Merge remote-tracking branch 'origin/main'

README.md

@@ -1,7 +1,7 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-# mb11CalculusPilot
+# Research compendium for Bartholdy et al. 2023
 
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/bbartholdy/mb11CalculusPilot/main?urlpath=rstudio)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7649825.svg)](https://zenodo.org/badge/DOI/10.5281/zenodo.7649825)
@@ -18,7 +18,7 @@ Our pre-print is online here:
 > 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 12 Sep 2023. Online at
+> Zenodo, Accessed 26 Sep 2023. Online at
 > <https://doi.org/10.5281/zenodo.7649151>
 
 ### How to cite
@@ -28,30 +28,36 @@ Use the above paper to cite this compendium.
 <!--
 Please cite this compendium as:
 
-> Bartholdy, B.P., Hasselstrøm, J.B., Sørensen, L.K., Casna, M., Hoogland, M., Historisch Genootschap Beemster, & Henry, A.G., (2023). _Compendium of R code and data for Multiproxy analysis exploring patterns of diet and disease in dental calculus and skeletal remains from a 19th century Dutch population_. Accessed 12 Sep 2023. Online at <https://doi.org/10.5281/zenodo.7649825>
+> Bartholdy, B.P., Hasselstrøm, J.B., Sørensen, L.K., Casna, M., Hoogland, M., Historisch Genootschap Beemster, & Henry, A.G., (2023). _Compendium of R code and data for Multiproxy analysis exploring patterns of diet and disease in dental calculus and skeletal remains from a 19th century Dutch population_. Accessed 26 Sep 2023. Online at <https://doi.org/10.5281/zenodo.7649825>
 -->
 
 ## Contents
 
+The **root** directory contains:
+
+- [:file_folder: data-raw](/data-raw/): R script to download and process
+  the raw data from Zenodo (<https://zenodo.org/record/8061483>).
+- [:file_folder: data](/data/): Data output from `data-raw/*.R`, used in
+  the analysis (*.rda*).
+- [:file_folder: R](/R/): R functions required in the analysis.
+
 The **analysis** directory contains:
 
 - [:file_folder: paper](/analysis/paper): Quarto source document for
   manuscript. Includes code to reproduce the figures and tables
   generated by the analysis.
-- [:file_folder: data](/data/): Data output from `data-raw/*.R`, used in
-  the analysis (*.rda*).
-- [:file_folder: analysis/figures](/analysis/figures): Plots and other
+- [:file_folder: figures](/analysis/figures): Plots and other
   illustrations
 - [:file_folder:
   supplementary-materials](/analysis/supplementary-materials):
   Supplementary materials including notes and other documents prepared
   and collected during the analysis.
-- [:file_folder: R](/R/): R functions required in the analysis.
-- [:file_folder: data-raw](/data-raw/): R script to download and process
-  the raw data from Zenodo (<https://zenodo.org/record/8061483>).
 
 ## 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
@@ -61,12 +67,22 @@ Desktop](https://rstudio.com/products/rstudio/download/), and
 [Quarto](https://quarto.org/docs/get-started/).
 
 You can download the compendium as a zip from from this URL:
-[main.zip](/archive/main.zip). After unzipping: - open the `.Rproj` file
-in RStudio - run `devtools::install()` to ensure you have the packages
-this analysis depends on (also listed in the [DESCRIPTION](/DESCRIPTION)
-file). - finally, open `analysis/paper/paper.qmd` and **render** to
-produce the PDF manuscript (`_output/`), or run
-`rmarkdown::render("analysis/paper/paper.qmd")` in the R console.
+
+[main.zip](/archive/refs/heads/main.zip).
+
+or clone the repository:
+
+`git clone git@github.com: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](/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