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Data Push Summaries

Source: vignettes/data-push-summaries.Rmd
data-push-summaries.Rmd
library(matos)
#> By continuing, you are agreeing to the ACT Network MATOS User Agreement and
#> Data Policy, Version 1.2:
#> 
#> <https://matos.asascience.com/static/MATOS.User.Agreement.V1.1.pdf>
#>

Oh, boy; oh, boy! Here it is: one of the three yearly data pushes and Kim has hit you with a slew of automated emails to let you know that the data you’ve recorded on your receivers has been matched to other projects in MATOS or one of the other OTN nodes.

What now? What’s been updated? Who might I contact for more information? Well, make_receiver_push_summary and make_tag_push_summary are here to help.

ACT members

If you’re an ACT member, the first thing you’ll want to do is list the projects for which you have access.

list_my_projects(read_access = T)
#> ! Please log in.
#> ✔ Login successful!
#>                                             name number
#> 32      Maryland Department of Natural Resources     90
#> 41              Navy Kennebec ME Telemetry Array    192
#> 45         NCBO-MD DNR Chesapeake Backbone North    181
#> 46           NCBO-VMRC Chesapeake Backbone South    164
#> 104 UMCES Black Sea Bass & Offshore Construction     97
#> 105              UMCES BOEM Offshore Wind Energy     87
#> 106           UMCES Chesapeake Backbone, Mid-Bay    161
#> 107  UMCES Lower Hudson Striped Bass Contingents    155
#> 108   UMCES Potomac River Striped Bass Migration     60
#> 109 UMCES Resident Hudson Striped Bass Migration    160
#> 110           UMCES Striped Bass Thermal Squeeze    152
#> 111    UMCES-NYSDEC Hudson Striped Bass Spawning    127
#>                                                 url
#> 32   https://matos.asascience.com/project/detail/90
#> 41  https://matos.asascience.com/project/detail/192
#> 45  https://matos.asascience.com/project/detail/181
#> 46  https://matos.asascience.com/project/detail/164
#> 104  https://matos.asascience.com/project/detail/97
#> 105  https://matos.asascience.com/project/detail/87
#> 106 https://matos.asascience.com/project/detail/161
#> 107 https://matos.asascience.com/project/detail/155
#> 108  https://matos.asascience.com/project/detail/60
#> 109 https://matos.asascience.com/project/detail/160
#> 110 https://matos.asascience.com/project/detail/152
#> 111 https://matos.asascience.com/project/detail/127

From here, you can just provide your project name or number and let it rip. Below, I provide the number associated with “UMCES BOEM Offshore Wind Energy”.

This function does a bit of data cleaning on the front end and then runs everything through a Quarto or RMarkdown report. The functions use Quarto by default, but RMarkdown will be selected if:

  1. Quarto is not installed on the computer, or
  2. the rmd argument is set to TRUE.
# Compiles with Quarto (default)
make_receiver_push_summary(87, rmd = F)

# Compiles with RMarkdown
make_receiver_push_summary(87, rmd = T)

Functionality is identical for make_tag_push_summary:

Other OTN-ites

If you are a member of OTN or an OTN node, such as FACT, your data extract files are compatible with make_receiver_push_summary and make_tag_push_summmary. The only difference is that you’ll have to manually provide your data files – matos is not set up to download them for you.

We’ll use data from Trudel 2018 (https://members.oceantrack.org/data/repository/pbsm) to show how this might work.

make_receiver_push_summary 

# Create a folder in your temporary directory to hold the sample files
td <- file.path(tempdir(), 'matos_test_files')
dir.create(td)

# Download deployment metadata
# Note "mode = 'wb'! Needed to download the file in binary
download.file('https://members.oceantrack.org/data/repository/pbsm/data-and-metadata/2018/pbsm-instrument-deployment-short-form-2018.xls',
              destfile = file.path(td, 'pbsm-instrument-deployment-short-form-2018.xls'),
              mode = 'wb')

# Download qualified detections
download.file('https://members.oceantrack.org/data/repository/pbsm/detection-extracts/pbsm_qualified_detections_2018.zip',
              destfile = file.path(td, 'pbsm_qualified_detections_2018.zip'))

# Download unqualified detections
download.file('https://members.oceantrack.org/data/repository/pbsm/detection-extracts/pbsm_unqualified_detections_2018.zip',
              destfile = file.path(td, 'pbsm_unqualified_detections_2018.zip'))

qualified_filepath <- file.path(td, 'pbsm_qualified_detections_2018.zip')
unqualified_filepath <- file.path(td, 'pbsm_unqualified_detections_2018.zip')
deployment_filepath <- file.path(td, 'pbsm-instrument-deployment-short-form-2018.xls')

When you have an ACT project, matos automatically uses the most-recent data push date as a reference point to let you know what has changed since the last time you’ve received new data. It doesn’t know this for other networks, but you can provide a date via the since argument.

make_receiver_push_summary(
  qualified = qualified_filepath,
  unqualified = unqualified_filepath,
  deployment = deployment_filepath,
  since = '2018-05-06'
)

There you go – you now have a report of detections picked up by your receiver array in your working directory!

make_tag_push_summary

The same process applies to summarize your deployed transmitters.

download.file('https://members.oceantrack.org/data/repository/pbsm/detection-extracts/pbsm_matched_detections_2018.zip',
               destfile = file.path(td, 'pbsm_matched_detections_2018.zip'))

matched_filepath <- file.path(td, 'pbsm_matched_detections_2018.zip')
make_tag_push_summary(matched = matched_filepath,
                      since = '2018-05-01')

Suggestions

I am always open to suggestions on what could be added to change to make this more useful for you. Please open an issue on GitHub or email me with your thoughts.

Errors and how to fix them 

Could not determine mime type for `~\Matcheddetections_layer.fgb'
Error: pandoc document conversion failed with error 63

This error is created by an old version of the mapview package (pre-June 2021) and has to do with the package’s switch to using a file geodatabase to increase plotting performance. To fix this, you have two options:

  1. Update mapview (suggested), or
  2. Run mapviewOptions(fgb = FALSE) before attempting to run make_receiver_push_summary or make_tag_push_summary. Note that this will make the report build more slowly.

References

Trudel, Marc. “A Pilot Study to Investigate the Migration of Atlantic Salmon Post-Smolts and Their Interactions with Aquaculture in Passamaquoddy Bay, New Brunswick, Canada.” Ocean Tracking Network, 2018. https://members.oceantrack.org/project?ccode=PBSM.