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I sincerely thank the R user community, `bookdown` authors, Zotero, and ISU Lunchinators for inspiration, coaching, and troubleshooting.
This current structure works best for me.
The following folders are populated as the manuscript submission progresses.
1-Background: motivation to conduct the research and relevant .pdf of the literature
2-Data: raw and clean data sheets
3-Doc: data management plan and logistical documents
4-Data-wrangling: `.R` files with codes to clean the raw data
5-Analysis: `.Rmd` executable files to analyze the data and render report. Each `.Rmd` file is devoted to address one hypothesis
6-Draft: to put everything together. `.bib` (the Zotero generated bibliography) `Introduction.Rmd`, `MandM.Rmd`, and `Discussion.Rmd` live here.
7-Extra: anything else relevant but does not fit into the previous 6 folders.
General workflow:
1 - Each `.Rmd` file is devoted to address one hypothesis.
2 - All the pieces are put together under `Draft.Rmd`. The execution of `Draft.Rmd` will generate:
i) a latex-figure folder with all the figures from the `.Rmd` files.
ii) a `.tex` file and a `.pdf` file.
3 - The `.tex` file is uploaded to Overleaf for final polishing that are very inconvenient or impossible to do in R.