Appendix
Uploading a local tag database
You can view live detections of your project's Lotek tags on the SensorGnomes web interface by following these steps.
Introduction
If you are installing a station that detects Lotek tags, it is often useful to know whether it is able to detect tags in real time, particularly if you are deploying tags in the vicinity. Thankfully this is possible by loading a local tag database on to the internal storage of the device. When the SensorGnome boots up, it checks for a tag database and will display any of those tags it "hears" on its web interface.
Viewing your live tag detections can also be useful when deploying tags or as a make-shift manual tracking device when a Lotek receiver is unavailable.
This works by using a local version of the tag finder algorithm (
find_tags_unifile) in comparison with the tag recordings provided during registration. Note that this local version differs from the version found on Motus, mainly in that Motus searches for tags from all projects across the network (but only those known to be actively deployed during the given time period) whereas this method will only compare raw radio data with the tag patterns it has been provided, regardless of deployment period.Steps
- 1.
- If there are multiple files to choose from, pick the last file in the list for the most recent set of tags.
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2. Connect to your SensorGnome with a computer using 'root' as both the username and password and navigate to the
ubootfolder.3. Rename the files
SG_tag_database.sqlite with the suffix ‘old’, or delete them all together.4. Copy the tag database you just downloaded from motus.org into the
uboot folder. Rename the file to SG_tag_database.sqlite5. Reboot the SensorGnome.
6. Load the SensorGnome's web interface and scroll down to near the bottom of the page where it says "Tag Database" and verify the list of tags includes tags from your project.
You are done! You can now view the "live known tags" pane at the top of the page to check whether your tags are being detected by this station.
Merging multiple tag databases into one
Tag database files are organized by yearly quarter, so tags that were registered in different quarters of the year will be provided in different files. As only one tag database can be loaded at a time, multiple databases will have to be merged into one prior to loading on to the SensorGnome. You can use or modify the script below to merge multiple databases in R.
It's important to remember the limitations of this method: it will only search for the tags that it has been provided, and it is incapable of discerning or handling ambiguous tag IDs.
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### merge tag databases ####
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# This function accepts a vector of file names
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# corresponding to the various tag databases to be merged.
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# It saves one tag database containing all the source dbs
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# named 'SG_tag_database.sqlite' for copying onto a SG
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# It also returns a data frame with the results for visual overview
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​
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merge_dbs <- function(db_list, out_db = 'SG_tag_database.sqlite'){
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library(RSQLite)
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out_df <- data.frame()
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# loop through the list of tag dbs to be merged
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for (i in db_list) {
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message('Processing ', i)
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# establish SQLite connection to the current tag database
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con <- dbConnect(SQLite(), i)
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# select all from the tags table of the tag database, as a data frame
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df <- dbGetQuery(con, 'SELECT * FROM tags')
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# bind (append) the resulting rows to the consolidated out_df data frame
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out_df <- rbind(out_df, df)
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# disconnect from the source tag database
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dbDisconnect(con)
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}
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# open a SQLite connection to your output file
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outdb <- dbConnect(SQLite(), out_db)
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# write the results to the new consolidated tag database
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# This will overwrite any existing SG_tag_database.sqlite file
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# if one already exists in the target directory
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dbWriteTable(outdb, 'tags', out_df, overwrite = T)
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# close the connection to the new consolidated tag database
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dbDisconnect(outdb)
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message(length(db_list), " tag sqlite files merged into ", out_db)
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return(out_df)
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}
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​
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# An example of how to use this function...
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# Call the function and pass in the paths of the tag databases to be merged.
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merged_db <- merge_dbs(c('D:/Downloads/project_322_2020-2_tag_database.sqlite',
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'D:/Downloads/project_322_2021-2_tag_database.sqlite'))
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​
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View(merged_db)
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