish is of high importance for fish culture facilities. However, tools or approved therapies for treating infestations on fish are limited. This paper summarizes results from four separate clinical field studies that evaluated the efficacy of hydrogen peroxide (H2O2; 35% PEROX-AID) for reducing Gyrodactylus spp. infestation densitAuthorsMaren T. Tuttle-Lau, Eric Leis, Aaron R. Cupp, Laura Lynne Peterman, Jillian Hebert, Richard A. Erickson, Susan M. Schleis, Mark P. GaikowskiIncorporating metapopulation dynamics to inform invasive species management: Evaluating bighead and silver carp control strategies in the Illinois River
1. Invasive species management can benefit from predictive models that incorporate spatially explicit demographics and dispersal to guide resource allocation decisions. 2. We used invasive bigheaded carps (Hypophthalmichthys spp.) in the Illinois River, USA as a case study to create a spatially explicit model to evaluate the allocation of future management efforts. Specifically, we compared additiAuthorsJahn Kallis, Richard A. Erickson, David P. Coulter, Alison A. Coulter, Marybeth K. Brey, Matt Catalano, John M. Dettmers, James E. Garvey, Kevin Irons, Elizabeth A. Marschall, Kenneth A Rose, Mark L. Wildhaber, David C. GloverBioLake: A first assessment of lake temperature-derived bioclimatic predictors for aquatic invasive species
Aquatic invasive species (AIS) present major ecological and economic challenges globally, endangering ecosystems and human livelihoods. Managers and policy makers thus need tools to predict invasion risk and prioritize species and areas of concern, and they often use native range climate matching to determine whether a species could persist in a new location. However, climate matching for AIS ofteAuthorsRyan C. Burner, Wesley Daniel, Peder S. Engelstad, Christopher J. Churchill, Richard A. EricksonTargeted metabolomics characterizes metabolite occurrence and variability in stable freshwater mussel populations
Freshwater mussels (order Unionida) play a key role in freshwater systems as ecosystem engineers and indicators of aquatic ecosystem health. The fauna is globally imperilled due to a diversity of suspected factors; however, causes for many population declines and mortality events remain unconfirmed due partly to limited health assessment tools. Mussel-monitoring activities often rely on populationAuthorsDiane L. Waller, Joel Putnam, John Steiner, Brant Fisher, Grant N. Burcham, John W. Oliver, Stephen B. Smith, Richard A. Erickson, Anne Remek, Nancy BodekerMetaIPM: Placing integral projection models into a metapopulation framework
Metapopulation models include spatial population dynamics such as dispersion and migration between subpopulations. Integral projection models (IPMs) can include demographic rates as a function of size. Traditionally, metapopulation models do not included detailed populaiton models such as IPMs. In some situations, both local population dynamics (e.g. size-based survival) and spatial dynamics are iAuthorsRichard A. Erickson, James P Peirce, Greg J. Sandland, Hannah Mann Thompson, Alison A. Coulter, David C. GloverReconstructing missing data by comparing interpolation techniques: Applications for long-term water quality data
Missing data are typical yet must be addressed for proper inferences or expanding datasets to guide our limnological understanding and management of aquatic systems. Interpolation methods (i.e., estimating missing values using known values within the dataset) can alleviate data gaps and common problems. We compared seven popular interpolation methods for predicting substantial missingness in a lonAuthorsDanelle M. Larson, Wako Bungula, Amber Lee, Alaina Stockdill, Casey McKean, Frederick Miller, Killian Davis, Richard A. Erickson, Enrika HlavacekObtaining and applying public data for training students in technical statistical writing: Case studies with data from U.S. Geological Survey and general ecological literature
Effective undergraduate statistical education requires training using real-world data. Textbook datasets seldom match the complexities and messiness of real-world data and finding these datasets can be challenging for educators. Consulting and industrial datasets often have nondisclosure agreements. Academic datasets often require subject area expertise beyond those of a general education or lackAuthorsBarb Bennie, Richard A. EricksonUsing integral projection models to explore management strategies for silver carp (Hypophthalmichthys molitrix)
Silver carp (Hypophthalmichthys molitrix) are planktivorous fish that were originally introduced to the United States for use in fish production ponds and have since escaped these enclosures and are invading the Mississippi River Basin. The silver carp invasion of the Illinois River has a myriad of negative effects on native ecosystems. In this paper, we introduce key dependencies that are likelyAuthorsCameron Coles, Elizabeth Balas, James P Peirce, Greg J. Sandland, Richard A. EricksonEfficacy of florfenicol and oxytetracycline administered in feed to control cisco mortality associated with Aeromonas salmonicida infections
Two medications (one with florfenicol and one with oxytetracycline) that are approved in the United States to control mortality due to furunculosis associated with Aeromonas salmonicida were assessed to determine their efficacy in medicated feeds to treat A. salmonicida-infected Cisco (also known as Lake Herring) Coregonus artedi. Cisco were subjected to static infection baths containing A. salmonAuthorsAaron R. Cupp, Maren T. Tuttle-Lau, Eric Leis, Samantha Lea Wolfe, Justin Smerud, John W. Oliver, Richard A. Erickson, Austin Hannah, Aaron Johnson, Rachel Grace Nelson, Isaac Standish, Joel Wils, Mark P. GaikowskiAnalysis of per capita contributions from a spatial model provides strategies for controlling spread of invasive carp
