inst/shiny/modules/rep_refPackages.md

In wallace: A Modular Platform for Reproducible Modeling of Species Niches and Distributions

Module: Reference Packages

BACKGROUND

Over the decade of the 2010s, scientific practice increasingly emphasized documentation and reproducibility. In biodiversity science, the area of modeling species niches/distributions has advanced rapidly in this regard via the emergence of various kinds of community-driven standards (see Fitzpatrick et al. 2021 for an overview). These include checklists for data and model reporting (Feng et al. 2019), standardized metadata frameworks (RMMS, Merow et al. 2019; occCite, Owens et al., 2021), and detailed protocols for reporting (ODMAP, Zurell et al. 2020). These tools facilitate the implementation of best-practice guidelines to assess the quality of a model, indicating whether it meets minimal standards for applied biodiversity uses (Araújo et al. 2019; Sofaer et al. 2019). Heavily leveraging ENMeval 2.0 and rangeModelMetadata, Wallace now uses Range Modeling Metadata Standards (RMMS) data objects (which also form the basis of ODMAP reporting) and allows the user to download them as a CSV file (or a ZIP file for multiple species). Wallace promotes documentation and downstream assessment of modeling quality by allowing users to download extensive information that includes sources of input data, methodological decisions, and results. One option for the documentation (see Module: Download Session Code) is a file that can be re-run in R to reproduce the analyses (if re-run on exactly the same versions of R and dependent packages). Many intermediate and advanced users of R likely will find this file useful as a template for modification. Additionally, Wallace now provides citations of the particular R packages (and their versions) used in a given analysis (Module: Reference Packages).

In publications and reports based on analyses run in Wallace, citation of all packages used both promotes documentation and gives credit to the developers of the packages with which Wallace is built. Dovetailing with the modular nature of Wallace, such citation should increase the incentive for researchers to formalize their code into R packages on CRAN and join the Wallace community to integrate them into future releases of the software.

IMPLEMENTATION

Users can download a list of references for the R packages used in the analyses. This module utilizes RefManageR and knitcitations (McLean 2020; Boettiger 2021). The list can be downloaded as a .pdf, HTML, or .doc file.

REFERENCES

Araújo, M.B., Anderson, R.P., Barbosa, A.M., Beale, C.M., Dormann, C.F., Early, R., Garcia, R.A., Guisan, A., Maiorano, L., Naimi, B., O’Hara, R.B., Zimmermann, N.E., & Rahbek, C. (2019). Standards for distribution models in biodiversity assessments. Science Advances, 5, 1. DOI: 10.1126/sciadv.aat4858

Boettiger, C. (2021). knitcitations: Citations for 'Knitr' Markdown Files. R package version 1.0.12. CRAN

Feng, X., Park, D.S., Walker, C., Peterson, A.T., Merow, C., & Papeş, M. (2019). A checklist for maximizing reproducibility of ecological niche models. Nature Ecology & Evolution, 3, 1382–1395. DOI: 10.1038/s41559-019-0972-5

Fitzpatrick, F.C., Lachmuth, S., & Haydt, N.T. (2021). The ODMAP protocol: a new tool for standardized reporting that could revolutionize species distribution modeling. Ecography, 44(7), 1067-1070.DOI: 10.1111/ecog.05700

Kass, J.M, Muscarella, R., Galante, P.J, Bohl, C.L., Pinilla-Buitrago, G.E., Boria, R.A., Soley-Guardia, M., & Anderson, R.P. (2021). ENMeval 2.0: Redesigned for customizable and reproducible modeling of species’ niches and distributions. Methods in Ecology and Evolution, 12(9), 1602– 1608. DOI: 10.1111/2041-210X.13628

McLean, M.W. (2020). RefManageR: Straightforward 'BibTeX' and 'BibLaTeX' Bibliography Management. R package version 1.3.0. CRAN

Merow, C., Maitner, B.S., Owens, H.L., Kass, J.M., Enquist, B.J., Jetz, W., & Guralnick, R.P. (2019). Species’ range model metadata standards: RMMS. Global Ecology and Biogeography, 28(12), 1912–1924. DOI: 10.1111/geb.12993

Owens, H. L., Merow, C., Maitner, B.S., Kass, J.M., Barve, V., & Guralnick, R.P. (2021). occCite: Tools for querying and managing large biodiversity occurrence datasets. Ecography, 44(8), 1228-1235. DOI: 10.1111/ecog.05618

Sofaer, H.R., Jarnevich, C.S., Pearse, I.S., Smyth, R.L, Auer, S., Cook, G.L., Edwards, T.C., Guala, G.F., Howard, T.G., Morisette, J.T., & Hamiliton, H. (2019). Development and delivery of species distribution models to inform decision-making. BioScience, 69(7), 544–557. DOI: 10.1093/biosci/biz045

Zurell, D., et al. (2020). A standard protocol for reporting species distribution models. Ecography, 43(9), 1261–1277. DOI: 10.1111/ecog.04960

wallace documentation built on Sept. 11, 2024, 9:16 p.m.