In 2019, a joint project called the “Synthesis of Gully MPA Oceanographic Monitoring Data” was initiated between Fisheries and Oceans Canada (DFO)’s Maritimes Region Canadian Science Advisory Secretariat (CSAS) and the Atlantic Zone Monitoring Program (AZMP). The aim of this project was to compile the physical, chemical and biological oceanographic data collected by the AZMP in the Gully MPA, and provide preliminary analyses of patterns in these conditions over a near 20-year period. Given that this represented the first synthesis and preliminary analysis of AZMP data that are biannually collected within the Gully MPA, one of the primary deliverables of this project was to create and archive reproducible R code that could be used to A) produce a template for reproducible analytical products designed to evaluate changes in oceanographic conditions in the MPA, and B) create a reproducible technical report to facilitate consistent reporting of these trends, as new data are collected.
R package csasdown was recently developed by members of DFO’s Pacific Region to facilitate the creation of reproducible CSAS documents using R Markdown and bookdown. The package also includes scripts for generating reproducible DFO technical reports (see Guide for the production of Fisheries and Oceans Canada science report series for more information).
The purpose of these instructions is two-fold: A) to provide a basic demonstration to new users of csasdown on how to create a reproducible DFO technical report, and B) to provide a guide to the scripts used to create the Canadian Technical Report of Hydrography and Ocean Sciences report titled “Ocean monitoring of the Gully MPA - A synopsis of data collected by the Atlantic Zone Monitoring Program”.
It is our hope that future initiatives aimed at analyzing and reporting on the oceanographic conditions of the Gully MPA could utilize these instructions and code to produce a report with consistent analytical products and formatting.
The csasdown GitHub website provides a README.md and PDF presentation on the use of the package to create DFO CSAS reports. The various files and subfolders that are included with the csasdown package are explained in the README.md. Below is a quick demonstration on the creation of a blank/template DFO technical report produced using csasdown.
We recommend using RStudio as the integrated development environment (IDE). If the user is using Windows then it is highly recommended to also install Rtools, which are tools to compile R packages from source; a feature that is occasionally required.
The renv package is used to create a new R environment containing only base R packages, and all of the additional R packages required to create the technical report.
Step 1. Created a new R project (we called this ReproducibleReport) in a new directory of the same name. This is done by selecting the menu item File -> New Project which open the New Project wizard (Figure 1).
Step 2. Click the New Directory option.
Step 3. Click the New Project option.
Step 4. Check the boxes next to the options “Create a git repository” and “Use renv with this project” before pressing the Create Project button. Note the “Open in a new session” option only needs to be checked if the user was already in an active R project.
These options were selected to:
- start the project with a clean R environment containing only the R base packages (renv), and
- allow the tracking of all changes to the code and files (git).
A new R environment will open. The following figures show how the environment looks within RStudio and in the file browser.
Re-creating a reproducible report requires the user to have knowledge of what R packages were used and their version numbers. R package renv tracks this information automatically with little user involvement.
One of the useful functions of renv is being able to see if your environment has changed; i.e., it is out of sync with the lockfile (a text file storing information about the packages that have been installed in the environment). Below is the current contents of the lockfile (renv.lock). Notice the only project package installed is renv.
{
"R": {
"Version": "4.0.5",
"Repositories": [
{
"Name": "CRAN",
"URL": "https://cran.rstudio.com"
}
]
},
"Packages": {
"renv": {
"Package": "renv",
"Version": "0.13.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "079cb1f03ff972b30401ed05623cbe92"
}
}
}To check if the environment is out of sync, execute the renv::status
command below. You will see that the project is synced with the
lockfile.
> renv::status()
* The project is already synchronized with the lockfile.Step 5. Now it is time to add the R packages required to create the reproducible report. Run the following commands to install the remotes and csasdown packages. The remotes package allows you to install remote repositories (i.e., from GitHub).
> install.packages("remotes")
Installing remotes [2.2.0] ...
OK [copied local binary]
> remotes::install_github("pbs-assess/csasdown")
Downloading GitHub repo pbs-assess/csasdown@HEAD
Downloading GitHub repo pbs-assess/rosettafish@HEAD
Installing 4 packages: stringi, magrittr, glue, stringr
Installing packages into ‘C:/DEV/GullyReproducibleReport/renv/library/R-4.0/x86_64-w64-mingw32’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/stringi_1.5.3.zip'
Content type 'application/zip' length 15243599 bytes (14.5 MB)
downloaded 14.5 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/magrittr_2.0.1.zip'
Content type 'application/zip' length 235751 bytes (230 KB)
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trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/glue_1.4.2.zip'
Content type 'application/zip' length 154900 bytes (151 KB)
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trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/stringr_1.4.0.zip'
Content type 'application/zip' length 216733 bytes (211 KB)
downloaded 211 KB
package ‘stringi’ successfully unpacked and MD5 sums checked
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package ‘bookdown’ successfully unpacked and MD5 sums checkedNote that if the package is already stored on your computer, a message may appear that says OK [copied local binary] when installing the package in a new R environment. If the package is not locally stored then it will be downloaded from the default R package repository or the repository specified in the function call if retrieving it from GitHub, for example.
Now that a host of new packages were installed, check if the environment is out of sync:
> renv::status()
* The project is already synchronized with the lockfile.Surprisingly, the project is not out of sync with the lockfile after installing new packages. This is because none of project’s current files depend on the new packages to compile (run). Thus the environment is officially unchanged; although new packages are stored within the renv subfolder.
