Create an example project: a small study, written as an easypaper paper

Writes the same project as create_paper(), with a short study in it instead of empty sections: the trees of Barro Colorado Island, Panama, as the vegan package distributes them (BCI), analysed, written up and cited. Every part of a manuscript is there, written the way the package expects it, to read, render and copy from:

Usage

create_example_paper(path, overwrite = FALSE, git = TRUE, open = FALSE)

Arguments

path: Directory to create, as a single non-empty string; ~ is expanded. Its base name becomes the name of the .Rproj file. A path that exists as a file is refused.
overwrite: Write into a directory that already has files in it. FALSE (the default) refuses, so an existing manuscript is never silently overwritten.
git: Initialise a git repository and make the first commit. TRUE by default: it is local and private, costs a second, and gives the manuscript a history from its first line instead of from the day you remember to start one. It has nothing to do with GitHub, which is a later and separate decision. Needs git on the PATH and a configured user.name / user.email; if either is missing, the project is still created and you are told what to run.
open: Open the new project in RStudio. Needs an RStudio session and the rstudioapi package; outside one, the project is created and a message says so.

Value

The absolute path of the created project, invisibly.

Details

manuscript.qmd              title, short title, authors with shared
                            affiliations and their ORCID iDs, the
                            corresponding author
_sections/01_abstract.qmd   the abstract, and the keywords under it
_sections/02_introduction   citations in brackets and in the sentence
_sections/03_methods        the text of the Methods, and a chunk that reads
                            the data from data/ for every analysis
_sections/04.1_richness     each analysis beside its text, in a file named
_sections/04.2_composition  after it: a GLM of richness; a PERMANOVA, a
                            PERMDISP and an NMDS of composition;
                            numbers written by inline R, never typed;
                            scientific names written by R, in italics
_sections/10_figures        two figures: an NMDS with names in italics
_sections/11_tables         two flextables, with the three rules
_sections/12.1_suppl        a supplementary figure and table
_sections/06-09             the statements at the end, filled in
data/                       the two tables of BCI, as .csv
references/                 the five references the text cites, one
                            with a species in its title, set in italics
                            by every render; the style is the
                            template's, Journal of Ecology

create_paper() stays the one to start a paper of your own with: it writes the structure and nothing else.

It needs one package, vegan: its BCI and BCI.env data are written into data/, and the analysis uses it. When it is missing, the function stops before writing anything, and says what to install. The data were collected by Condit et al. (2002), Science 295: 666–669, doi:10.1126/science.1066854 : cite them, not this example, if you use them. The authors of the example are borrowed from the history of the field – Charles Darwin and Alfred Russel Wallace, who never wrote it – and their affiliations, emails and ORCID iDs are made up.

Examples