In fishsciences/ybt: Yolo Bypass Telemetry Project Analysis Package

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This is a subtopic of the Database workflow. It covers all handling of the detection data, from the files downloaded in the field to appending the database.

General detections workflow

1. Download acoustic receivers in the field
2. Copy all vrls from a given field download range into a new subfolder of YB_Vemco/ using the ybt::copy_vrls() function.
3. Create a new .vdb in that subfolder, following the naming conventions below.
4. Process data in VUE, including drift-correction and exporting to .csv
5. Format the detection .csv(s) in R with the ybt::format_VUE_detections() function
6. Append the resulting detections dataframe to SQLite database using the ybt::ybt_db_append() function
7. Back up updated database to cloud and/or external storage

1. Download Receivers in the field

• Create a VUE database (.vdb) for field downloads

  • Filename convention: "YB_fieldyyyy_mmdd.vdb"

    • for example: "YB_field2020_0321.vdb" for a download occurring on March 21st 2020.

  • Put the .vdb, along with each individual .vrl and its RLD file, into its own subdirectory of the "FieldDownloads" folder. Example:

YB_Vemco
 |-- YBFieldDownloads
 |    |-- Field2020_0901
 |        `--Field2020_0901.vdb
 |        `--VR2W_104440_20200901_1.vrl
 |        `--VR2W-RLD_104440_20200901_1.vrl
 |        `--VR2W_123456_20200901_1.vrl
 |        `--VR2W-RLD_123456_20200901_1.vrl

• Do this for each field download day until final downloads for the season are complete (this will typically be by June 30th of each year, depending on conditions).

2. Copy all vrls from a given field download range into a new subfolder of YB_Vemco/ using the ybt::copy_vrls() function.

Name the new subfolder with the range of download dates covered and a "_vrls" suffix. This will result in a directory structure like the following:

YB_Vemco
 |-- YBDetections_2020_0901-2021_0523_vrls
    `--VR2W_104440_20200901_1.vrl
    `--VR2W_123456_20200901_1.vrl
    `--VR2W_104440_20210523_1.vrl
    `--VR2W_123456_20210523_1.vrl
 |-- YBFieldDownloads
 |    |-- Field2020_0901
 |        `--Field2020_0901.vdb
 |        `--VR2W_104440_20200901_1.vrl
 |        `--VR2W-RLD_104440_20200901_1.vrl
 |        `--VR2W_123456_20200901_1.vrl
 |        `--VR2W-RLD_123456_20200901_1.vrl
 |    |-- Field2021_0523
 |        `--Field2020_0901.vdb
 |        `--VR2W_104440_20210523_1.vrl
 |        `--VR2W-RLD_104440_20210523_1.vrl
 |        `--VR2W_123456_20210523_1.vrl
 |        `--VR2W-RLD_123456_20210523_1.vrl

3. Create a new _dc.vdb in that subfolder, following the naming conventions below.

• Create _dc.vdb (with correct naming convention; see below) and place within the corresponding download range's _dc subfolder (which was created in the previous step). Example:

YB_Vemco
 |-- YBDetections_2020_0901-2021_0523_vrls
        |-- YBDetections_2020_0901-2021_0523_dc
            `-- YBDetections_2020_0901-2021_0523_dc.vdb
 |-- YBFieldDownloads

• Edit VUE options to "copy .vrl files" into the correct _dc subfolder so that all edited .vrl files will end up in the _dc subfolder during import.

4. Drift-correct and export all detections for detection year

• Import raw field .vrls with the VRL editor tool and drift-correct upon import; accept the default appendix to filenames ("_edited.vrl").

• If any errors are reported in the import log, save the import log as a .txt file with and _error tag, i.e.: "YBDetections_2020_0901-2021_0523_dc_Log_todaysdate_error.txt", within the _dc subfolder. If we run into weird issues during the analysis, this is a good starting point to help us trace problematic or missing detection files. NO need to save the log if everything imports successfully.

• Export drift-corrected detections as one .csv into the same _dc subfolder.

  • naming convention: "YBDetections_2020_0901-2021_0523_dc.csv" (specific date range will vary).

5. Format the detection .csv(s) in R with the ybt::format_VUE_detections() function

The formatting function does the following:

• Formats column headings
• Formats dates/times (POSIXct, PST, yyyy-mm-dd hh:mm:ss) and saves them as text in preparation for database appending
• Checks for simultaneous detections within receivers and tags; discard duplicates (there really shouldn't be any if VUE is functioning properly)

6. Append the resulting detections dataframe to SQLite database

This is done using the ybt::ybt_db_append() function; see vignettes('Database', package = 'ybt')

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