Data and Tools

I am working on two R packages now, i.e., enmRoute and PhenMap, they were deposited in my GitHub: the former package aims to develop and optimize survey route for planning field survey of early established populations, whereas the latter aims to mapping critical phonological events. They were designed to promote detection of early established invasive populations, in right time and place.

enmRoute package

The aim of this package is to use habitat suitability prediction (i.e., from ecological niche model) to optimize biodiversity survey in an expected area. Our primary results show that field surveys by using our ecological niche model-based tool could help us to promote the detection. We hope this model-based route could help field biologists design sampling routes for regional and national surveys. Check out the tutorial here: https://github.com/gpzhu/enmRoute. We are also developing a shiny app to facilitate the application of enmRoute: https://enmapp.shinyapps.io/enmroute.

In our framework, the candidate survey polygon patches were assembled from the buffer of incursion population distribution and niche model suitability prediction. Regional habitat suitability prediction is changed into binary predictions and transformed into polygon patches (Step 1). Candidate polygon patches were prioritized by removing small and low CCI ranked patches, the centroids of remaining candidate polygons are used to generate the optimal survey route (Step 2). Iterations of procedure in red arrows can assess the relationship (panel in dashed line) between survey expenses (i.e., inter patch driving time, and the accumulated inner patch survey expense, which is scaled with accumulated CCI) and the number of patches to be sampled, which can be used to determine how many and which patches should be used in survey network given available time and resources.

**Schematic overview of the survey route optimization framework, where arrows indicate data flows and outputs.**

Key Words: Survey route, Optimization, Ecological Niche Model, Habitat suitability, Carrying Capacity Index (CCI)

PhenMap package

The PhenMap package intends to map phenology events via process- and correlative- approaches.

Other Data and R code:

All data and R code that accompany my publication were also deposited in my Open Science Framework.