In benmarwick/researchcompendium:

knitr::opts_chunk$set(echo = FALSE)
project_start_date <- "2017-06-01"
# checkpoint::checkpoint(snapshotDate = project_start_date, use.knitr = TRUE)

Introduction

R Markdown

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com.

When you click the Knit button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

In Table \@ref(tab:carstab) we can see some data about the relationship between pressure and tempurature. We can reference the table by the ID of the code chunk that produces the table, like this: \@ref(tab:carstab)

library(knitr)
kable(head(mtcars), caption = "Data about cars")

Including Plots

You can also embed plots, for example:

plot(pressure)

In Figure \@ref(fig:pressureplot) we can see some data about pressure. We can cross-reference the figure like this: \@ref(fig:pressureplot), using the chunk ID as the key to link the cross-reference to the figure.

Note that the echo = FALSE parameter was added to the code chunk to prevent printing of the R code that generated the plot.

Citations and References

We can have a citation, using a .bib file that holds all the details. To get this: [@Marwick2016repro] we type [@Marwick2016repro]. The text after the @ is the bibtex key that links the in-text citation to the full details in the .bib file.

All of the usual variations on in-text citation formatting are possible in markdown, and listed for reference here: http://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html

Customising

After cloning this repo, I can replace 'researchcompendium' by the name of the new repo in every file where it occurs with this line in my bash terminal:

find . -type f -exec sed -i 's/foo/bar/g' {} +

I also need to switch on the new repo at https://travis-ci.com/, https://circleci.com/ & https://hub.docker.com and enter my details so that circle-ci can push to docker hub

Colophon

This report was generated on r Sys.time() using the following computational environment and dependencies:

# which R packages and versions?
kable(data.frame(Setting = names(devtools::session_info()$platform),
                 Value = sapply(devtools::session_info()$platform, `[`, 1),
                 stringsAsFactors = FALSE,
                 row.names = NULL),
      caption = "R session information")

kable(devtools::session_info()$packages,
      caption = "Packages that this report depends on")

# what commit is this file at?
library(git2r)
repo <- repository(path = "../..")
last_commit <- commits(repo)[[1]]

The current git commit of this file is r last_commit@sha, which is on the r branches(repo)[[1]]@name branch and was made by r last_commit@committer@name on r when(last_commit). The current commit message is "r last_commit@summary".