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Agenda

Practicing and Teaching Reproducibility and Replicability in the Human-Environment and Geographical Sciences

Introduction

  • Support
  • Introductions:
    • Name
    • Institution
    • Research or teaching project related to R&R
  • Defining R&R
  • Practicing R&R
  • Teaching R&R
  • Seminar Objectives
  • Research Objectives
  • State of the Research
  • Findings from Reproductions

Part I: Overview of R&R in HEGS

Vignette: Spatial Accessibility in Illinois

  • Reproduce studies with Jupyter Notebook on CyberGISX
  • Reproduction and Replication studies by Derrick Burt
  • Reanalysis by Kufre Udoh
  • Reprodution study with the Spring 2021 class and Summer 2021 research assistants

Reproducibility and Replicability in the Geographical Sciences

  • Sciences
    • Science under COVID-19
    • How do we trust science?
  • Spatial autocorrelation and heterogeneity
  • Reproduction for credibility and scientific progress
  • Literature highlights
  • Highlights of R&R in geography

Practical Computational Reproducibility

  • Conditions for reproducibility
  • Improving R&R
  • Infrastructure

R&R Pedagogy

  • Project-based learning
  • Rethinking the learning goals
  • Open Source GIScience curriculum
  • Vision for R&R in geography

Discussion session I

  • What are our individual and collective motivations for trying reproduction studies?
  • Any failures, concerns, and misgiving?

Part II: Research Compendium in Git & GitHub

GitHub Overview

  • Challenges
  • Git & GitHub version control
  • GitHub features
  • Tips, Tricks & Limitation

Template for R&R Research in HEGS

  • Executable research compendium
  • Repository template for HEGS research
  • Use .gitignore and code to manage data

Managing GitHub Repositories

Discussion session II

  • Are there any specific ways you want to integrate Git version control into your scholarship?
  • Are there specific reasons that you wish you had already adopted Git in the past?
  • Any concerns or misgivings?

Part III: Plan and Register a Reproduction / Replication Study

Pre-analysis Plan Overview

  • Reproduction study worked example
  • Pre-analysis planning & registration
  • OSF pre-analysis plan registration
  • R&R pre-analysis plan
  • Workflow diagram
  • Activity

The Spatial Scan Statistics

  • SaTScan
    • SaTScan input
    • SaTScan analysis
    • SaTScan advanced options
  • Generalized Estimating Equations

Discussion session III

  • Have we already learned more from researching its data sources and planning a workflow? What?
  • Do you notice any errors or missing information? If you were peer reviewing this study or planning to reproduce it, what more would you want to know?
  • Have you developed any concerns about the study?

Discussion session IV

  • Does the “spatial is special” phrase apply to pre-analysis plan registration?
  • Are there ways in which spatial data and spatial analysis require additional attention to detail and scrutiny if pre-analysis planning is to support enhanced replicability?

Part IV: Execute a Computational Notebook in RStudio

RStudio and R Markdown Overview

  • GUI for R
  • R Markdown computational notebook
  • Reading R
  • R Markdown practices

Execute R Markdown Computational Notebooks

Reproduction Study Result

  • Comparing GEE results
  • Reproduction report

Discussion session V

  • Was this reproduction an exact success? Approximate success? Failure?
  • Why?

Discussion session VI

  • Have we learned anything about Chakraborty’s study that we did not know based on the paper? What?
  • Can you imagine ways in which the reproduction study could be replicated, reanalyzed, or extended?

Discussion session VII

  • Are there specific ways you can imagine benefitting from R&R practices into your ongoing and future scholarly activity?
  • Are there specific barriers to adopting R&R practices into your ongoing and future scholarly activity?

Discussion session VII

  • If we can work out R&R in geography, can you envision ways in which geography could contribute to other sciences or to convergent / interdisciplinary research?
  • Interest in trying a reproduction or replication project in a course you are teaching?

Appreciation