In PredictiveEcology/SpaDES.Workshops: Training workshops for ecological modeling with SpaDES

knitr::opts_chunk$set(cache = TRUE, echo = TRUE, eval = FALSE)

Reproducible pipeline

*…This places an obligation on all creators of software to program in such a way that the computations can be understood and trusted. This obligation I label the Prime Directive.*

• John Chambers (Software for Data Analysis: Programming with R)

Adaptive management

• Ideally, we can rerun all decision support tools over and over again
• Must be MUCH easier the second, third, etc. time
• If there is an incremental change in input data, then we shouldn't need to redo the same effort as the first time around (e.g., Cache).

Why reproducible?

• Rerun analysis/model
• New computer or new team member
• Rebuild a figure (e.g., for publication)
• Address reviewer comments prior to publication
• Quickly update with new data
• Quickly update downstream reporting
• Defendability & transparency

Beyond reproducibility: reusablility

Open-ness and accessibility

• facilitate reusability & sharing
• increased densibility & transparency
• should be freely available

Interoperability

• modular design
• facilitate integration

Continuous workflow

Automatic testing

• R package infrastructure is tested daily by CRAN
• SpaDES family of packages tested everytime code committed

but what about SpaDES modules?

• unit tests (currently need to be run manually)

The 'PERFICT' approach

Predictive Ecology that is

• Reusable,
• Freely available,
• Interoperable,
• use a Continuous workflow,
• Tested automatically.

Substantial immediate and long-term benefits, at the [minor] cost of (re)learning and modifying current workflows

Data-to-decisions

What is SpaDES?

a. an R package (or family of packages) for sequencing model events;
b. a modelling philosophy;
c. an implementation of PERFICT;
d. all of the above.

*Bringing the best science, data, models into the hands of policy makers in real time, on their phones*

Best practices

Working with spatial data and simulations

http://www.alexchubaty.com/r-talks/spatial-data-best-practices/spatial-data-best-practices.html#/4

PredictiveEcology/SpaDES.Workshops documentation built on Jan. 30, 2021, 6:52 p.m.