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 quantitative ecologist who studies the interactions between people and their environment. Specificlly, 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.
Education and Certifications
Texas Tech University (Env. Tox., Math minor), PhD 2013
Texas Tech University (Env. Tox.), MS 2013
University of Wisconsin-Stevens Point (Wildlife and Biology, Chem. minor), BS 2007
Science and Products
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
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
Indiana Bat Project data
Analysis of per capita contributions from a spatial model provides strategies for controlling spread of invasive carp
Quantitative method development to determine feed consumption using a dye
FishStan: Hierarchical Bayesian models for fisheries
Emerging control strategies for integrated pest management of invasive carps
Use of an artificial stream to monitor avoidance behavior of larval sea lamprey in response to TFM and niclosamide
Paths to computational fluency for natural resource educators, researchers, and managers
Demographic and potential biological removal models identify raptor species sensitive to current and future wind energy
Asian carp population modeling to support an adaptive management framework
Demographic rate variability of Bighead and Silver Carps along an invasion gradient
Use of an artificial stream to monitor avoidance behavior of larval sea lamprey in response to TFM and niclosamide
Using Markov chains to quantitatively assess movement patterns of invasive fishes impacted by a carbon dioxide barrier in outdoor ponds
Toxicity of carbon dioxide to freshwater fishes: Implications for aquatic invasive species management
High-throughput calculations of climatch scores
Analysis code for Quantitative method development to determine feed consumption using a dye
A comparison of statistical modeling approaches for hierarchical data: A simulation study and application to ecology data
occStan: Occupancy models with RStan
climatchR: An implementation of Climatch in R
MetaIPM
eDNAoccupancy
Science and Products
- Science
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
Bat 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 studyIndiana 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: 60
Analysis 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.Quantitative method development to determine feed consumption using a dye
Although there are many methods to determine ingestion and absorption of aquafeeds, none exist that are simple, cost-effective, and quantitative and that can mark fish with a long-lasting, visible indicator. In addition to aquafeed development, selective baits are needed that can be used for aquatic invasive species removal efforts, including for Grass Carp Ctenopharyngodon idella. Bait incorporatFishStan: Hierarchical Bayesian models for fisheries
Fisheries managers and ecologists use statistical models to estimate population-level relations and demographic rates (e.g., length-maturity curves, growth curves, and mortality rates). These relations and rates provide insight into populations and inputs for other models. For example, growth curves may vary across lakes showing fish populations differ due to management actions or underlying envirEmerging control strategies for integrated pest management of invasive carps
Invasive carps are ecologically and economically problematic fish species in many large river basins in the United States and pose a threat to aquatic ecosystems throughout much of North America. Four species of invasive carps: black carp (Mylopharyngodon piceus), grass carp (Ctenopharyngodon idella), silver carp (Hypophthalmichthys molitrix) and bighead carp (Hypophthalmichthys nobilis), are partUse of an artificial stream to monitor avoidance behavior of larval sea lamprey in response to TFM and niclosamide
The lampricide 3-trifluoromethyl-4-nitrophenol (TFM) has been used in liquid form to control larval sea lamprey (Petromyzon marinus) in Great Lakes tributaries since the late 1950s. In the 1980s a dissolvable TFM bar was developed as a supplemental tool for application to small tributaries as a deterrent to larvae seeking water not activated with TFM. The size, mass, and number of bars needed in sPaths to computational fluency for natural resource educators, researchers, and managers
Natural resource management and supporting research teams need computational fluency in the data and model-rich 21st century. Computational fluency describes the ability of practitioners and scientists to conduct research and represent natural systems within the computer's environment. Advancement in information synthesis for natural resource management requires more sophisticated computational apDemographic and potential biological removal models identify raptor species sensitive to current and future wind energy
A central challenge in applied ecology is understanding the effect of anthropogenic fatalities on wildlife populations and predicting which populations may be particularly vulnerable and in greatest need of management attention. We used 3 approaches to investigate potential effects of fatalities from collisions with wind turbines on 14 raptor species for both current (106 GW) and anticipated futurByEcosystems, Energy Resources Program, Species Management Research Program, Forest and Rangeland Ecosystem Science Center, Geology, Energy & Minerals Science Center, Geosciences and Environmental Change Science Center, Northern Prairie Wildlife Research Center, Upper Midwest Environmental Sciences CenterAsian carp population modeling to support an adaptive management framework
This Monitoring and Response Plan provides the Asian Carp Regional Coordinating Committee (ACRCC) with updates on FWS and USGS modeling efforts for the Spatially Explicit Asian carp Population (SEAcarP) model. For FY2020, efforts are underway to parameterize and analyze the SEAcarP model. Themes: invasive species; Asian carp; Great Lakes.Demographic rate variability of Bighead and Silver Carps along an invasion gradient
Invasive Bighead Carp Hypophthalmichthys nobilis and Silver Carp H. molitrix have infested and caused largescale ecological and economic damage to the Illinois, Mississippi, and Ohio rivers. We compiled demographic data from 42,995 fish from 23 pools in the Illinois, Mississippi, and Ohio rivers, which universities and management agencies previously collected as part of management, monitoring, andUse of an artificial stream to monitor avoidance behavior of larval sea lamprey in response to TFM and niclosamide
The lampricide 3-trifluoromethyl-4-nitrophenol (TFM) has been used in liquid form to control larval sea lamprey (Petromyzon marinus) in Great Lakes tributaries since the late 1950s. In the 1980s a dissolvable TFM bar was developed as a supplemental tool for application to small tributaries as a deterrent to larvae seeking water not activated with TFM. The size, mass, and number of bars needed in sUsing Markov chains to quantitatively assess movement patterns of invasive fishes impacted by a carbon dioxide barrier in outdoor ponds
Natural resource managers use barriers to deter the movement of aquatic invasive species. Research and development of new invasive species barriers is often evaluated in pond and field scales using high‐resolution telemetry data. Telemetry data sets can be a rich source of data about fish movement and behavior but can be difficult to analyze due to the size of these data sets as well as their irreToxicity of carbon dioxide to freshwater fishes: Implications for aquatic invasive species management
Carbon dioxide (CO2) has been approved by the US Environmental Protection Agency as a new aquatic pesticide to control invasive Asian carps and other aquatic nuisance species in the United States. However, limited CO2 toxicity data could make it challenging for resource managers to characterize the potential risk to nontarget species during CO2 applications. The present study quantified the toxici - Software
High-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.Analysis code for Quantitative method development to determine feed consumption using a dye
This repository contains code for the analysis of a The purpose of the repository is to document what analysis was run for publication and is intended for an archive rather than a production or development type repository.A comparison of statistical modeling approaches for hierarchical data: A simulation study and application to ecology data
The repository contains code to analyze the differences in model results when nested design structures differ. The code for this project assumes the reader is familiar with R, nested designs, and mixed effects linear modeling.occStan: Occupancy models with RStan
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 occupancyclimatchR: An implementation of Climatch in R
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 autoMetaIPM
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.eDNAoccupancy
This repository contains the source code and package for the eDNAoccupancy package. This readme file contains the installation instructions for the package. The purpose of the R package is to fit three-level occupancy models. Although designed with eDNA-based observations, the package can be used for any occupancy situation with sampling and sub-sampling. - News