Step 6. Install the version of LaTeX that will be used to generate the PDF version of the report. This wiki page provides instructions for installing LaTeX for use with csasdown: https://github.com/pbs-assess/csasdown/wiki/Latex-Installation-for-csasdown.
> tinytex::install_tinytex()
trying URL 'https://yihui.org/tinytex/TinyTeX-1.zip'
Content type 'application/octet-stream' length 103777374 bytes (99.0 MB)
downloaded 99.0 MBThe outputs from the installation of tinytex may vary, but should resemble the following:
tlmgr install IEEEtran adjustbox algorithmicx algorithms appendix arydshln babel-english blindtext bookmark caption chngcntr cite collectbox colortbl datetime2 datetime2-english doi enumitem environ eso-pic etex-pkg everypage fancyhdr fp grfext hanging ifmtarg ifnextok import lastpage linegoal lineno lipsum luatex85 makecell marginnote microtype ms multirow ncctools nowidow oberdiek parskip pdfcomment pdfcrop pdflscape pdfpages pgf placeins ragged2e realboxes relsize rsfs scalerel sectsty setspace siunitx soul soulpos soulutf8 subfig tabu textcase textpos threeparttable threeparttablex titlecaps tlshell tocbibind tocloft tracklang trimspaces ulem varwidth was wrapfig xifthen xltabular zref
tlmgr.pl install: package IEEEtran not present in repository.
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tlmgr.pl: action install returned an error; continuing.
running mktexlsr ...
done running mktexlsr.
running updmap-sys ...
tlmgr.pl: An error has occurred. See above messages. Exiting.
done running updmap-sys.
tlmgr.pl: package log updated: C:/Users/JacksonJ/AppData/Roaming/TinyTeX/texmf-var/web2c/tlmgr.log
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tlmgr update --self
tlmgr install IEEEtran adjustbox algorithmicx algorithms appendix arydshln babel-english blindtext bookmark caption chngcntr cite collectbox colortbl datetime2 datetime2-english doi enumitem environ eso-pic etex-pkg everypage fancyhdr fp grfext hanging ifmtarg ifnextok import lastpage linegoal lineno lipsum luatex85 makecell marginnote microtype ms multirow ncctools nowidow oberdiek parskip pdfcomment pdfcrop pdflscape pdfpages pgf placeins ragged2e realboxes relsize rsfs scalerel sectsty setspace siunitx soul soulpos soulutf8 subfig tabu textcase textpos threeparttable threeparttablex titlecaps tlshell tocbibind tocloft tracklang trimspaces ulem varwidth was wrapfig xifthen xltabular zref
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tlmgr.pl: action install returned an error; continuing.
running mktexlsr ...
done running mktexlsr.
tlmgr.pl: An error has occurred. See above messages. Exiting.
tlmgr.pl: package log updated: C:/Users/JacksonJ/AppData/Roaming/TinyTeX/texmf-var/web2c/tlmgr.log
tlmgr.pl: command log updated: C:/Users/JacksonJ/AppData/Roaming/TinyTeX/texmf-var/web2c/tlmgr-commands.logStep 7. The draft function of R package csasdown is a wrapper
around the rmarkdown::draft function, and allows the user to create
reports that adhere to the template outlined by DFO CSAS publications
(csasdown::draft(“resdoc”) and (csasdown::draft(“sr”) for Research
Documents and Science Responses, respectively) and DFO secondary science
publications (csasdown::draft(“techreport”).
Secondary science publications include the DFO series ‘Canadian Technical Report of Fisheries and Aquatic Sciences’, ‘Canadian Data Report of Fisheries and Aquatic Sciences’, ‘Canadian Industry Report of Fisheries and Aquatic Sciences’, ‘Canadian Manuscript Report of Fisheries and Aquatic Sciences’, and ‘Canadian Hydrography and Ocean Sciences – Technical Reports’, among other series. These technical reports often contain preliminary scientific findings, and the Department normally provides the only review for these documents. For more information on DFO’s secondary publication series, please refer to: http://intra.dfo-mpo.gc.ca/science/publications/policy-politique/index-eng.html#24
Execute the draft function, setting “techreport” as the ‘type’:
> csasdown::draft("techreport")You will now see that a number of R markdown files and subfolders were unpacked into both the R environment and project directory.
Among these files includes several .Rmd files: 01_introduction.Rmd, 02_methods.Rmd, 03_results.Rmd, 04_discussion.Rmd, 05_appendix.Rmd, and 06_bibliography.Rmd. These .Rmd files form the various chapters of the technical report (introduction, methods, results, conclusion, etc.). If starting a new report, the user would simply write the text of each chapter directly into the .Rmd files, instead of using a word processor.
The index.Rmd file then ‘knits’ all the individual .Rmd chapters together to create a single Markdown (.md) file. This Markdown file is then converted to a LaTeX (.tex) file, and this .tex file is translated into the final PDF technical report document.
The _bookdown.yml file specifies which .Rmd files will be ‘knit’ when you press the knit button in index.Rmd:
book_filename: "techreport"
rmd_files: ["index.Rmd",
"01_introduction.Rmd",
"02_methods.Rmd",
"03_results.Rmd",
"04_discussion.Rmd",
"05_appendix.Rmd",
"06_bibliography.Rmd"]
delete_merged_file: trueWhen creating a new technical report, the user can rename these files to a custom naming convention, or add additional chapters as required. The **_bookdown.yml** file is very useful because you can comment out one or more lines/chapters so when the project is knit, only certain chapters are included. This allows the user to slowly build the report, checking the resulting output as content is added sequentially.
