In fishsciences/ybt: Yolo Bypass Telemetry Project Analysis Package

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Analysis is the third and final workflow of the Yolo Bypass Telemetry project. It begins after the database has been appended with new (formatted) detections and you are ready to generate the annual reproducible Telemetry Report.

General Analysis workflow

1. QAQC the data (there is an inst/setup.R script of the ybt package source files)
2. Save the QAQC'd tables to individual .rds files, or however you like to access them
3. Knit the current year's version of the annual reproducible Telemetry Report, using the QAQC'd data.

1. Install the ybt package

By running:

devtools::install_github("fishsciences/ybt", build_vignettes = TRUE)

This will install all dependencies of the package as well.

2. Knit the Reproducible Report for the current year

• First, download the YBT_Reports repository. Open with Rstudio.

• Save a new copy of Reports/AnnualTelemetrySummary.Rmd - I suggest saving it to a new directory created to hold all of the reports (example filename convention: ATS_YYYY.Rmd)

• Customize the setup for the report. Things that need to be altered are commented. These include:

• setting the correct file paths for your QAQC'd data
• focus_yr (i.e. 2018)
• focus_tg This is the name of the tag group as it appears in the tags table of the database. Naming convention is the species abbreviation (fca for fall Chinook adult) + underscore + the calendar year in which they were all tagged, i.e. wst_2012 or fca_2017.

• relative file paths to the database and the detections, for false detection screening data.

• Knit the report. This will generate both an html document and a Word document. The figures in the Word document may not display optimally, so you may need to go through the code in the .Rmd and individually export figures with ggsave().

Things to remember about the analysis workflow

• Don't take the reproducible report at face value - always read through it carefully to make sure it passes basic sanity checks. There may be unpredictable inconsistencies in each year's data that the report doesn't know how to handle automatically - make sure you include fixes for those in the individual year's .Rmd, not the template.

• The template will need to be updated every so often; it's very basic and there's plenty of room for improvement. A good way to learn is to start by customizing the appearance! Eventually we could get it to a fully parameterized R Markdown Report :)

fishsciences/ybt documentation built on March 11, 2021, 8:45 a.m.