The code in this repository are written in the R language and can be used to process data collected by an In-Situ Aqua TROLL 600 Multiparameter sonde. The data are collected by the non-profit Florida Commercial Watermen's Conservation (FCWC) and is a group of commercial fishermen located in southwest Florida. The data are transmitted to scientists at NOAA's Southeast Fisheries Science Center (SEFSC), NOAA's Atlantic Oceanographic and Meteorological Laboratory (AOML), and University of Miami's Cooperative Institute for Marine and Atmospheric Studies (CIMAS) for processing and distribution. The data undergo quality assurance and quality control (QA/QC) and then visualized products are sent back to the collaborating fishermen and other stakeholders. The data products are a work in progress with the goal of being responsive to the needs of the fishermen and to produce informative data products that can be used for planning purposes.
The original files are directly uploaded to GoogleDrive by the VuSitu App as an htm. The R functions in this repository are designed to perform a few different tasks:
- aquatroll_fields a helper function that just lists the standard parameters reported in aquatroll htm files
- summary_aquatroll takes an .htm or .csv and returns a summary data.frame of the data including if parameters were missing from the input file or if there was sensor drop out, both of which has been an issue
- data_extract_aquatroll takes an .htm or .csv and extract all the raw data and put it into a data.frame
- qaqc_automation performs quality assurance and quality control based upon Integrated Ocean Observing System (IOOS) recommendations
- interp_aquatroll takes the data.frame output of data_extract_aquatroll and smooths and interpolates selected parameters for downstream visualization
- bottom_finder is useful to find bottom for plotting profiles
- breaks makes handy breaks for color palettes
- running calculates a moving linear regression slope and moving average
Code to automate QA/QC is under development using guidelines outlined by the IOOS Quality Assurance / Quality Control of Real Time Oceanographic Data (QARTOD). The summary_aquatroll function will return missing parameters from a list of expected parameters and a list of parameters that dropped out. Drop out is when the parameter has some measurements but not for the whole time the unit was recording. This can happen when there is a bad connection or other sensor failure. If this happens, it is recommended that In-Situ technical support be contacted for further help.
The overall objective of the code is produce a visual data product that can be distributed to various stakeholders, including the fishermen that collect the data.
This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project code is provided on an ‘as is’ basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.
To do
- add QA/QC processing functions (in progess)
- make shiny app to display data https://shiny.rstudio.com/
- update .md using: https://r4ds.had.co.nz/r-markdown-formats.html or https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet or https://rmarkdown.rstudio.com/ examples