Initial commit

.Rbuildignore

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+^mininglucc\.Rproj$
+^\.Rproj\.user$
+^LICENSE\.md$
+^README\.Rmd$
+^README-.*\.png$
+^CONDUCT\.md$
+^CONTRIBUTING\.md$
+analysis

.gitignore

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+.Rproj.user
+.Rhistory
+.RData

CONDUCT.md

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+# Contributor Code of Conduct
+
+As contributors and maintainers of this project, we pledge to respect all people who 
+contribute through reporting issues, posting feature requests, updating documentation,
+submitting pull requests or patches, and other activities.
+
+We are committed to making participation in this project a harassment-free experience for
+everyone, regardless of level of experience, gender, gender identity and expression,
+sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.
+
+Examples of unacceptable behavior by participants include the use of sexual language or
+imagery, derogatory comments or personal attacks, trolling, public or private harassment,
+insults, or other unprofessional conduct.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments,
+commits, code, wiki edits, issues, and other contributions that are not aligned to this 
+Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed 
+from the project team.
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by 
+opening an issue or contacting one or more of the project maintainers.
+
+This Code of Conduct is adapted from the Contributor Covenant 
+(http:contributor-covenant.org), version 1.0.0, available at 
+http://contributor-covenant.org/version/1/0/0/

CONTRIBUTING.md

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+# Contributing
+
+We love pull requests from everyone. By participating in this project, you
+agree to abide by our [code of conduct](CONDUCT.md).
+
+## Getting Started
+
+* Make sure you have a [GitHub account](https://github.com/signup/free). If you are not familar with git and GitHub, take a look at <http://happygitwithr.com/> to get started.
+* [Submit a post for your issue](https://github.com/<USERNAME>/<REPO>/issues/), assuming one does not already exist.
+  * Clearly describe your issue, including steps to reproduce when it is a bug, or some justification for a proposed improvement.
+* [Fork](https://github.com/<USERNAME>/<REPO>/#fork-destination-box) the repository on GitHub to make a copy of the repository on your account. Or use this line in your shell terminal:
+
+    `git clone [email protected]:your-username/<REPO>.git`
+
+## Making changes
+
+* Edit the files, save often, and make commits of logical units, where each commit indicates one concept
+* Follow our [style guide](http://adv-r.had.co.nz/Style.html).
+* Make sure you write [good commit messages](http://tbaggery.com/2008/04/19/a-note-about-git-commit-messages.html).
+* Make sure you have added the necessary tests for your code changes.
+* Run _all_ the tests using `devtools::check()` to assure nothing else was accidentally broken.
+* If you need help or unsure about anything, post an update to [your issue](https://github.com/<USERNAME>/<REPO>/issues/).
+
+## Submitting your changes
+
+Push to your fork and [submit a pull request](https://github.com/<USERNAME>/<REPO>/compare/).
+
+At this point you're waiting on us. We like to at least comment on pull requests
+within a few days (and, typically, one business day). We may suggest
+some changes or improvements or alternatives.
+
+Some things you can do that will increase the chance that your pull request is accepted:
+
+* Engage in discussion on [your issue](https://github.com/<USERNAME>/<REPO>/issues/).
+* Be familiar with the backround literature cited in the [README](README.Rmd)
+* Write tests that pass.
+* Follow our [code style guide](http://adv-r.had.co.nz/Style.html).
+* Write a [good commit message](http://tbaggery.com/2008/04/19/a-note-about-git-commit-messages.html).
+
+
+

DESCRIPTION

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+Package: mininglucc
+Title: What the Package Does (One Line, Title Case)
+Version: 0.0.0.9000
+Authors@R:
+    person(given = "First",
+           family = "Last",
+           role = c("aut", "cre"),
+           email = "[email protected]")
+Description: What the package does (one paragraph).
+License: GPL-3
+ByteCompile: true
+Encoding: UTF-8
+LazyData: true
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.1.1
+Imports: bookdown,
+    here
+Suggests: devtools,
+    git2r

