shinyReport_receivers

Data Visualisations: Receiver Array Report

Source: vignettes/shinyReport_receivers.Rmd

The remora package includes statistics and data visualisations for acoustic telemetry receiver array and tagging projects. The shinyReport() function allows users to create an interactive data report for their projects, which comprises a range of visualisations and analytical tools to aid data exploration and project management. The resulting plots and tables can be downloaded for further use and analysis. This interactive report is an exploratory tool and should not be considered an extensive analysis toolkit.

Currently, the focus of the remora package is to integrate animal telemetry data and oceanographic observations collated by Australia’s Integrated Marine Observing System. Therefore, the geographical scope of available datasets is currently restricted to the Australasia region.

Receiver Array Report

The receiver array report provides users with basic summary statistics and data visualisations for their acoustic telemetry receiver array project. When called, the function produces an interactive Shiny App that will open in the user’s default internet browser.

Run Shiny App

The remora package should be installed prior to calling the functions described in this vignette.

The shinyReport() function requires the user to specify the type of report to produce. Two options are available depending on whether the user wishes to produce a report for their receiver array project (receivers) or tagging project (transmitters).

This vignette describes the receiver array (receivers) report.


The shinyReport() function will generate a pop-up window enabling the user to navigate and select the detections data .CSV file for the receiver array project of their choice. Once this file is loaded, another pop-up window will appear prompting the user to select the corresponding receiver deployment metadata file. Note: the pop-up windows appear in the background of RStudio for some OS.

These files can be accessed via the IMOS Australian Animal Acoustic Telemetry Database.

For the detections file, the user can access the Detections tab, filter by “Receiver Deployment Project Name”, and download the data.



For the receiver metadata file, the user can access the Receiver Deployments tab, filter by the same project selected above, and download the data.


Alternatively, the user can select their own data, previously formatted to match the IMOS database output format.

In this vignette, multi-year and multi-species data from the IMOS Heron Island receiver array project are presented as an example.

Detections map


Map of the detections recorded at each station in the receiver array. The user can select different datasets to overlay on the map including the number of detections, transmitters or species detected. Additionally, the date range can be modified with the time slider on the left panel. Hovering on the markers reveals pop-up text including the station name, installation name, number of detections, number of species, number of transmitters and the coordinates of the receiver station.


Detections overview


Bar plot presenting the number of detections recorded at each station, colour-coded according to the different species detected in the array. The user can filter by station and/or species to explore patterns in the data. Hovering on each bar will reveal additional information including the station name, species common name and number of detections recorded.

The plot can be saved by clicking on the camera icon in the top right corner.

The summary table on the left panel summarises the number of detections per species per station within the receiver array. This summary table is refreshed as the user selects different filter options. This table can be saved as .CSV, Excel or .PDF file by clicking on the respective buttons.


Transmitters overview


Bar plot presenting the number of transmitters detected at each receiver station, colour-coded by according to the different species detected in the array. The user can filter by station and/or species, as required. Hovering on each bar will reveal additional information including the station name, species common name and number of transmitters detected.

The plot can be saved by clicking on the camera icon in the top right corner.

The summary table on the left panel summarises the number of transmitters detected per species at per station. When the user selects different filters the summary table will be modified accordingly. This table can be saved as .CSV, Excel or .PDF by clicking on the respective buttons.


Detections over time

Detections per station


Scatter plot presenting the number of detections per day recorded at a receiver station, colour-coded according to the receiver deployed. The user can filter by installation, station, month and/or species to explore patterns in the data. Additionally, the user can select a different timezone (default timezone is UTC; WARNING modifying the timezone may incur some delays to update the plot).Hovering on the data points reveals additional information including the date, number of detections recorded and the receiver name.

The plot can be saved by clicking on the camera icon in the top right corner.


Detections per hour


Box plot presenting the number of detections recorded per hour. The user can filter by installation, station, month and/or species. Additionally, the user can select a different timezone (default timezone is UTC; WARNING modifying the timezone may incur some delays to update the plot).Hovering on the plot will reveal additional information including the maximum value, upper fence, Q3, median and Q1.

The plot can be saved by clicking on the camera icon in the top right corner.


Array performance


Plot of the Station Efficiency Index, modified from Ellis et al. (2019) and based on the resonATe toolkit. This index assesses the performance of a station in the context of the entire receiver array. Values range from 0 to 1, with higher values indicating higher performance.

\[ SEI = \frac{T_s}{T_a} \cdot \frac{S_s}{S_a} \cdot \frac{DD_s}{DD_a} \cdot \frac{D_a}{D_s} \] Where:

  • \(SEI\) = Station Efficiency Index
  • \(T_s\) = Number of tags detected on the station for the date range selected
  • \(T_a\) = Number of tags detected across all stations for the date range selected
  • \(S_s\) = Number of species detected on the station for the date range selected
  • \(S_a\) = Number of species detected across all stations for the date range selected
  • \(DD_s\) = Number of unique days with detections for the station and date range selected
  • \(DD_a\) = Number of unique days for the date range selected
  • \(D_a\) = Number of days for the date range selected
  • \(D_s\) = Number of days that the station was active*

*Note:

  • If the station was active for more days than the date range selected \(D_a = D_s\)

  • If the station was active before the date range selected, the start date of \(D_s\) will be the same as the start date for \(D_a\)

  • If the station was active until after the end date for the date range selected, the end date of \(D_s\) will be the same as the end date for \(D_a\)


The user can filter by installation and date range (i.e. days where the station was considered active). Hovering on the plot will reveal additional information including the value of the index for each station. The plot can be saved by clicking on the camera icon in the top right corner.

The table on the left panel summarises the names of the receivers deployed at each station for the installation and date range selected. This table can be saved as .CSV, Excel or .PDF by clicking on the respective buttons.


Note: To explore and visualise data relative to a tagging project, head over to the shinyReport_transmitters vignette

References

  1. Ellis, R.D., Flaherty-Walia, K.E., Collins, A.B., Bickford, J.W., Boucek, R., Walters Burnsed S.L., Lowerre-Barbieri, S.K. (2019) Acoustic telemetry array evolution: From species- and project-specific designs to large-scale, multispecies, cooperative networks. Fisheries Research (209): 186-195. https://doi.org/10.1016/j.fishres.2018.09.015

  2. IMOS (2021). Animal Tracking Database. https://animaltracking.aodn.org.au. Accessed: 2021-10-11.


Vignette version 0.0.5 (5 Nov 2021)