Create example repo

.gitignore

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+**/.DS_Store
+
 # History files
 .Rhistory
 .Rapp.history

README.md

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-# starter_folder
+# starter_folder
+
+This repo....
+
+It is organised as follows...

outputs/paper/paper.Rmd

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+---
+title: "TBD"
+subtitle: "TBD"
+author: "TBD"
+thanks: "Code and data are available at: LINK."
+date: "`r format(Sys.time(), '%d %B %Y')`"
+abstract: "First sentence. Second sentence. Third sentence. Fourth sentence."
+output:
+  bookdown::pdf_document2:
+toc: FALSE
+bibliography: references.bib
+---
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+
+library(tidyverse)
+library(palmerpenguins)
+```
+
+# Introduction
+
+
+
+
+# Data
+
+Our data is of penguins (Figure \@ref(fig:bills)).
+
+```{r bills, fig.cap="Bills of penguins", echo = FALSE}
+ggplot(penguins, aes(x = island, fill = species)) +
+  geom_bar(alpha = 0.8) +
+  scale_fill_manual(values = c("darkorange","purple","cyan4"),
+                    guide = FALSE) +
+  theme_minimal() +
+  facet_wrap(~species, ncol = 1) +
+  coord_flip()
+```
+
+Talk more about it.
+
+Also bills and their average (Figure \@ref(fig:billssssss)). (Notice how you can change the height and width so they don't take the whole page?)
+
+```{r billssssss, fig.cap="More bills of penguins", echo = FALSE, fig.width=8, fig.height=4}
+
+# This needs to be about the random data tha tI sasmpled?
+ggplot(penguins, aes(x = island, fill = species)) +
+  geom_bar(alpha = 0.8) +
+  scale_fill_manual(values = c("darkorange","purple","cyan4"),
+                    guide = FALSE) +
+  theme_minimal() +
+  facet_wrap(~species, ncol = 1) +
+  coord_flip()
+```
+
+Talk way more about it. 
+
+
+
+# Model
+
+\begin{equation}
+Pr(\theta | y) = \frac{Pr(y | \theta) Pr(\theta)}{Pr(y)}  (\#eq:bayes)
+\end{equation}
+
+Equation \@ref(eq:bayes) seems useful, eh?
+
+Here's a dumb example of how to use some references: In paper we run our analysis in `R` [@citeR]. We also use the `tidyverse` which was written by @thereferencecanbewhatever If we were interested in baseball data then @citeLahman could be useful. 
+
+
+# Results
+
+# Discussion
+
+## First discussion point
+
+If my paper were 10 pages, then should be be at least 2.5 pages. The discussion is a chance to show off what you know and what you learnt from all this. 
+
+## Second discussion point
+
+## Third discussion point
+
+## Weaknesses and next steps
+
+Weaknesses and next steps should also be included.
+
+\newpage
+
+# Appendix {-}
+
+\newpage
+
+
+# References
+
+

outputs/paper/references.bib

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+@Manual{citeR,
+    title = {R: A Language and Environment for Statistical Computing},
+    author = {{R Core Team}},
+    organization = {R Foundation for Statistical Computing},
+    address = {Vienna, Austria},
+    year = {2020},
+    url = {https://www.R-project.org/},
+  }
+  
+  
+@Article{thereferencecanbewhatever,
+    title = {Welcome to the {tidyverse}},
+    author = {Hadley Wickham and Mara Averick and Jennifer Bryan and Winston Chang and Lucy D'Agostino McGowan and Romain François and Garrett Grolemund and Alex Hayes and Lionel Henry and Jim Hester and Max Kuhn and Thomas Lin Pedersen and Evan Miller and Stephan Milton Bache and Kirill Müller and Jeroen Ooms and David Robinson and Dana Paige Seidel and Vitalie Spinu and Kohske Takahashi and Davis Vaughan and Claus Wilke and Kara Woo and Hiroaki Yutani},
+    year = {2019},
+    journal = {Journal of Open Source Software},
+    volume = {4},
+    number = {43},
+    pages = {1686},
+    doi = {10.21105/joss.01686},
+  }  
+  
+  
+@Manual{citeLahman,
+    title = {Lahman: Sean `Lahman' Baseball Database},
+    author = {Michael Friendly and Chris Dalzell and Martin Monkman and Dennis Murphy},
+    year = {2020},
+    note = {R package version 8.0-0},
+    url = {https://CRAN.R-project.org/package=Lahman},
+  }  

starter_folder.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX