Last updated: 2020-06-30
Checks: 1 1
Knit directory: Fiber_Intervention_Study/
This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
The R Markdown file has unstaged changes. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.
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 d377778. 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: .Rhistory
Ignored: .Rproj.user/
Ignored: code/.Rhistory
Ignored: reference-papers/Dietary_Variables.xlsx
Ignored: reference-papers/Johnson_2019.pdf
Ignored: renv/library/
Ignored: renv/staging/
Untracked files:
Untracked: analysis/hei_data_doublecheck.Rmd
Untracked: fig/figure6.pdf
Untracked: fig/figures-2020-06-21.zip
Untracked: fig/figures-2020-06-21/
Untracked: fig/figures-2020-06-23.zip
Untracked: fig/figures-2020-06-23/
Untracked: manuscript/Figures_2020_06_26.pdf
Untracked: manuscript/Manuscript Draft 2020-06-26[2].docx
Untracked: manuscript/Manuscript Draft 2020-06-28-NP.docx
Unstaged changes:
Modified: analysis/analysis_anthropometric.Rmd
Modified: analysis/index.Rmd
Deleted: fig/figure1_alpha_diversity.pdf
Deleted: fig/figure1_legend.pdf
Deleted: fig/figure2_individual_beta_diversity_over_study.pdf
Deleted: fig/figure3_PCoA_analysis_results_beta_diversity_between_groups.pdf
Deleted: fig/figure3_legend.pdf
Deleted: fig/figure4_final_microbiome_diet_variables_over_time.pdf
Deleted: fig/figure4_legend.pdf
Deleted: fig/figure5_glmm_genus.pdf
Deleted: fig/figure5_glmm_phylum.pdf
Deleted: fig/figure6_change_in_BMI.pdf
Modified: fig/figures-2020-06-17.zip
Modified: tab/results_glmm_microbiome_genus.csv
Modified: tab/results_glmm_microbiome_phylum.csv
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/index.Rmd) and HTML (docs/index.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 |
|---|---|---|---|---|
| Rmd | d377778 | noah-padgett | 2020-06-17 | updated genus level analyses |
| html | d377778 | noah-padgett | 2020-06-17 | updated genus level analyses |
| html | 9da43aa | noah-padgett | 2020-06-08 | Build site. |
| Rmd | 774d405 | noah-padgett | 2020-06-01 | updated glmm and figures |
| html | 774d405 | noah-padgett | 2020-06-01 | updated glmm and figures |
| html | 0733fe5 | noah-padgett | 2020-05-21 | Build site. |
| Rmd | e5d2921 | noah-padgett | 2020-05-14 | updated index |
| html | e5d2921 | noah-padgett | 2020-05-14 | updated index |
| Rmd | 25bfffd | noah-padgett | 2020-05-07 | fixed index references |
| html | 25bfffd | noah-padgett | 2020-05-07 | fixed index references |
| Rmd | 774a55f | noah-padgett | 2020-04-16 | updated beta diversity and permanova |
| html | 774a55f | noah-padgett | 2020-04-16 | updated beta diversity and permanova |
| html | 51b6275 | noah-padgett | 2020-02-20 | Build site. |
| Rmd | 1c719ff | noah-padgett | 2020-02-20 | updated output window size |
| html | 1c719ff | noah-padgett | 2020-02-20 | updated output window size |
| html | 6de5819 | noah-padgett | 2020-02-06 | Build site. |
| Rmd | b076219 | noah-padgett | 2020-02-06 | glmm results added |
| html | bc47d52 | noah-padgett | 2020-02-06 | Build site. |
| Rmd | cf9504e | noah-padgett | 2020-02-06 | glmm results added |
| html | cf9504e | noah-padgett | 2020-02-06 | glmm results added |
| Rmd | 4aac91f | noah-padgett | 2020-01-30 | update home page |
| html | 4aac91f | noah-padgett | 2020-01-30 | update home page |
| html | c1bce73 | noah-padgett | 2019-12-11 | Build site. |
| Rmd | d0fce22 | noah-padgett | 2019-12-11 | wflow_git_commit(all = T, force = T) |
| html | d0fce22 | noah-padgett | 2019-12-11 | wflow_git_commit(all = T, force = T) |
| html | f275c59 | noah-padgett | 2019-12-10 | Initial commit - Noah |
| Rmd | 9d0b939 | noah-padgett | 2019-12-10 | wflow_git_commit(all = T) |
| Rmd | 46f9359 | noah-padgett | 2019-12-10 | Start workflowr project. |
Welcome to our research website. This page will contain links to the results pages from our study.
Describing the data and pre-processing steps.
This page gives the results of testing the changes in anthropometric variables (BMI, LBM, VFL, Weight) between the beginning and end of the study. This page tests the changes in clinical measures (e.g., Glucose, BUN, Creatinine, Chloride, HDL, Insulin, PYY, etc.). In summary, no significance differences were detectable after controlling for multiple comparisons.
This file gives the code that generates Figure 4: the plot describing the change in microbiome relative abundance (phylum-level) over time and the change in diet variables over time.
*Microbiome and Diet Trends over Time
Next, we double checked the some data w.r.t. fat and HEI scores
Alpha diversity was measures using richness (Observed OTUs) and evenness (Shannon and Inverse Simpson). This first page gives general overview of how alpha diversity metrics varied among subjects, between intervention groups, and over time. No statistical analyses were conducted, these were helpful for getting a sense of how alpha diversity varied prior to moving into analyses.
On this page, we conducted more formal investigations of changes in alpha diversity using linear mixed effects models. These results were inconclusive as to the effect of the intervention on alpha diversity metrics.
*Beta Diversity Analyses This page describes the beta-diversity analyses used and the results of PERMANOVAs.
These two pages describe the models and results used to test the changes in microbiome abundance over time. We used generalized linear mixed effects models. In summary, eight separate models were hypothesized and tested and final results are presented describing which microbiome (phylum/genus-level) abundances changed over time with respect to the intervention. The results presented in text are from model 6 (the last set of results presented). *Modeling changes in Phylum-level abundance
*Modeling changes in Genus-level abundance
Next, we focused on the genus level analyses in more detail.
*Genera relative abundance information
*Focused analysis of prevotella and bacteroides
This page describes the relationships between microbiome abundance and different food metrics (HEI scores). *Microbiome and Food Plot