Once draft("techreport") is executed, the R environment becomes out of
sync. Use renv::status() to check the status of the environment:
> renv::status()
The following package(s) are installed but not recorded in the lockfile:
_
svglite [2.0.0]
lattice [0.20-41]
ps [1.6.0]
digest [0.6.27]
utf8 [1.2.1]
mime [0.11]
R6 [2.5.0]
csasdown [pbs-assess/csasdown@HEAD]
sys [3.4]
evaluate [0.14]
httr [1.4.2]
ggplot2 [3.3.5]
highr [0.9]
pillar [1.6.1]
rlang [0.4.11]
uuid [0.1-4]
curl [4.3.2]
rstudioapi [0.13]
callr [3.7.0]
Matrix [1.3-2]
rmarkdown [2.9]
labeling [0.4.2]
webshot [0.5.2]
readr [1.4.0]
stringr [1.4.0]
selectr [0.4-2]
munsell [0.5.0]
tinytex [0.32]
xfun [0.24]
pkgconfig [2.0.3]
askpass [1.1]
systemfonts [1.0.2]
base64enc [0.1-3]
clipr [0.7.1]
mgcv [1.8-34]
htmltools [0.5.1.1]
openssl [1.4.4]
tidyselect [1.1.1]
tibble [3.1.2]
bookdown [0.22]
fansi [0.5.0]
viridisLite [0.4.0]
crayon [1.4.1]
dplyr [1.0.7]
withr [2.4.2]
MASS [7.3-53.1]
BH [1.75.0-0]
nlme [3.1-152]
jsonlite [1.7.2]
gtable [0.3.0]
lifecycle [1.0.0]
magrittr [2.0.1]
scales [1.1.1]
zip [2.2.0]
cli [3.0.0]
stringi [1.6.2]
farver [2.1.0]
xml2 [1.3.2]
ellipsis [0.3.2]
generics [0.1.0]
vctrs [0.3.8]
kableExtra [1.3.4]
RColorBrewer [1.1-2]
glue [1.4.2]
officer [0.3.18]
markdown [1.1]
purrr [0.3.4]
hms [1.1.0]
processx [3.5.2]
yaml [2.2.1]
colorspace [2.0-2]
rosettafish [pbs-assess/rosettafish@HEAD]
rvest [1.0.0]
isoband [0.2.5]
cpp11 [0.3.1]
knitr [1.33]Use renv::snapshot() to add these packages to your lockfile, and to
save the current state of the project.
> renv::snapshot()
The following package(s) will be updated in the lockfile:
# CRAN ===============================
- BH [* -> 1.75.0-0]
- MASS [* -> 7.3-53.1]
- Matrix [* -> 1.3-2]
- R6 [* -> 2.5.0]
- RColorBrewer [* -> 1.1-2]
- askpass [* -> 1.1]
- base64enc [* -> 0.1-3]
- bookdown [* -> 0.22]
- callr [* -> 3.7.0]
- cli [* -> 3.0.0]
- clipr [* -> 0.7.1]
- colorspace [* -> 2.0-2]
- cpp11 [* -> 0.3.1]
- crayon [* -> 1.4.1]
- curl [* -> 4.3.2]
- digest [* -> 0.6.27]
- dplyr [* -> 1.0.7]
- ellipsis [* -> 0.3.2]
- evaluate [* -> 0.14]
- fansi [* -> 0.5.0]
- farver [* -> 2.1.0]
- generics [* -> 0.1.0]
- ggplot2 [* -> 3.3.5]
- glue [* -> 1.4.2]
- gtable [* -> 0.3.0]
- highr [* -> 0.9]
- hms [* -> 1.1.0]
- htmltools [* -> 0.5.1.1]
- httr [* -> 1.4.2]
- isoband [* -> 0.2.5]
- jsonlite [* -> 1.7.2]
- kableExtra [* -> 1.3.4]
- knitr [* -> 1.33]
- labeling [* -> 0.4.2]
- lattice [* -> 0.20-41]
- lifecycle [* -> 1.0.0]
- magrittr [* -> 2.0.1]
- markdown [* -> 1.1]
- mgcv [* -> 1.8-34]
- mime [* -> 0.11]
- munsell [* -> 0.5.0]
- nlme [* -> 3.1-152]
- officer [* -> 0.3.18]
- openssl [* -> 1.4.4]
- pillar [* -> 1.6.1]
- pkgconfig [* -> 2.0.3]
- processx [* -> 3.5.2]
- ps [* -> 1.6.0]
- purrr [* -> 0.3.4]
- readr [* -> 1.4.0]
- rlang [* -> 0.4.11]
- rmarkdown [* -> 2.9]
- rstudioapi [* -> 0.13]
- rvest [* -> 1.0.0]
- scales [* -> 1.1.1]
- selectr [* -> 0.4-2]
- stringi [* -> 1.6.2]
- stringr [* -> 1.4.0]
- svglite [* -> 2.0.0]
- sys [* -> 3.4]
- systemfonts [* -> 1.0.2]
- tibble [* -> 3.1.2]
- tidyselect [* -> 1.1.1]
- tinytex [* -> 0.32]
- utf8 [* -> 1.2.1]
- uuid [* -> 0.1-4]
- vctrs [* -> 0.3.8]
- viridisLite [* -> 0.4.0]
- webshot [* -> 0.5.2]
- withr [* -> 2.4.2]
- xfun [* -> 0.24]
- xml2 [* -> 1.3.2]
- yaml [* -> 2.2.1]
- zip [* -> 2.2.0]
# GitHub =============================
- csasdown [* -> pbs-assess/csasdown@HEAD]
- rosettafish [* -> pbs-assess/rosettafish@HEAD]
Do you want to proceed? [y/N]: y
* Lockfile written to 'C:/DEV/ReproducibleReport/renv.lock'.Step 8. Open the index.Rmd file in the project directory and press the ‘Knit’ button. This will knit all the .Rmd report sections together, to produce the final PDF report.
