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Using R for ecological modeling in USACE

6 Background on habitat models in USACE

The U.S. Army Corps of Engineers (USACE) engages in many decisions that affect ecological outcomes (e.g., ecosystem restoration of oyster reefs, environmental flows for imperiled fishes, dredge material management impacting bird breeding grounds). In such scenarios, ecological models are used to quantify environmental impacts and benefits throughout project life-cycles, including the planning, engineering, construction, operations, and maintenance phases.

Ecological models have become widely-used tools for informing decisions related to the management of complex ecological processes. Models span the breadth of potential ecological management applications such as seafood harvest limits, transport of nutrients into freshwaters, bioaccumulation of contaminants, management of imperiled taxa, and wetland impact assessment. In addition to diverse outcomes, ecological models often take on a variety of theoretical constructs ranging from theoretical, analytical models to statistical correlations of variables to agent-based simulations of animal movement (see Swannack et al. 2012 for a review of ecological model types). This diversity of ecological endpoints and model constructs has led to a wide array of tools applicable to ecosystem management and restoration.

Habitat suitability models are a common approach to ecological modeling of environmental impacts and benefits that reflect on quantity and quality of habitat. Habitat suitability index models use an index-based scoring method to quantify a habitat’s ability to support a target taxon (USFWS 1981). These “index” models (Swannack et al. 2012) were originally developed for species-specific applications (e.g., slider turtles), but the general approach has also been adapted to guilds (e.g., salmonids), communities (e.g., floodplain vegetation), and ecosystem processes (e.g., the Hydrogeomorphic Method). Habitat suitability index (HSI) models are commonly used across the Corps to support and evaluate restoration endpoints.

6.0.0.1 More information on index-based ecological models

Index models are a family of techniques that quantitatively translate multiple features or processes into a relative assessment of habitat suitability for a given organism or a relative assessment of ecosystem condition (Tirpak et al. 2009, Swannack et al. 2012). More specifically, index models combine assessments of habitat or ecosystem quality and quantity into an overarching metric for assessing the relative condition of a site (e.g., a “habitat unit” or “functional capacity unit”). Quantity is commonly expressed as a metric of area such as acres or hectares; however, other metrics may be appropriate to specific applications (e.g., river length or lake volume). Quality is then assessed by identifying key variables correlated with habitat or ecosystem condition. Each variable is translated into a suitability index curve, which transforms dimensional quantities such as flow velocity into dimensionless values of quality ranging from zero (completely unsuitable) to one (optimal habitat). Multiple suitability curves are then combined through various equational forms into an overarching assessment of habitat quality (e.g., a “habitat suitability index” or “functional capacity index”).

Index models may be derived from a variety of methods and resources. Like all models, many index model developers have emphasized that these algorithms simplify complex ecosystems, and thus, these tools should be considered adaptable hypotheses rather than mechanistic, cause-effect relationships. The value of index models lies in their utility for quantitatively comparing the relative merits of alternative management actions and testing hypotheses. The following represent the most common sources of index models applied to USACE ecosystem restoration projects:

  • U.S. Fish and Wildlife Service (USFWS) Habitat Suitability Index (HSI) Models: The HSI approach quantitatively relates potential for species presence to habitat characteristics. Species have complex relationships with their environment, and HSI models provide a simple method for characterizing potential for habitat to support target species across a landscape. The USFWS led the development of 500+ HSI models in the 1970-1980s to support environmental management decisions nationwide (https://www.nwrc.usgs.gov/wdb/pub/hsi/hsiindex.htm). The quantitative relationships between species and habitat were generally based on a combination of literature, field studies, and expert opinion, and the reports are colloquially referred to as the “blue books” because of the blue covers binding the original publications.
  • Hydrogeomorphic Method (HGM) of Wetland Assessment: Similarly, the HGM approach is a common technique for rapidly assessing wetland function. The HGM methodology for model development is thoroughly documented (Brinson 1993, Smith et al. 1995), and models are available for 30+ wetland types nationwide (https://wetlands.el.erdc.dren.mil/guidebooks.cfm).
  • Literature-Based Index Models: Index models also appear within the peer-reviewed and grey literature in a variety of formats. Some of the original HSI models have been subsequently adapted to local conditions or updated as new data became available (e.g., the bluegill model by Stuber et al. 1982 was adapted by Palesh and Anderson 1990). Updated models also appear in the peer-reviewed literature as new data become available, such as recent revisions to the oyster suitability model that expand its breadth of applicability (Swannack et al. 2014).
  • Project- or Objective-Centric Index Models: Specific restoration projects may build models unique to a set of project objectives (McKay et al. 2019), which can evolve as a project proceeds from preliminary screening to detailed alternatives analysis (e.g., McKay et al. 2018ab). More recently, Carrillo et al. (2020) proposed a Toolkit for interActive Modeling (TAM), which facilitates development of index models in real-time for mediated modeling workshop settings (Herman et al. 2019).

6.0.0.2 Calculating and applying index-based ecological models

One of the challenges in applying index-based models is that no standard platform exists for computing outcomes. As a result, users often develop ad hoc spreadsheet models, which may be highly prone to numerical errors (McKay 2009). However, the common quantity-quality structure of index models provides an opportunity to develop a consistent, error-checked index modeling calculator adaptable to a variety of applications across the Corps. In the next module, we will introduce ecorest, an R package created to facilitate application of HSI models in a user-friendly setting.