Metapopulation models may be applied to inform natural resource management to guide actions targeted at location-specific subpopulations. Model insights frequently help to understand which subpopulations to target and highlight the importance of connections among subpopulations. For example, managers often treat aquatic invasive species populations as discrete populations due to hydrological (e.g.AuthorsDonald Schoolmaster, Alison A. Coulter, Jahn L. Kallis, David C. Glover, John M. Dettmers, Richard A. EricksonValidation of a portable eDNA detection kit for invasive carps
Loop-mediated isothermal amplification (LAMP) is a rapid molecular detection technique that has been used as a diagnostic tool for detecting human and animal pathogens for over 20 years and is promising for detecting environmental DNA shed by invasive species. We designed a LAMP assay to detect the invasive carps, silver carp (Hypophthalmichthys molitrix), bighead carp (Hypophthalmichthys nobilis)AuthorsStacie A. Kageyama, Matthew Regh Hoogland, Tariq Tajjioui, Theresa M. Schreier, Richard A. Erickson, Christopher M. Merkes - Software
Filter Total Items: 21
Simulations for assessing the suitability of YY-males as a control method across life histories
This repository contains code to simulate the use of YY-males as a control tool for different aquatic invasive species. The code uses the Meta-IPM Python package (https://doi.org/10.5066/P9PW673G) The code for this project assumes the reader is familiar with Jupyter Notebooks, enough Conda and Python to install the Meta-IPM package, and population ecology.Monosex control within integrated pest management
This repository contains code to simulate the use of YY-males and direct mortality such as harvest or pesticide applicaion as a control tools for different aquatic invasive species.SEIcarP
SEIcarP is an R package (R Core Team 2021) implementing the Spatially Explicit Invasive Carp (SEICarP; sometimes stylize as SEIcarP) population model for the Illinois River. This repository contains the SEIcarP model plus two additional packages required for the main model package to run. These are the SEIcarP Bighead Carp (BH) data (SEIcarPdataBHCP) and the SEIcarP Silver Carp (SV) data (SEIcarPdApplication of the SEICarP Model to the Illinois River
This repository contains code to run the Spatially Explicit Invasive Carp Population (SEICarP) model in the Illinois Rive. The code uses the `SEICarP` R package. The code for this project assumes the reader is familiar with R, population modeling, and quantitative fisheries methods.Example application of MetaIPM to the Illinois River
This repository contains an example application of the `Meta-IPM` Python package (https://doi.org/10.5066/P9PW673G). The specific application focuses on the Illinois River using existing public data.Indiana mussel metabolomics data analysis
This repository contains code to cluster a sample of Mussels based up their metabolic levels via Non-Metric Multidimensional Scaling (NMDS) and distance based-Redundancy Analysis (db-RDA). Mussel sample is broken down and examined by catch location, sex, and species. The code for this project assumes the reader is familiar with R and clustering techniques.Calculations of BioLake climate data
Climate data allow people to examine species distributions and possible distributions. This script takes ERA5-Land climate estimates (https://www.ecmwf.int/en/forecasts/datasets/reanalysis-datasets/era5) for precipitation and lake temperature and processes them to create summary climate layers for use with biological organisms in lakes. This code could be modified to use a different subset of yearInterpolating missing water quality data
This repository contains analysis codes to interpolate missing data from the Upper Mississippi River LTRM dataset.Coregonid
This repository contains code for the analysis from a study that examined mortality and qPCR detection in 4 groups of fish: an uninfected control group, an infected control group, and two treatment groups. The main goals were to determine if their were differences in mortality and qPCR detection of the parasite among the differing groups. Mortality was addressed using a Generalized Linear Mixed MAnalysis of Grass Carp eDNA Data
This product contains code to analyze a dataset that was collected to compare a LAMP assay and a qPCR assay for Grass Carp in a pond study. This repository contains the RMarkdown and R files used to analyze the data. It was created to allow for reproducible results. The code assumes the user is experience with R, especially the Tidyverse, and Stan.BatTool R package
This R package was developed to help the USFWS understand the effects of wind turbine mortality and WNS on the Indiana bat. The model has been described in a peer-reviewd (and open access publication). The package includes both a GUI and command line interface. The GUI only works for Myotis spp., although the command line tool has been expanded for two other genera of bats: Lasiurus spp. and PipisHigh-throughput calculations of climatch scores
Matching climate envelopes allows people to examine how potential invasive species may match habitats. This repository contains code for using the climatchR package for high-throughput calculations of climatch scores for species using GBIF data. Climatch is based upon the climatch algorithm as implemented through the climatchR package. - News