If the code has run successfully, a viewer should open that contains the template technical report PDF. The .tex and .pdf report are also saved in the _book subfolder in the project directory.
The cover of the technical report (tech-report-cover.docx) must be manually edited and the report type (e.g., Canadian Technical Report of Fisheries and Aquatic Sciences, Canadian Technical Report of Hydrographic and Ocean Sciences) changed, depending on which report series is being targeted for publication.
If the code does not run successfully (probably indicated by missing libraries with the file extension .sty) then it may be necessary to do a full install of the full suite of TinyTex libraries using the command:
tinytex::tlmgr_install('scheme-full')
The installation of the full suite of TinyTex libraries will take quite a while; possibly an hour or more.
And this concludes a demonstration of how to generate a reproducible DFO technical report using R package csasdown!
The repository of code, data, and figures used to create the Canadian Technical Report of Hydrography and Ocean Sciences report titled ‘Oceanographic monitoring of the Gully MPA - A synopsis of data collected by the Atlantic Zone Monitoring Program’ can be found here: https://github.com/AtlanticR/reproducible-gully-report.
To reproduce the report stored in this repository, the user must have R, RStudio and Rtools installed on their computer.
It also helps to eliminate possible errors by installing the devtools R package.
Step 1. Download the repository from GitHub by clicking the Code button, and ‘Download ZIP’ option. Unzip the contents of the project directory.
You will see that the ‘chapter’ .Rmd files are slightly different from
those unpacked from draft("techreport"). Additional chapters were
added, and their naming convention customized to reflect the contents
presented in the Gully technical report. Users who wish to utilize this
code for future iterations of this report, or other reports designed to
evaluate changes in oceanographic conditions can re-write the text in
each .Rmd file.
Step 2. Double-click on the R project titled GullyReproducibleReport.RProj, or open the project from within RStudio. This will open the R environment in which the project was saved.
The first time the project is opened there will be a message (see following) about the environment being out of sync with the lockfile (see renv).
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
# Bootstrapping renv 0.13.2 --------------------------------------------------
* Downloading renv 0.13.2 ... OK (downloaded binary)
* Installing renv 0.13.2 ... Done!
* Successfully installed and loaded renv 0.13.2.
* Project 'C:/DEV/new-gully-report' loaded. [renv 0.13.2]
* The project library is out of sync with the lockfile.
* Use `renv::restore()` to install packages recorded in the lockfile.To re-sync the environment, execute the following:
> renv::restore()
The following package(s) will be updated:
# CRAN ===============================
- BH [* -> 1.75.0-0]
- DBI [* -> 1.1.1]
- R6 [* -> 2.5.0]
- RColorBrewer [* -> 1.1-2]
- Rcpp [* -> 1.0.6]
- askpass [* -> 1.1]
- base64enc [* -> 0.1-3]
- bookdown [* -> 0.22]
- brio [* -> 1.1.1]
- callr [* -> 3.6.0]
- classInt [* -> 0.4-3]
- cli [* -> 2.4.0]
- clipr [* -> 0.7.1]
- colorspace [* -> 2.0-0]
- cpp11 [* -> 0.2.7]
- crayon [* -> 1.4.1]
- curl [* -> 4.3]
- desc [* -> 1.3.0]
- diffobj [* -> 0.3.4]
- digest [* -> 0.6.27]
- dplyr [* -> 1.0.5]
- e1071 [* -> 1.7-6]
- ellipsis [* -> 0.3.1]
- evaluate [* -> 0.14]
- fansi [* -> 0.4.2]
- farver [* -> 2.1.0]
- generics [* -> 0.1.0]
- ggplot2 [* -> 3.3.3]
- glue [* -> 1.4.2]
- gsw [* -> 1.0-5]
- gtable [* -> 0.3.0]
- highr [* -> 0.8]
- hms [* -> 1.0.0]
- htmltools [* -> 0.5.1.1]
- httr [* -> 1.4.2]
- isoband [* -> 0.2.4]
- jsonlite [* -> 1.7.2]
- kableExtra [* -> 1.3.4]
- knitr [* -> 1.33]
- labeling [* -> 0.4.2]
- lifecycle [* -> 1.0.0]
- lubridate [* -> 1.7.10]
- magrittr [* -> 2.0.1]
- markdown [* -> 1.1]
- mime [* -> 0.10]
- munsell [* -> 0.5.0]
- officer [* -> 0.3.18]
- openssl [* -> 1.4.3]
- pillar [* -> 1.6.0]
- pkgconfig [* -> 2.0.3]
- pkgload [* -> 1.2.1]
- praise [* -> 1.0.0]
- processx [* -> 3.5.1]
- proxy [* -> 0.4-25]
- ps [* -> 1.6.0]
- purrr [* -> 0.3.4]
- readr [* -> 1.4.0]
- rematch2 [* -> 2.1.2]
- rlang [* -> 0.4.10]
- rmarkdown [* -> 2.8]
- rprojroot [* -> 2.0.2]
- rstudioapi [* -> 0.13]
- rvest [* -> 1.0.0]
- scales [* -> 1.1.1]
- selectr [* -> 0.4-2]
- sf [* -> 0.9-8]
- stringi [* -> 1.5.3]
- stringr [* -> 1.4.0]
- svglite [* -> 2.0.0]
- sys [* -> 3.4]
- systemfonts [* -> 1.0.1]
- testthat [* -> 3.0.2]
- tibble [* -> 3.1.1]
- tidyselect [* -> 1.1.0]
- tinytex [* -> 0.31]
- units [* -> 0.7-1]
- utf8 [* -> 1.2.1]
- uuid [* -> 0.1-4]
- vctrs [* -> 0.3.7]
- viridisLite [* -> 0.3.0]
- waldo [* -> 0.2.5]
- webshot [* -> 0.5.2]
- withr [* -> 2.4.1]
- xfun [* -> 0.22]
- xml2 [* -> 1.3.2]
- yaml [* -> 2.2.1]
- zip [* -> 2.1.1]
# GitHub =============================
- csasdown [* -> pbs-assess/csasdown@HEAD]
- oce [* -> dankelley/oce@develop]
- rosettafish [* -> pbs-assess/rosettafish@HEAD]
Do you want to proceed? [y/N]: y
Installing BH [1.75.0-0] ...
