bbartholdy/mb11calculuspilot

Multiproxy analysis exploring patterns of diet and disease in dental calculus and skeletal remains from a 19th century Dutch population

Research compendium for Bartholdy et al. 2023

This repository contains the data and code for our paper:

Bartholdy, B.P., Hasselstrøm, J.B., Sørensen, L.K., Casna, M., Hoogland, M., Historisch Genootschap Beemster, & Henry, A.G. (2023). Multiproxy analysis exploring patterns of diet and disease in dental calculus and skeletal remains from a 19th century Dutch population. Zenodo, Accessed 26 Sep 2023. Online at https://doi.org/10.5281/zenodo.7649151

How to cite

Use the above paper to cite this compendium.

Contents

The root directory contains:

• 📁 data-raw: R script to download and process the raw data from Zenodo (https://zenodo.org/record/8061483).
• 📁 data: Data output from data-raw/*.R, used in the analysis (.rda).
• 📁 R: R functions required in the analysis.

The analysis directory contains:

• 📁 paper: Quarto source document for manuscript. Includes code to reproduce the figures and tables generated by the analysis.
• 📁 figures: Plots and other illustrations
• 📁 supplementary-materials: Supplementary materials including notes and other documents prepared and collected during the analysis.

How to run in your browser or download and run locally

If you are running Linux, you will need to install gfortran, e.g. sudo apt install gfortran for Ubuntu.

This research compendium has been developed using the statistical programming language R. To work with the compendium, you will need installed on your computer the R software itself, optionally (but recommended) RStudio Desktop, and Quarto.

You can download the compendium as a zip from from this URL:

main.zip.

or clone the repository:

git clone [email protected]:bbartholdy/mb11CalculusPilot.git

Then:

• open the .Rproj file in RStudio
• run devtools::install() to ensure you have the packages this analysis depends on (also listed in the DESCRIPTION file).
• finally, open analysis/paper/paper.qmd and render to produce the PDF manuscript (_output/), or run quarto::quarto_render("analysis/paper/paper.qmd") in the R console.

Licenses

Text and figures : CC-BY-4.0

Code : See the DESCRIPTION file

Data : CC-0 attribution requested in reuse

Contributions

We welcome contributions from everyone. Before you get started, please see our contributor guidelines. Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

mb11calculuspilot's Issues

codecheck feedback from SJE

hi Bjorn, I'm trying to render your doc.

As I had renv installed, I had to go through and install a heap of extra packages via renv

rmarkdown
here
dplyr
tidy
ggplot2
ggcorrplot
psych
patchwork
readr
devtools
rbbt

but then when I render from the CLI using markdown, I get an almost empty HTML.

rmarkdown::render('analysis/paper/paper.qmd')

should I be using quarto instead?

If I try quarto, I get a bit further:

> system("quarto render paper.qmd")

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union


Attaching package: ‘psych’

The following objects are masked from ‘package:ggplot2’:

    %+%, alpha

ℹ Loading mb11CalculusPilot
Error : Can't connect to the Better BibTeX endpoint. Is Zotero running?
`summarise()` has grouped output by 'sample'. You can override using the
`.groups` argument.
Joining, by = c("sample", "batch")
Warning message:
Removed 143 rows containing missing values. 
Joining, by = "id"
Error in `mutate()`:
! Problem while computing `caries_count = if_else(caries == "none", 0L,
  1L, missing = NA)`.
Caused by error in `if_else()`:
! `missing` must be an integer vector, not a logical vector.
Backtrace:
     ▆
  1. ├─... %>% ungroup()
  2. ├─dplyr::ungroup(.)
  3. ├─mb11CalculusPilot::tooth_position(.)
  4. │ └─.data %>% ... at mb11CalculusPilot/R/utils.R:45:2
  5. ├─dplyr::mutate(...)
  6. ├─dplyr::summarise(., count = sum(caries_count), )
  7. ├─dplyr::group_by(., id, tooth)
  8. ├─dplyr::mutate(...)
  9. ├─dplyr:::mutate.data.frame(., caries_count = if_else(caries == "none", 0L, 1L, missing = NA))
 10. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
 11. │   ├─base::withCallingHandlers(...)
 12. │   └─mask$eval_all_mutate(quo)
 13. └─dplyr::if_else(caries == "none", 0L, 1L, missing = NA)
 14.   └─dplyr:::replace_with(...)
 15.     └─dplyr:::check_type(val, x, name, error_call = error_call)
 16.       └─rlang::abort(msg, call = error_call)
Execution halted



processing file: paper.qmd
  |                                                                             |                                                                      |   0  |                                                                             |....                                                                  |   5%
label: setup (with options) 
List of 2
 $ include: logi FALSE
 $ cache  : logi FALSE

Quitting from lines 2-12 (paper.qmd) 
Error in `mutate()`:
! Problem while computing `caries_count = if_else(caries == "none", 0L,
  1L, missing = NA)`.
Caused by error in `if_else()`:
! `missing` must be an integer vector, not a logical vector.
Backtrace:
  1. ... %>% ungroup()
 13. dplyr::if_else(caries == "none", 0L, 1L, missing = NA)

Execution halted
> 

CC: @nuest