Summary
- Began to know about the workflow when using R as suggested. https://www.tellingstorieswithdata.com/workflow.html#developing-research-questions. Basic knowledge: R Markdown, R projects, relevant skills to access data, write code comments, etc.
- Set up R project for all the documents used to practice with: Example data, R scripts, RMarkdown files and output files, Summary documents for each meeting, etc.
- Have installed
rstan and brms packages in RStudio.
- Read Chapter 1,2,3 and 9 of “Statistical Rethinking” using
rstan as well as brms: https://bookdown.org/content/4857/markov-chain-monte-carlo.html. Reproduced the output of the “Terrain Ruggedness” example: “rugged” data pre-processing, sampling from posterior probability of 3 parameters, how to set up # of chains & cores, sample visualizations, check the chains with trace plots and trank plots, tuning superparameters like iter, warmup.
- Had a glance at the recommended article (comparison between BUGS and STAN): https://besjournals.onlinelibrary.wiley.com/doi/epdf/10.1111/2041-210X.12681.
- Materials about origin or concepts of HMC that I read once or am currently reading:
- BRMS package preferred: Now reading “Advanced Bayesian Multilevel Modeling with the R Package brms” (Paul-Christian Bürkner, 2018): https://journal.r-project.org/archive/2018/RJ-2018-017/RJ-2018-017.pdf. Trying all the examples included in this article.
- Tried to use RMarkdown to present the output, analysis results of some examples for practice. (saved as .html). Learning some commands commonly used.
Questions
- Requirement for numbers of words or pages?
- Presents novel models/methods?
- Medical data, where to get?
- A timeline of the statistic project.
- Next steps:
- continue exploring
brms.
- start looking for the topics and data for the final dissertation.
- review and learn more about HMC.
- use RMarkdown to write the general framework for the dissertation.
- Q: What else?
- Leapfrog method. Neal’s review, MCMC using Hamiltonian dynamics (Neal, 2012): https://arxiv.org/pdf/1206.1901.pdf, page 8 & 14
knitr::include_graphics("images/leapfrog algorithm.png")

knitr::include_graphics("images/leapfrog raw codes.png")