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+

README.Rmd

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+---
+output: github_document
+---
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+```{r, echo = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  fig.path = "README-"
+)
+# Please put your title here to include it in the file below.
+Title <- "Title of your paper goes here"
+```
+
+# mininglucc
+
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh///master?urlpath=rstudio)
+
+This repository contains the data and code for our paper:
+
+> Authors, (YYYY). _`r Title`_. Name of journal/book <https://doi.org/xxx/xxx>
+
+Our pre-print is online here:
+
+> Authors, (YYYY). _`r Title`_. Name of journal/book, Accessed `r format(Sys.Date(), "%d %b %Y")`. Online at <https://doi.org/xxx/xxx>
+
+
+### How to cite
+
+Please cite this compendium as:
+
+> Authors, (`r format(Sys.Date(), "%Y")`). _Compendium of R code and data for `r Title`_. Accessed `r format(Sys.Date(), "%d %b %Y")`. Online at <https://doi.org/xxx/xxx>
+
+## Contents
+
+The **analysis** directory contains:
+
+  - [:file\_folder: paper](/analysis/paper): R Markdown source document
+    for manuscript. Includes code to reproduce the figures and tables
+    generated by the analysis. It also has a rendered version,
+    `paper.docx`, suitable for reading (the code is replaced by figures
+    and tables in this file)
+  - [:file\_folder: data](/analysis/data): Data used in the analysis.
+  - [: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.
+
+## How to run in your broswer or download and run locally
+
+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](https://cloud.r-project.org/)
+itself and optionally [RStudio Desktop](https://rstudio.com/products/rstudio/download/).
+
+The simplest way to explore the text, code and data is to click on
+[binder](https://mybinder.org/v2/gh///master?urlpath=rstudio)
+to open an instance of RStudio in your browser, which will have the
+compendium files ready to work with. Binder uses rocker-project.org
+Docker images to ensure a consistent and reproducible computational
+environment. These Docker images can also be used locally.
+
+You can download the compendium as a zip from from this URL:
+[master.zip](/archive/master.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.Rmd` and knit to produce the `paper.docx`, or run `rmarkdown::render("analysis/paper/paper.Rmd")` in the R console
+
+### Licenses
+
+**Text and figures :**  [CC-BY-4.0](http://creativecommons.org/licenses/by/4.0/)
+
+**Code :** See the [DESCRIPTION](DESCRIPTION) file
+
+**Data :** [CC-0](http://creativecommons.org/publicdomain/zero/1.0/) attribution requested in reuse
+
+### Contributions
+
+We welcome contributions from everyone. Before you get started, please see our [contributor guidelines](CONTRIBUTING.md). Please note that this project is released with a [Contributor Code of Conduct](CONDUCT.md). By participating in this project you agree to abide by its terms.
+

README.md

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+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+# mininglucc
+
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh///master?urlpath=rstudio)
+
+This repository contains the data and code for our paper:
+
+> Authors, (YYYY). *Title of your paper goes here*. Name of journal/book
+> <https://doi.org/xxx/xxx>
+
+Our pre-print is online here:
+
+> Authors, (YYYY). *Title of your paper goes here*. Name of
+> journal/book, Accessed 06 Nov 2020. Online at
+> <https://doi.org/xxx/xxx>
+
+### How to cite
+
+Please cite this compendium as:
+
+> Authors, (2020). *Compendium of R code and data for Title of your
+> paper goes here*. Accessed 06 Nov 2020. Online at
+> <https://doi.org/xxx/xxx>
+
+## Contents
+
+The **analysis** directory contains:
+
+  - [:file\_folder: paper](/analysis/paper): R Markdown source document
+    for manuscript. Includes code to reproduce the figures and tables
+    generated by the analysis. It also has a rendered version,
+    `paper.docx`, suitable for reading (the code is replaced by figures
+    and tables in this file)
+  - [:file\_folder: data](/analysis/data): Data used in the analysis.
+  - [: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.
+
+## How to run in your broswer or download and run locally
+
+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](https://cloud.r-project.org/) itself and optionally [RStudio
+Desktop](https://rstudio.com/products/rstudio/download/).
+
+The simplest way to explore the text, code and data is to click on
+[binder](https://mybinder.org/v2/gh///master?urlpath=rstudio) to open an
+instance of RStudio in your browser, which will have the compendium
+files ready to work with. Binder uses rocker-project.org Docker images
+to ensure a consistent and reproducible computational environment. These
+Docker images can also be used locally.
+
+You can download the compendium as a zip from from this URL:
+[master.zip](/archive/master.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.Rmd` and knit to produce the `paper.docx`, or run
+`rmarkdown::render("analysis/paper/paper.Rmd")` in the R console
+
+### Licenses
+
+**Text and figures :**
+[CC-BY-4.0](http://creativecommons.org/licenses/by/4.0/)
+
+**Code :** See the [DESCRIPTION](DESCRIPTION) file
+
+**Data :** [CC-0](http://creativecommons.org/publicdomain/zero/1.0/)
+attribution requested in reuse
+
+### Contributions
+
+We welcome contributions from everyone. Before you get started, please
+see our [contributor guidelines](CONTRIBUTING.md). Please note that this
+project is released with a [Contributor Code of Conduct](CONDUCT.md). By
+participating in this project you agree to abide by its terms.

