## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(collapse = TRUE, comment = "#>")

## ----eval = FALSE-------------------------------------------------------------
# set_paper(".")           # once a session: the project to work on
# 
# # while you write
# render_html()            # the manuscript, in seconds
# preview()                # live: reloads every time you save
# 
# # documents to read, in output/
# render_docx()            # the .docx, in the journal's style
# render_pdf()             # the .pdf
# render_supplementary()   # the supplement, with its own references
# render_all()             # the three above, and the analysis code
# 
# # what you send, in submission/
# make_preprint()          # the preprint and its data deposit
# make_submission()        # the journal's folder, double-blind

## ----eval = FALSE-------------------------------------------------------------
# library(easypaper)
# 
# create_paper("my_paper",
#              title   = "Manuscript title here",
#              authors = c("Charles Darwin", "Alfred Russel Wallace"))

## ----eval = FALSE-------------------------------------------------------------
# library(easypaper)
# set_paper(".")

## ----eval = FALSE-------------------------------------------------------------
# create_example_paper("example_paper")   # needs the vegan package

## ----eval = FALSE-------------------------------------------------------------
# list_journals()                  # the styles you have
# add_journal("ecology-letters")   # -> references/ecology-letters.csl
# render_docx("ecology-letters")   # this render only, in that style

## ----eval = FALSE-------------------------------------------------------------
# convert_data("originals/counts.xlsx")   # one workbook, one .csv per sheet
# convert_data("originals")               # a whole folder at once

## ----eval = FALSE-------------------------------------------------------------
# make_submission()                        # own document
# make_submission(suppl_figures = "main")  # end of the main text

## ----eval = FALSE-------------------------------------------------------------
# td_upload("02_introduction")     # the section, as a Google Doc
# td_download("02_introduction")   # their edits, back into the .qmd
# td_update("02_introduction")     # your local version, over the Google Doc

## ----eval = FALSE-------------------------------------------------------------
# check_species_text()

## ----eval = FALSE-------------------------------------------------------------
# check_packages()    # packages the manuscript loads that are not installed
# check_citations()   # @keys with no entry in references/: the render stops
# check_crossrefs()   # @fig-/@tbl- with no target, and figures nobody cites
# check_title()       # does the manuscript still have the template's title?
# check_renv()        # is renv.lock there, and does it match what you use?
# check_data()        # files in data/ that the analysis never reads
# check_species()     # scientific names of the references left in doubt

## ----eval = FALSE-------------------------------------------------------------
# manuscript_stats()
# #> Manuscript summary
# #>   Title                          87 characters
# #>   Title, without spaces          75 characters
# #>   Short title                    38 characters
# #>   Short title, without spaces    34 characters
# #>   Abstract                      243 words
# #>   Keywords                        5
# #>   Main text                    6120 words
# #>   Main text + references       7480 words
# #>   References                     61
# #>   Figures                         5
# #>   Tables                          2
# #>   Supplementary figures           3
# #>   Supplementary tables            1

## ----eval = FALSE-------------------------------------------------------------
# render_html()                       # seconds, while you write
# render_docx()                       # the .docx, in the journal manuscript.qmd names
# render_pdf()                        # the .pdf, for a preprint server or for reading
# render_all()                        # docx and pdf, with their supplements, and the code

## ----eval = FALSE-------------------------------------------------------------
# make_preprint()                       # -> submission/bioRxiv/
# make_preprint(label = "EcoEvoRxiv")   # another server
# make_preprint()                       # again: submission/bioRxiv_v2/
# make_preprint(line_numbers = FALSE, line_spacing = 2)  # unnumbered, double-spaced

## ----eval = FALSE-------------------------------------------------------------
# make_preprint()                     # builds data_and_code.zip (or make_submission())
# deposit_zenodo(sandbox = TRUE)      # try it on Zenodo's sandbox first
# deposit_zenodo()                    # the real draft, and its DOI

## ----eval = FALSE-------------------------------------------------------------
# edit_metadata("attributes")   # what each column means, and its units
# edit_metadata("biblio")       # what the dataset is, when and where
# edit_metadata("write")        # dataspice.json and its web page

## ----eval = FALSE-------------------------------------------------------------
# make_submission()                                     # -> submission/JournalofEcology/, double-blind
# make_submission(blind = FALSE)                        # signed, for a journal that is not blind
# make_submission()                                     # again: submission/JournalofEcology_v2/

## ----eval = FALSE-------------------------------------------------------------
# make_submission(line_numbers = FALSE, line_spacing = 1.5)
# make_submission(figure_format = "png", suppl_figures = "main")

## ----eval = FALSE-------------------------------------------------------------
# convert_data("originals", also = "las")   # LiDAR point clouds, copied too

## ----eval = FALSE-------------------------------------------------------------
# # in the first chunk of any .qmd or .Rmd, which runs before pandoc reads it
# easypaper::italicize_species("references.bib", "references_italic.json")

## ----eval = FALSE-------------------------------------------------------------
# render_docx(caption_style = "abbrev")              # Fig. 1. / Table 1.
# make_submission("ecology-letters", caption_style = "colon")

## ----eval = FALSE-------------------------------------------------------------
# render_docx(caption_style = "custom")   # Fig. 1: ... / Tab. 1: ... / Fig. S1: ...

## ----eval = FALSE-------------------------------------------------------------
# citation("easypaper")