Section 7 History

7.1 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 new set of results and major changes to the model structure, code, or datasets.
  • Y is the minor version, which will be incremented when there is a new set of results and minor changes in the model code or datasets (but no change in model structure).
  • 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.

7.2 Change Log

  • v2.1.0 | Jan 4, 2024 Re-calibrate model with updated stream temperature model v1.4.0 results through 2022.
  • v2.0.0 | Jul 8, 2022 Removed all fixed effects except for mean July stream temperature due to cross-correlation between stream temperatures and other covariates (e.g., forest cover). Changed random effect levels from HUC10 to HUC8.
  • v1.4.0 | Sep 8, 2021
    Re-calibrate model with updated stream temperature model v1.3.0 results through 2020, removed July stream temperature scenarios from predictions (these have been replaced by the air temperature scenarios)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 v1.2.0 results through 2019
  • 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 v1.1 results
  • 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 stream temperature model v1.0 results.
  • v1.0.0 | Oct 25, 2018
    Recalibrate model using stream temperature model v1.0 results.
  • 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.
Bates, D., Mächler, M., Bolker, B., and Walker, S. (2015). Fitting linear mixed-effects models using lme4. Journal of Statistical Software, 67(1), 1–48.
Bolker, B. M., Brooks, M. E., Clark, C. J., Geange, S. W., Poulsen, J. R., Stevens, M. H. H., and White, J.-S. S. (2009). Generalized linear mixed models: A practical guide for ecology and evolution. Trends in Ecology & Evolution, 24(3), 127–135.
Kanno, Y., Letcher, B. H., Rosner, A. L., O’Neil, K. P., and Nislow, K. H. (2015). Environmental Factors Affecting Brook Trout Occurrence in Headwater Stream Segments. Transactions of the American Fisheries Society, 144(2), 373–382.
Kuhn, M. (2022). Caret: Classification and regression training.
Zuur, A. F., Ieno, E. N., Walker, N., Saveliev, A. A., and Smith, G. M. (2009). Mixed effects models and extensions in ecology with R. New York, NY: Springer New York.