Malcomb et al Reanalysis

Oct-12 : In this lesson, we will reanalyze the vulnerability model for Malawi and test robustness.

The purpose of this lab is to:

• choose a parameter or set of interdependent parameters of the Malcomb et al climate vulnerability model for Malawi which represents a subjective researcher decision
• change the parameter or set of parameters
• test the vulnerability model’s robustness to the change
• visualize and interpret your results in the context of theory on error and uncertainty in spatial models in general and vulnerability models in particular

Procedure

• identify an error, uncertain decision, or opportunity for improving reproducibility or study design. Everyone can contribute to the following on this reproduction:
  1. Finalize one cohesive report. I will do as much of this as I can before lab…
  2. Investigate metadata documentation for the data sources and integrate what you learn into the report. Metadata is found in the data/metadata folder. and the data_metadata.csv file tells you which metadata files are associated with which data inputs. This investigation may lead to aspects of the study that you want to change.
• write a plan for modifications in markdown, including:
  1. title and author (yourself)
  2. description of modification(s) with rationale(s)
  3. plan for visualizing/comparing/interpreting of results
  4. save as docs/reports/<name>-analysis-plan.md, e.g. docs/reports/holler-analysis-plan.md
  5. commit the plan and push to GitHub
  6. this is a small-scale version of a preregistration
• modify the main 01-Rpr-Malcomb-2014.Rmd analysis plan & code to address the issue identified above
• implement the change in code
• interpret the results of your change(s) in the rmarkdown report
• knit a new study report html form. See this video
• enable GitHub Pages on the repository to serve the html version of the report to the web. (see previous video)
• write a blog post highlighting what you have learned from and contributed to with this reproduction and reanalysis study. In particular, the report and blog should address error and uncertainty in the Malcomb et al study in the context of Longley’s and Tate’s frameworks.
  • Keep in mind, a blog post is for highlights : aim for a post to be a short and impactful advertisement for the full study… no more than two paragraphs.
• Link to your full study from the blog post

Timeline

• Thursday, October 12 Lab: Finalize analysis plan and commit the plan to GitHub
• Before Thursday, October 19 Lab: Commit finalized analysis report and blog post to GitHub

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