OK [linked cache]
Installing DBI [1.1.1] ...
OK [linked cache]
Installing R6 [2.5.0] ...
OK [linked cache]
Installing RColorBrewer [1.1-2] ...
OK [linked cache]
Installing Rcpp [1.0.6] ...
OK [linked cache]
Installing sys [3.4] ...
OK [linked cache]
Installing askpass [1.1] ...
OK [linked cache]
Installing base64enc [0.1-3] ...
OK [linked cache]
Installing digest [0.6.27] ...
OK [linked cache]
Installing rlang [0.4.10] ...
OK [linked cache]
Installing htmltools [0.5.1.1] ...
OK [linked cache]
Installing evaluate [0.14] ...
OK [linked cache]
Installing highr [0.8] ...
OK [linked cache]
Installing xfun [0.22] ...
OK [linked cache]
Installing mime [0.10] ...
OK [linked cache]
Installing markdown [1.1] ...
OK [linked cache]
Installing glue [1.4.2] ...
OK [linked cache]
Installing magrittr [2.0.1] ...
OK [linked cache]
Installing stringi [1.5.3] ...
OK [linked cache]
Installing stringr [1.4.0] ...
OK [linked cache]
Installing yaml [2.2.1] ...
OK [linked cache]
Installing knitr [1.33] ...
OK [linked cache]
Installing jsonlite [1.7.2] ...
OK [linked cache]
Installing tinytex [0.31] ...
OK [linked cache]
Installing rmarkdown [2.8] ...
OK [linked cache]
Installing bookdown [0.22] ...
OK [linked cache]
Installing brio [1.1.1] ...
OK [linked cache]
Installing ps [1.6.0] ...
OK [linked cache]
Installing processx [3.5.1] ...
OK [linked cache]
Installing callr [3.6.0] ...
OK [linked cache]
Installing proxy [0.4-25] ...
OK [linked cache]
Installing e1071 [1.7-6] ...
OK [linked cache]
Installing classInt [0.4-3] ...
OK [linked cache]
Installing cli [2.4.0] ...
OK [linked cache]
Installing clipr [0.7.1] ...
OK [linked cache]
Installing colorspace [2.0-0] ...
OK [linked cache]
Installing cpp11 [0.2.7] ...
OK [linked cache]
Installing crayon [1.4.1] ...
OK [linked cache]
Installing ellipsis [0.3.1] ...
OK [linked cache]
Installing generics [0.1.0] ...
OK [linked cache]
Installing lifecycle [1.0.0] ...
OK [linked cache]
Installing fansi [0.4.2] ...
OK [linked cache]
Installing utf8 [1.2.1] ...
OK [linked cache]
Installing vctrs [0.3.7] ...
OK [linked cache]
Installing pillar [1.6.0] ...
OK [linked cache]
Installing pkgconfig [2.0.3] ...
OK [linked cache]
Installing tibble [3.1.1] ...
OK [linked cache]
Installing purrr [0.3.4] ...
OK [linked cache]
Installing tidyselect [1.1.0] ...
OK [linked cache]
Installing dplyr [1.0.5] ...
OK [linked cache]
Installing gtable [0.3.0] ...
OK [linked cache]
Installing isoband [0.2.4] ...
OK [linked cache]
Installing farver [2.1.0] ...
OK [linked cache]
Installing labeling [0.4.2] ...
OK [linked cache]
Installing munsell [0.5.0] ...
OK [linked cache]
Installing viridisLite [0.3.0] ...
OK [linked cache]
Installing scales [1.1.1] ...
OK [linked cache]
Installing withr [2.4.1] ...
OK [linked cache]
Installing ggplot2 [3.3.3] ...
OK [linked cache]
Installing xml2 [1.3.2] ...
OK [linked cache]
Installing curl [4.3] ...
OK [linked cache]
Installing openssl [1.4.3] ...
OK [linked cache]
Installing httr [1.4.2] ...
