Section 1 Introduction

The SHEDS brook trout occupancy model predicts probability of occupancy for catchments smaller than 200 km^2 in the northeastern U.S. from Maine to Virginia.

The documentation is divided into the following sections:

  1. Introduction : provides an overview the model and its documentation, as well as a snapshot of the current calibration
  2. Theory : describes how the model works including the underlying structure and theory
  3. Data Sources : describes the datasets used as inputs to the model
  4. Data Processing : describes how input datasets are processed prior to model fitting (i.e. QAQC procedures)
  5. Calibration and Validation : describes how well the model predicts occupancy based on observations that were included (calibration) and excluded (validation) from the model fitting process
  6. Predictions : describes how predictions are generated after the model is calibrated and describes the various summary metrics that are computed for each catchment
  7. Download : provides links to download the model predictions, catchment delineation (shapefiles), and covariates dataset.

The model will be periodically updated and re-calibrated (approximately once every 6 months) to incorporate any newly available data or updated stream temperature model results, and to make any necessary revisions to the data processing and/or model structure. With each update, a new version will be assigned to the model, and this documentation website will be updated to reflect the most recent performance of the model. A brief summary of the changes associated with each new version is provided in the Change Log below.

1.1 Model Overview

1.2 Current Snapshot

Table 1.1 provides a snapshot of the calibration and validation performance for the current version of the model (v1.4.0). More details about the model performance can be found in the Calibration and Validation section.

Table 1.1: Summary statistics of model calibration and validation
Calibration Validation
# Catchments 10,302 2,839
Sensitivity 0.660 0.620
Specificity 0.797 0.715
False Negative Rate 0.050 0.087
False Positive Rate 0.059 0.120
Accuracy 0.708 0.654
Error Rate 0.109 0.207
AUC 0.957 0.835

1.3 Model Versioning

The model uses semantic versioning of the form: vX.Y.Z

  • X is the major version, which will be incremented when there is a major change to the model theory, code, or datasets.
  • Y is the minor version, which will be incremented when there is a new set of results due to changes in the model code, datasets, processing procedures, etc.
  • Z is the patch version, which will be incremented only when there is a change to the documentation or code that does not yield different results.

1.4 Source Code

The source code for the model itself and this documentation is available in the Github repository walkerjeffd/sheds-bto-model. Each version of the model will be included under the list of Releases.

1.5 Change Log

  • v1.4.0 (Sep 8, 2021)
    Re-calibrate model with updated stream temperature model results through 2020 (v1.3.0), removed July stream temperature scenarios from predictions (these have been replaced by the air temperature scenarios)
  • v1.3.0 (Jul 13, 2020)
    Re-run calibration with updated stream temperature model results through 2019 (v1.2.0)
  • v1.2.2 (Jan 17, 2020)
    Rename prediction metrics to be more consistent
  • v1.2.1 (Jan 16, 2020)
    Added predictions for air temperature scenarios (+2, +4, +6 degC), remove 0.5 degC increments from July stream temperature scenarios, revise method for estimating max temperature increases to achieve occupancy thresholds using linear interpolation
  • v1.2.0 (Dec 3, 2019)
    Re-run calibration with updated stream temperature model results (v1.1)
  • v1.1.1 (Mar 26, 2019)
    Update documentation, add Download section containing links to model predictions, catchment delineation, and covariates.
  • v1.1.0 (Mar 25, 2019)
    Add observation data from MA DFW. Recalibrate model using v1.0 of stream temperature model.
  • v1.0.0 (Oct 25, 2018)
    Recalibrate model using v1.0 of stream temperature model.
  • v0.9.0 (Aug 16, 2018)
    Preliminary release of the new model framework and documentation.
  • Previous Versions (prior to 2018)
    Previous versions of the brook trout occupancy model can be found here. That website is now deprecated, but will remain available for future reference. Beginning with v1.0.0 of the new framework and codebase, all model changes and results will be tracked and made available.