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This PR is looking great! Please address my inline comments, and try to get all the automated checks to pass; if you have questions about any of those checks, please tag me in a comment on this PR, and we can discuss them when we meet.
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| I think the commented-out section above is not necessary in this .qmd file. I would like to generate simulated data from the longitudinal data for this .qmd file only. The section above will be handled in the _ses_outtakes-data-load.qmd file. |
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I agree with taking this part out; in fact, let's limit this .qmd even further; it should only contain the code that fits the longitudinal model to the real longitudinal data, performs MCMC diagnostics, and graphs the fitted model.
Simulating longitudinal data from an existing seroresponse model should be a separate .qmd.
| curve_params_shigella <- jags.post |> postprocess_jags_output() | ||
| usethis::use_data(curve_params_shigella, overwrite = TRUE) | ||
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| #curve_params_shigella <- jags.post |> postprocess_jags_output() #somehow it doesn't work |
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| #curve_params_shigella <- jags.post |> postprocess_jags_output() #somehow it doesn't work | ||
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| # Use Sam's package rather than my current R function |
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The version of postprocess_jags_data() in the {serodynamics} package is an extended version of your function from this project.
We can remove the original version from this project, and we can use and extend the {serodynamics} version going forward;
it's not inherently specific to shigella, so it belongs in the serodynamics package.
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Suggestion for line 2:
generate_final_table <- function(results_list, sample_size = attr(results_list, "sample_size")) {See related change to end of simulated_seroincidence2(); metadata such as sample size should stay connected to the corresponding object
the output of generate_final_table() should also have attributes sample_size and age_range
| ggplot(summary_metrics_combined, aes(x = sample_size, y = empirical_se, color = Age_Group)) + | ||
| geom_line() + | ||
| geom_point() + | ||
| labs( | ||
| title = "IpaB-IgG with the Smallest Lambda", | ||
| x = "Sample Size", | ||
| y = "Empirical Standard Error", | ||
| color = "Age Group" | ||
| ) + | ||
| theme_minimal() |
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let's turn all this ggplot code (lines 136-145) into a function?
Co-authored-by: Douglas Ezra Morrison <demorrison@ucdavis.edu>
Co-authored-by: Douglas Ezra Morrison <demorrison@ucdavis.edu>
Co-authored-by: Douglas Ezra Morrison <demorrison@ucdavis.edu>
Co-authored-by: Douglas Ezra Morrison <demorrison@ucdavis.edu>
Co-authored-by: Douglas Ezra Morrison <demorrison@ucdavis.edu>
Co-authored-by: Douglas Ezra Morrison <demorrison@ucdavis.edu>
Co-authored-by: Douglas Ezra Morrison <demorrison@ucdavis.edu>
Co-authored-by: Douglas Ezra Morrison <demorrison@ucdavis.edu>
Co-authored-by: Douglas Ezra Morrison <demorrison@ucdavis.edu>
Co-authored-by: Douglas Ezra Morrison <demorrison@ucdavis.edu>
Co-authored-by: Douglas Ezra Morrison <demorrison@ucdavis.edu>
Merge branch 'practice_Kwan' of https://github.com/UCD-SERG/shigella into practice_Kwan # Please enter a commit message to explain why this merge is necessary, # especially if it merges an updated upstream into a topic branch. # # Lines starting with '#' will be ignored, and an empty message aborts # the commit.
2 participants
I modified two .qmd files and added one new .qmd file. I also added some R function files. I think I may need to delete some unnecessary R function files.
There are three .qmd files. Please review them step by step:
Please go through the .qmd files above in order.