Initiate a directory that contains all of the files needed for a stock assessment document written with sa4ss.
draft(
authors,
species = "Species name",
latin = "Scientific name",
coast = "U.S. West Coast",
type = c("sa"),
create_dir = FALSE,
edit = FALSE,
...
)A vector of author names. For example,
"John R. Doe" without first name first. The middle
initial or name is optional. Entries must exactly match
those used in the "data-raw\authors.csv" file.
If you need additional authors added to this file
please contact the package maintainers or add them to the
.csv file and run the R script also found in that
folder prior to submitting a pull request. Following this
workflow ensures that the author's address is also added.
A vector of character strings providing species names for
all species included in the stock assessment. Typically, there will only
be one species, but this template can accommodate a species complex as well.
Each species should be capitalized as you would like to see it used in the middle
of a sentence. For example,
"Pacific Hake" is used in the stock assessment of hake;
not "pacific hake" because Pacific Hake is the preferred name, not
pacific hake. The text can be called in the document using spp for the
form to be used in the middle of a sentence and Spp when placed at the
beginning of a sentence.
A character string specifying the Latin name without italic formatting. Please capitalize as you want it to be used in the document though because case will not be altered.
A character string specifying which part of the coast the stock
assessment includes. For example, "U.S. West Coast", which is the
default, will be used to create the following title: "Status of common
name (latin name) along the U.S. West Coast in 2010". Previously, the word
coast was added internally to the text, this is no longer the default
behavior of sa4ss and instead you must explicitly add the word, which
allows users to have more flexibility. For example, "California Coast from
Point Conception north" is a viable option.
The name of the template you want to initiate. The default
template is sa, which stands for stock assessment. As development for
sa4ss progresses, expect to see more templates become available.
Available templates are listed in the default function call. Specify a
single character value from those available if you want to change the type
from the default.
A logical value that leads to the draft document being
placed in its own directory called "doc". The default value of
FALSE uses the current working directory rather than containing all
of the files in a new directory, which is helpful if you want to use your
own name for the directory. TRUE will create the new directory
"doc" and copy of the necessary files into it. A third option also
exists, "default", which allows rmarkdown::draft(), to determine the
appropriate directory structure.
A logical value, with a default of FALSE, specifying if
you want to open the indexing file for editing by default. The software
chosen by R is normally not ideal and the file is not a file that is
normally edited by users, which is why sa4ss does not follow the
default value used by rmarkdown::draft().
Additional arguments that you wish to pass to
rmarkdown::draft(). See args(rmarkdown::draft).
Invisibly returns the file name of the document, which will be the main
indexing file that links to the auxiliary files. If edit = TRUE, this file
will be opened for editing.
rmarkdown::draft()The function is based on rmarkdown::draft() that creates new R Markdown
documents based on templates stored within R packages. The
rticles R package stores the most
templates, mainly for the submission of manuscripts to journals.
User input for parameters such as authors and species help customize the
draft to your stock assessment document. Therefore, users should focus on
the input arguments that come before type = because these will be specific
to the stock assessment and are used to set up the initial file structure.
A template contains two mandatory objects,
template.yaml
skeleton/skeleton.Rmd,
and optional files include those in a directory named resources and
additional files within the skeleton directory. Because it is not known what
your directory will be named, the skeleton file is renamed to 00a.Rmd by
this function to ensure that it comes first in bookdown's rendering of all
of the .Rmd files, which is done alphabetically unless users specify all the
files, an option that we do not really want to use.
See draft.
if (FALSE) { # \dontrun{
sa4ss::draft()
} # }