OK [linked cache]
Installing selectr [0.4-2] ...
OK [linked cache]
Installing rvest [1.0.0] ...
OK [linked cache]
Installing rstudioapi [0.13] ...
OK [linked cache]
Installing webshot [0.5.2] ...
OK [linked cache]
Installing systemfonts [1.0.1] ...
OK [linked cache]
Installing svglite [2.0.0] ...
OK [linked cache]
Installing kableExtra [1.3.4] ...
OK [linked cache]
Installing zip [2.1.1] ...
OK [linked cache]
Installing uuid [0.1-4] ...
OK [linked cache]
Installing officer [0.3.18] ...
OK [linked cache]
Installing hms [1.0.0] ...
OK [linked cache]
Installing readr [1.4.0] ...
OK [linked cache]
Installing rosettafish [0.0.0.9000] ...
OK [linked cache]
Installing csasdown [0.0.10.9000] ...
OK [linked cache]
Installing rprojroot [2.0.2] ...
OK [linked cache]
Installing desc [1.3.0] ...
OK [linked cache]
Installing diffobj [0.3.4] ...
OK [linked cache]
Installing pkgload [1.2.1] ...
OK [linked cache]
Installing praise [1.0.0] ...
OK [linked cache]
Installing rematch2 [2.1.2] ...
OK [linked cache]
Installing waldo [0.2.5] ...
OK [linked cache]
Installing testthat [3.0.2] ...
OK [linked cache]
Installing gsw [1.0-5] ...
OK [linked cache]
Installing lubridate [1.7.10] ...
OK [linked cache]
Installing units [0.7-1] ...
OK [linked cache]
Installing sf [0.9-8] ...
OK [linked cache]
Installing oce [1.4-0] ...
OK [linked cache]Next check the status of the environment (lock file) to see if everything is now in sync.
> renv::status()
The following package(s) are out of sync:
Package Lockfile Version Library Version
KernSmooth 2.23-20 2.23-18
MASS 7.3-54 7.3-53
Matrix 1.3-4 1.3-2
boot 1.3-28 1.3-26
class 7.3-19 7.3-18
cluster 2.1.2 2.1.0
lattice 0.20-44 0.20-41
mgcv 1.8-36 1.8-33
nnet 7.3-16 7.3-15
oce 1.5-0 1.4-0
ocedata 0.1.9 0.1.8
pkgload 1.2.1 1.2.2
spatial 7.3-14 7.3-13
survival 3.2-13 3.2-7
Use `renv::snapshot()` to save the state of your library to the lockfile.
Use `renv::restore()` to restore your library from the lockfile.If it is not in sync then execute the renv::snapshot command to
synchronize the environment again.
> renv::snapshot()At this step you may receive an error that R package oce failed to install. This will be re-installed below once the Index.Rmd file is opened.
Step 4. Install the remotes and csasdown packages:
> install.packages("remotes")
> remotes::install_github("pbs-assess/csasdown")Using renv::status, you will see that the project is out of sync with
the lockfile. Use renv::snapshot to sync the project and lockfile.
Step 5. Open the index.Rmd file. An R Markdown pane will appear in the R environment with the Console, Terminal and Jobs panes visible. You may receive a message indicating that several dependencies of the Index.Rmd file are not installed, including R package oce. Select the Install option to install these packages.
Use renv::status() to check the that the project is in sync with the
lockfile, and if not, execute renv::snapshot().
Press the Knit button to compile the various .Rmd chapters into a single report. The output in the R Markdown pane will resemble the following:
processing file: techreport.Rmd
|. | 1%
ordinary text without R code
|.. | 2%
label: setup (with options)
List of 5
$ echo : logi FALSE
$ cache : logi FALSE
$ message: logi FALSE
$ results: chr "hide"
$ warning: logi FALSE
|.. | 3%
ordinary text without R code
|... | 4%
label: load-libraries (with options)
List of 1
$ cache: logi FALSE
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Attaching package: 'kableExtra'
The following object is masked from 'package:dplyr':
group_rows
Attaching package: 'lubridate'
The following objects are masked from 'package:base':
date, intersect, setdiff, union
Loading required package: gsw
Loading required package: testthat
Attaching package: 'testthat'
The following object is masked from 'package:dplyr':
matches
Loading required package: sf
Linking to GEOS 3.9.0, GDAL 3.2.1, PROJ 7.2.1
Attaching package: 'scales'
The following object is masked from 'package:readr':
col_factor
The following object is masked from 'package:oce':
rescale
|.... | 6%
inline R code fragments
|..... | 7%
label: table1 (with options)
List of 3
$ results: chr "asis"
$ include: logi TRUE
$ echo : logi FALSE
Attaching package: 'tidyr'
The following object is masked from 'package:testthat':
matches
|...... | 8%
ordinary text without R code
|...... | 9%
label: table2 (with options)
List of 3
$ results: chr "asis"
$ include: logi TRUE
$ echo : logi FALSE
|....... | 10%
ordinary text without R code
|........ | 11%
label: table3 (with options)
List of 3
$ results: chr "asis"
$ include: logi TRUE
$ echo : logi FALSE
|......... | 12%
ordinary text without R code
|......... | 13%
label: table4 (with options)
List of 3
$ results: chr "asis"
$ include: logi TRUE
$ echo : logi FALSE
Joining, by = "years"
|.......... | 15%
ordinary text without R code
|........... | 16%
label: table5 (with options)
List of 3
$ results: chr "asis"
$ include: logi TRUE
$ echo : logi FALSE
|............ | 17%
ordinary text without R code
|............. | 18%
label: table6 (with options)
List of 3
$ results: chr "asis"
$ include: logi TRUE
$ echo : logi FALSE
|............. | 19%
ordinary text without R code
|.............. | 20%