analysis/paper/paper.Rmd

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+---
+title: "Title Goes Here"
+author:
+  - Myfirstname Mylastname:
+      email: [email protected]
+      institute: [UofO]
+      correspondence: true
+  - Yourfirstname Yourlastname:
+      email: [email protected]
+      institute: [UofA]
+      correspondence: false
+institute:
+  - UofO: University of One Place
+  - UofA: University of Another Place
+date: "`r format(Sys.time(), '%d %B, %Y')`"
+output: 
+    bookdown::word_document2:
+      fig_caption: yes
+      reference_docx: "../templates/template.docx" # Insert path for the DOCX file
+      pandoc_args:
+      - --lua-filter=../templates/scholarly-metadata.lua
+      - --lua-filter=../templates/author-info-blocks.lua
+      - --lua-filter=../templates/pagebreak.lua
+bibliography: references.bib
+csl: "../templates/journal-of-archaeological-science.csl" # Insert path for the bib-style
+abstract: |
+  Text of abstract
+keywords: |
+  keyword 1; keyword 2; keyword 3
+highlights: |
+  These are the highlights. 
+---
+
+<!-- This is the format for text comments that will be ignored during renderings. Do not put R code in these comments because it will not be ignored. -->
+
+<!-- With the following code you can access and display values from the yml header above. -->
+
+Keywords: `r rmarkdown::metadata$keywords`
+
+Highlights: `r rmarkdown::metadata$highlights`
+
+<!-- The following code chunk defines some general settings how code chunks should behave. -->
+
+```{r setup, echo = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  warning = FALSE,
+  message = FALSE,
+  echo = FALSE,
+  comment = "#>",
+  fig.path = "../figures/",
+  dpi = 300
+)
+```
+
+<!-- The actual document text starts here: -->
+
+# Introduction
+
+Here is a citation [@Marwick2017]
+
+# Background
+
+# Methods
+
+# Results
+
+<!-- Here's some example analysis code: -->
+
+```{r get-data, eval = FALSE}
+# Note the path that we need to use to access our data files when rendering this document
+my_data <- read.csv(here::here('analysis/data/raw_data/my_csv_file.csv'))
+```
+
+```{r demo-plot, fig.cap="A plot of random numbers"}
+plot(rnorm(10))
+```
+
+Figure \@ref(fig:demo-plot) shows how we can have a caption and cross-reference for a plot
+
+```{r demo-inline-code}
+x <- round(pi, 2)
+```
+
+Here is an example of inline code `r x` in the middle of a sentence. 
+
+# Discussion
+
+# Conclusion
+
+# Acknowledgements
+
+<!-- The following line inserts a page break  -->
+
+\newpage
+
+# References 
+
+<!-- The following line ensures the references appear here for the MS Word or HTML output files, rather than right at the end of the document (this will not work for PDF files):  -->
+
+<div id="refs"></div>
+
+\newpage
+
+### Colophon
+
+This report was generated on `r Sys.time()` using the following computational environment and dependencies: 
+
+```{r colophon, cache = FALSE}
+# which R packages and versions?
+if ("devtools" %in% installed.packages()) devtools::session_info()
+```
+
+The current Git commit details are:
+
+```{r}
+# what commit is this file at? 
+if ("git2r" %in% installed.packages() & git2r::in_repository(path = ".")) git2r::repository(here::here())  
+```