List methodology in the order in which results are presented.
Typically the order is:
If a table/graph (or analysis) is not discussed in the paper, it should not be included in the paper.
This also extends to the methods section: we only describe methods that are used in the paper.
The tables included after Table 1 typically correspond to research questions/hypotheses.
For each table, indicate what outcome was modeled, what method was used to model it, and any relevant notes about the modeling.
The tables included after Table 1 typically correspond to research questions/hypotheses.
We also want to explicitly state how the results are displayed in the tables.
Finally, we include technical details about how the data was handled during the analysis.
We always state (and cite) the software used to produce information for the paper.
Every software has its preferences on how use should be cited in papers.
To cite R in publications use:
R Core Team (2025). _R: A Language and Environment for Statistical
Computing_. R Foundation for Statistical Computing, Vienna, Austria.
<https://www.R-project.org/>.
A BibTeX entry for LaTeX users is
@Manual{,
title = {R: A Language and Environment for Statistical Computing},
author = {{R Core Team}},
organization = {R Foundation for Statistical Computing},
address = {Vienna, Austria},
year = {2025},
url = {https://www.R-project.org/},
}
We have invested a lot of time and effort in creating R, please cite it
when using it for data analysis. See also 'citation("pkgname")' for
citing R packages.
To cite package 'tidyverse' in publications use:
Wickham H, Averick M, Bryan J, Chang W, McGowan LD, François R,
Grolemund G, Hayes A, Henry L, Hester J, Kuhn M, Pedersen TL, Miller
E, Bache SM, Müller K, Ooms J, Robinson D, Seidel DP, Spinu V,
Takahashi K, Vaughan D, Wilke C, Woo K, Yutani H (2019). "Welcome to
the tidyverse." _Journal of Open Source Software_, *4*(43), 1686.
doi:10.21105/joss.01686 <https://doi.org/10.21105/joss.01686>.
A BibTeX entry for LaTeX users is
@Article{,
title = {Welcome to the {tidyverse}},
author = {Hadley Wickham and Mara Averick and Jennifer Bryan and Winston Chang and Lucy D'Agostino McGowan and Romain François and Garrett Grolemund and Alex Hayes and Lionel Henry and Jim Hester and Max Kuhn and Thomas Lin Pedersen and Evan Miller and Stephan Milton Bache and Kirill Müller and Jeroen Ooms and David Robinson and Dana Paige Seidel and Vitalie Spinu and Kohske Takahashi and Davis Vaughan and Claus Wilke and Kara Woo and Hiroaki Yutani},
year = {2019},
journal = {Journal of Open Source Software},
volume = {4},
number = {43},
pages = {1686},
doi = {10.21105/joss.01686},
}
To cite bayesrules package in publications use:
Mine Dogucu, Alicia Johnson, Miles Ott (2021). bayesrules: Datasets
and Supplemental Functions from Bayes Rules! Book Retrieved from
https://github.com/bayes-rules/bayesrules R package version 0.0.2.900
A BibTeX entry for LaTeX users is
@Manual{,
title = {bayesrules: Datasets and Supplemental Functions from Bayes Rules! Book},
author = {Mine Dogucu and Alicia Johnson and Miles Ott},
year = {2021},
url = {https://github.com/bayes-rules/bayesrules},
note = {R package version 0.0.2.9000},
}
Finally (finally!), we should state the a priori significance level if we are analyzing under the frequentist framework.
If we are analyzing under the Bayesian framework, that will be obvious when we describe our modeling approach.
Descriptive data are shown as median (range) or n (%), as appropriate. What numbers are shown in the cells of the table?
Continuous variables were compared using the Kruskal-Wallis test. Categorical variables were compared using the \chi^2 or Fisher’s exact tests, as appropriate. How were p-values generated?
Note the informative footnote!
Descriptive data are shown as median (range) or n (%), as appropriate. Continuous variables were compared using the Kruskal-Wallis test. Categorical variables were compared using the \chi^2 or Fisher’s exact tests, as appropriate.
Hospital mortality and use of extracorporeal membrane oxygenation were modeled using logistic regression. Regression results are shown as odds ratio (95% confidence interval; CI). Significance of predictors was assessed using the omnibus Wald \chi^2 test. When appropriate, pairwise comparisons were made using the Bonferroni adjustment.
Data management and analysis were performed using SAS software, Version 9.3 (SAS Institute, Inc., Cary, NC). A priori significance was defined as p < 0.05.
We just need to make sure that information is noted somewhere.
Example of recently-published supplement: click here.
The original rule still applies, though: if there is no mention of it in the paper, it should not be included in the supplementary materials.
Why are we talking about this? (Adding details for interpretations.)
You will be expected to provide basic examples of how to interpret coefficients in the model(s) you are using in this analysis.
Again, only include what is necessary to understand the results.
When working with others & disagreeing on what should be included, I will ask myself, “is this my hill to die on?”
Battles I have won:
Battles I have not won:
I do not write this section until after the results section is finalized and/or I know exactly what tables and graphs are being included in the paper.
Note that generally, tables take the same appearance. I make sure we are consistent with how results are displayed across tables in a paper, which also helps with writing the methods section.
However, sometimes a journal has requirements for tables. Fields have different ways they present model results.
Today we have talked about the basics of writing a statistical methods section corresponding to the analysis you performed.
While this discussion is in the academic context, you can still employ these methods outside of academic papers:
STA6349 - Applied Bayesian Analysis - Fall 2025