label: table7 (with options)
List of 3
$ results: chr "asis"
$ include: logi TRUE
$ echo : logi FALSE
|............... | 21%
ordinary text without R code
|................ | 22%
label: table8 (with options)
List of 3
$ results: chr "asis"
$ include: logi TRUE
$ echo : logi FALSE
|................. | 24%
ordinary text without R code
|................. | 25%
label: figure1 (with options)
List of 2
$ fig.align: chr "center"
$ fig.cap : chr "(ref:fig1-caption)"
|.................. | 26%
ordinary text without R code
|................... | 27%
label: figure2 (with options)
List of 2
$ fig.align: chr "center"
$ fig.cap : chr "(ref:fig2-caption)"
|.................... | 28%
ordinary text without R code
|.................... | 29%
label: figure3 (with options)
List of 2
$ fig.align: chr "center"
$ fig.cap : chr "(ref:fig3-caption)"
|..................... | 30%
ordinary text without R code
|...................... | 31%
label: figure4 (with options)
List of 2
$ fig.align: chr "center"
$ fig.cap : chr "(ref:fig4-caption)"
|....................... | 33%
ordinary text without R code
|........................ | 34%
label: figure5 (with options)
List of 3
$ fig.align: chr "center"
$ fig.cap : chr "(ref:fig5-caption)"
$ out.width: chr "7.75in"
|........................ | 35%
ordinary text without R code
|......................... | 36%
label: figure6 (with options)
List of 3
$ fig.align: chr "center"
$ fig.cap : chr "(ref:fig6-caption)"
$ out.width: chr "7.75in"
|.......................... | 37%
ordinary text without R code
|........................... | 38%
label: figure7 (with options)
List of 3
$ fig.align: chr "center"
$ fig.cap : chr "(ref:fig7-caption)"
$ out.width: chr "7.75in"
|............................ | 39%
ordinary text without R code
|............................ | 40%
label: figure8 (with options)
List of 3
$ fig.align: chr "center"
$ fig.cap : chr "(ref:fig8-caption)"
$ out.width: chr "9.25in"
|............................. | 42%
ordinary text without R code
|.............................. | 43%
label: figure9 (with options)
List of 3
$ fig.align: chr "center"
$ fig.cap : chr "(ref:fig9-caption)"
$ out.width: chr "9.0in"
|............................... | 44%
ordinary text without R code
|............................... | 45%
label: figure10 (with options)
List of 2
$ fig.align: chr "center"
$ fig.cap : chr "(ref:fig10-caption)"
|................................ | 46%
ordinary text without R code
|................................. | 47%
label: figure11 (with options)
List of 2
$ fig.align: chr "center"
$ fig.cap : chr "(ref:fig11-caption)"
|.................................. | 48%
ordinary text without R code
|................................... | 49%
label: figure12 (with options)
List of 2
$ fig.align: chr "center"
$ fig.cap : chr "(ref:fig12-caption)"
|................................... | 51%
ordinary text without R code
|.................................... | 52%
label: figure13 (with options)
List of 3
$ fig.align: chr "center"
$ fig.cap : chr "(ref:fig13-caption)"
$ out.width: chr "9.5in"
|..................................... | 53%
ordinary text without R code
|...................................... | 54%
label: figure14 (with options)
List of 2
$ fig.align: chr "center"
$ fig.cap : chr "(ref:fig14-caption)"
|....................................... | 55%
ordinary text without R code
|....................................... | 56%
label: figure15 (with options)
List of 3
$ fig.align: chr "center"
$ fig.cap : chr "(ref:fig15-caption)"
$ out.width: chr "5.0in"
|........................................ | 57%
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output file: techreport.knit.md
"C:/Users/JacksonJ/ANACON~1/Scripts/pandoc" +RTS -K512m -RTS techreport.knit.md --to latex --from markdown+autolink_bare_uris+tex_math_single_backslash --output techreport.tex --lua-filter "C:\Users\JacksonJ\AppData\Local\renv\cache\v5\R-4.0\x86_64-w64-mingw32\bookdown\0.22\8fb0b67dfdf9d751fc93cb0036def3cc\bookdown\rmarkdown\lua\custom-environment.lua" --lua-filter "C:\Users\JacksonJ\AppData\Local\renv\cache\v5\R-4.0\x86_64-w64-mingw32\rmarkdown\2.8\f518ba47713f92d0d603eec7c6888faf\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\JacksonJ\AppData\Local\renv\cache\v5\R-4.0\x86_64-w64-mingw32\rmarkdown\2.8\f518ba47713f92d0d603eec7c6888faf\rmarkdown\rmarkdown\lua\latex-div.lua" --metadata-file "C:\Users\JacksonJ\AppData\Local\Temp\1\RtmpgBRgxg\file54bc2460464f" --self-contained --table-of-contents --toc-depth 2 --template "C:\Users\JacksonJ\AppData\Local\renv\cache\v5\R-4.0\x86_64-w64-mingw32\csasdown\0.0.10.9000\57f2cf63e839d922570cf1fe22c1f26b\csasdown\csas-tex\tech-report.tex" --number-sections --highlight-style tango --pdf-engine xelatex --top-level-division=chapter --wrap=none --default-image-extension=png --include-in-header "C:\Users\JacksonJ\AppData\Local\Temp\1\RtmpgBRgxg\rmarkdown-str54bc371224f.html" --variable tables=yes --standalone -Mhas-frontmatter=false --citeproc
[1] "C:/DEV/new-gully-report/_book/techreport.pdf"
Output created: _book/techreport.pdf
Warning messages:
1: In eval(expr, envir, enclos) : NAs introduced by coercion
2: LaTeX Warning: Command \underbar has changed.
