SeaFlow_cruise_report

This repository consists of a knitR file and supporting documents to build an R and LaTeX cruise report for SeaFlow data. To customise the report for your cruise:

• Knitting this report together requires a plethora of packages in both R and LaTeX. Check the .Rnw file to make sure you have them all.
• Download all the files (except README) in this repository and put them in the same directory. In the terminal cd to this directory.
• Ensure you are connected to the SeaFlow-OPP drive. Otherwise, change path to a local directory containing the database, OPP files, and VCT files for the cruise.
• Cruise identifiers will be pulled from the Google sheets file "SeaFlow instrument log." To authorize R to access this worksheet, copy the link provided in your terminal during your first knitr run and paste it in a browser. You should only have to do this once.
• Tweak the outlier detection for temperature and salinity in the hydro block.

In a bash shell, use R to knit a LaTeX .tex file:

Rscript -e "library(knitr); knit('SeaFlow_cruise_report.Rnw')" cruise_name

Build the pdf from the LaTeX file. You may need to do this 3 times sequentially to get all the labels and references complete.

WARNING: The "--shell-escape" option allows a shell to download files from our GitHub repository required to build the LaTeX file. Double check that these are all files you trust.

pdflatex --shell-escape SeaFlow_cruise_report.tex

To get the bibliography, use BibTeX:

bibtex SeaFlow_cruise_report

Then LaTeX the .tex file again once or thrice as above.