Matimmune.knit.md

Last updated: 2024-06-09

Checks: 2 0

Knit directory: madi-brussels-pertussis-thailand/

This reproducible R Markdown analysis was created with workflowr (version 1.7.1). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Repository version: 59a1721

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version 59a1721. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:


Ignored files:
    Ignored:    .RData
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/

Untracked files:
    Untracked:  analysis/cluster_pca_single4_old.Rmd
    Untracked:  withelisa.csv
    Untracked:  withelist1.csv

Unstaged changes:
    Modified:   analysis/antigenPCA_single.Rmd
    Modified:   analysis/apwp_pca_single.Rmd
    Modified:   analysis/cluster_pca_single4.Rmd
    Modified:   analysis/cluster_single.Rmd
    Modified:   analysis/doublepca1.Rmd
    Modified:   analysis/mediation_individual.Rmd
    Modified:   analysis/mediation_multiple.Rmd
    Modified:   analysis/mediation_pca.Rmd
    Modified:   analysis/mediation_pls_3.Rmd
    Modified:   analysis/mediation_verification.Rmd
    Modified:   data/dirEffect_wp_nocofounder_pca.Rd
    Modified:   data/dirEffect_wp_nocofounder_pls_3.Rd
    Modified:   data/medEffect_wp_nocofounder_pca.Rd
    Modified:   data/medEffect_wp_nocofounder_pls_3.Rd
    Modified:   data/totalEffect_wp_nocofounder_pca.Rd

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/Matimmune.Rmd) and HTML (docs/Matimmune.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
html	8c46744	Jie Zhou	2024-06-03	remove antigen elisa
Rmd	1b36bb0	Jie Zhou	2024-05-13	added the first apwp results
html	1b36bb0	Jie Zhou	2024-05-13	added the first apwp results

0.1 Causal Mediation Analysis

In the Causal Mediation Analysis section, the direct effects of the study treatments may be mediated by Cord blood (at birth) total IgG or Prevaccinated infant serum (Month 2). Response variables are of three types.