Check if current package is valid.
LaTeX Warning: Command \underline has changed.
Check if current package is valid. Once the document is knit together a PDF file (techreport.pdf) will appear in the viewer. The PDF will also be stored in the _book folder that is generated upon execution of the Knit function.
A number of additional R packages were added to the GullyReproducibleReport.Rproj at various stages to allow certain functionality, such as adding special characters and symbols not accessible in base R:
-
Added LaTeX package xfrac so that I could add the code for creating the ¾ symbol.
-
Added LaTeX package gensymb so that I could use the code for the degree symbol.
-
Added LaTeX package multirow so that I could collapse more than one row using the kableExtra function collapse_rows.
-
Added LaTeX packages colortbl and xcolor to use colors in tables using the “striped” or “background” kable options.
-
Added LaTeX package bookmark to allow more options when configuring bookmarks (cross-reference commands to create hypertext links).
-
Added LaTeX package mathptmx which gives mathematical expressions the same or similar font as the normal text.
It is also required to download and install the free version of Ghostscript.
The path (e.g. (C:\Program Files\gs\gs9.54.0\bin)) to the Ghostscript executable must be added to the Windows user PATH variable.
One of the authors created the report in Microsoft Word. The text was copied and pasted into the various RMarkdown files. Some of the symbols that were in the Word document had to be replaced with their LaTeX equivalents for them to be output correctly in the PDF document; for example:
plus/minus symbol: ± changed to $\pm$
Three-quarters symbol: ¾ change to $\textthreequarters$
Greek letter Mu: µ changed to $\mu$
Degree symbol: ⁰ changed to $\degree$Some other useful features that were discovered during the generation of this report were:
To make a subscript 2 use the following type of format to do it: \textsubscript{2}
To make a superscript th use the following type of format to do it: \textsuperscript{th}
To make it so that some text strings in a data frame are italicized in the output table, I used the LaTeX command: \textit{}
For example: zoopl <- c("LL\_07/Fall“,”Year“,”\textit{C. finmarchicus}“,”\textit{Clausocalanus}“,”\textit{Microcalanus}“,”GULD\_03/Fall“,”Year“,”\textit{Clausocalanus}“,”\textit{M. lucens}“,”HL\_06/Fall“,”Year“,”\textit{C. finmarchicus}“,”\textit{M. clausi}“,”\textit{M. lucens}“,”\textit{O. atlantica}“,”\textit{O. similis}“,”\textit{Paracalanus}“,”\textit{Pleuromamma}")
There were horizontal lines in the header and footer of landscape pages. To remove these from the PDF document, I deleted the two identical lines (seen below) from the techreport.sty file.
{\rotatebox{90}{\rule{9in}{0.25pt}}}\end{textblock}
Note that the csasdown package creators may change things so that this is removed already so it might not be an issue in future report projects.
There are two formatting issues that need to be fixed but it involves the editing of the intermediate LaTeX file (techreport.tex) that was generated from the RMarkdown files. It is stored in the _book sub-folder where the techreport.pdf file is also located. The LaTeX file is used to generate the PDF document.
Before editing the LaTeX file it must be copied from the _book sub-folder to the main folder.
Problem 1: The TABLES and FIGURES are subsections of the REFERENCES section instead of being their own sections.
Solution: Removed the "sub" prefix from the TABLES and FIGURES sections.
\hypertarget{sec:tables}{%
\subsection{TABLES}\label{sec:tables}}
became
\hypertarget{sec:tables}{%
\section{TABLES}\label{sec:tables}}
and
\hypertarget{sec:figures}{%
\subsection{FIGURES}\label{sec:figures}}
became
\hypertarget{sec:figures}{%
\section{FIGURES}\label{sec:figures}}Problem 2: Inline references when there are more than two authors are indicated with the format <Primary Author> et al.. Normally this et al. phrase, which is the abbreviated version of the Latin phrase "et alia" meaning "and others", is italicized. I could not achieve this in RMarkdown.
Solution: Did a search in the LaTeX document to find and replace all occurrences of "et al." with "\textit{et al.}". All 51 occurrences were changed.
Since the intermediate LaTeX file was edited it has to be converted to PDF format outside of RStudio.
This is done within an operating system console window (using Windows 10 Anaconda command prompt in this instance but you can use the Terminal window within RStudio just as easily) by executing the following command:
(base) PS C:\dev\new-gully-report> xelatex techreport.tex
One will notice at first glance that:
- the resulting PDF document has the correct section numbers for the Tables and Figures,
- the "et al." phrases are all italicized, but
- the Table of Contents (TOC) is totally empty, and
- some in-document links to the tables and figures may be invalid as indicated by question marks.
Checking the console window one will notice two warnings at the end of compilation, which are:
-
LaTeX Warning: There were undefined references.
-
LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.
Re-running the command will generate the TOC and fix the in-document links to tables and figures but still one of the two warnings remained. Executing the command a third time gets rid of the last warning.