activating hyperlinks.

adding time bin example
Adding ref to ATN
renaming webpage for consistancy with eDNA.
updating config to new page name

_config.yml

@@ -121,7 +121,7 @@ extras_order:
   - helpful-tutorials
   - figures
   - edna-extension
-  - special-data-type-acoustic-telemetry
+  - acoustic-telemetry
 
 # Specify that things in the episodes collection should be output.
 collections:

_extras/special-data-type-acoustic-telemetry.md → _extras/acoustic-telemetry.md

@@ -1,5 +1,5 @@
 ---
-title: "Specific Data Examples - Acoustic (and Satellite) Telemetry"
+title: "Acoustic (and Satellite) Telemetry"
 teaching: 15
 exercises: 0
 questions:
@@ -35,13 +35,48 @@ keypoints:
  Each of the telemetry networks produce for their investigators a data report that takes into account every compatible listening device across all of the networks that has heard their tagged animals. This report is intended to be the best, most complete report available for all possible detections of the studied animals from all participating partners worldwide. These reports can run into the millions of detections for anadromous fish, closed system monitoring, or where an animal may be resident near a listening device (or deceased near one). The Ocean Tracking Network has created a data pipeline for projects that combine all the observations for a certain project into a Darwin Core Event Core archive, based on a shared standard built between the European Tracking Network and the Ocean Tracking Network that can produce an Occurrence Core or Event Core dataset.
 
  When preparing to submit animal telemetry data to the Ocean Biodiversity Information System, we as data managers must consider how to put these tens or hundreds of thousands of individual animal locations into the context of the broader database. By making time-binned summaries of the animal position data, and by using the organismID field to denote multiple positions for a single known individual organism, the OTN publication process allows telemetry data to contribute fully to the OBIS database without creating too much data density or losing the details of each individual animal's movement history.
-
+
+ Below is a small table highlighting how one might make a time-binned summary of observations. In this example, we truncate the date-times down to the day+hour, then see if there are duplicate values. If so, we keep the first value but drop the other values that fall in that same hour.
+
+| time                 | dayhr         | Keep?   |
+|:---------------------|:--------------|:--------|
+| 2009-09-23T00:00:00Z | 2009-09-23T00 | True    |
+| 2009-09-25T06:42:00Z | 2009-09-25T06 | True    |
+| 2009-09-25T11:09:00Z | 2009-09-25T11 | True    |
+| 2009-09-25T11:11:00Z | 2009-09-25T11 | False   |
+| 2009-09-25T11:30:00Z | 2009-09-25T11 | False   |
+| 2009-09-27T17:58:00Z | 2009-09-27T17 | True    |
+| 2009-09-30T05:01:00Z | 2009-09-30T05 | True    |
+| 2009-10-08T20:24:00Z | 2009-10-08T20 | True    |
+| 2009-10-15T11:05:00Z | 2009-10-15T11 | True    |
+| 2009-10-17T06:11:00Z | 2009-10-17T06 | True    |
+| 2009-10-17T09:00:00Z | 2009-10-17T09 | True    |
+| 2009-10-17T10:38:00Z | 2009-10-17T10 | True    |
+| 2009-10-18T08:48:00Z | 2009-10-18T08 | True    |
+| 2009-10-18T10:26:00Z | 2009-10-18T10 | True    |
+| 2009-10-18T11:15:00Z | 2009-10-18T11 | True    |
+| 2009-10-19T10:20:00Z | 2009-10-19T10 | True    |
+| 2009-10-23T23:52:00Z | 2009-10-23T23 | True    |
+| 2009-10-24T00:06:00Z | 2009-10-24T00 | True    |
+| 2009-10-26T10:53:00Z | 2009-10-26T10 | True    |
+| 2009-10-26T11:22:00Z | 2009-10-26T11 | True    |
+| 2009-10-27T16:21:00Z | 2009-10-27T16 | True    |
+| 2009-10-27T16:22:00Z | 2009-10-27T16 | False   |
+| 2009-10-27T16:42:00Z | 2009-10-27T16 | False   |
+| 2009-10-29T11:53:00Z | 2009-10-29T11 | True    |
+| 2009-10-30T10:03:00Z | 2009-10-30T10 | True    |
+| 2009-10-31T19:48:00Z | 2009-10-31T19 | True    |
+| 2009-10-31T21:15:00Z | 2009-10-31T21 | True    |
+| 2009-11-01T21:04:00Z | 2009-11-01T21 | True    |
+| 2009-11-06T17:53:00Z | 2009-11-06T17 | True    |
+| 2009-11-13T18:48:00Z | 2009-11-13T18 | True    |
+| 2009-11-23T05:12:00Z | 2009-11-23T05 | True    |
 
 ### Mapping example
 
 OTN maintains this wiki entry example of how to populate each of the Darwin Core fields for an acoustic telemetry-sourced data Darwin Core archive. 
 
-https://github.com/tdwg/dwc-for-biologging/wiki/Acoustic-sensor-enabled-tracking-of-blue-sharks 
+<https://github.com/tdwg/dwc-for-biologging/wiki/Acoustic-sensor-enabled-tracking-of-blue-sharks>
 
 The key features of this schema are:
 
@@ -61,14 +96,16 @@ The key features of this schema are:
 * Event records with parent Event records for any co-deployed instruments at a receiver deployment.
 * Optional eMoF records associated with the instrument deployment.
 
-Data provided to the Ocean Tracking Network or its Nodes (see https://members.oceantrack.org for the map of current Nodes ) can produce these packages automatically based on currently-reported data. The published datasets are available via OBIS, and OTN's OBIS Node at https://members.oceantrack.org/ipt/.
+Data provided to the Ocean Tracking Network or its Nodes (see <https://members.oceantrack.org> for the map of current Nodes ) can produce these packages automatically based on currently-reported data. The published datasets are available via OBIS, and OTN's OBIS Node at <https://members.oceantrack.org/ipt/>.
 
 
 ## Satellite telemetry, light-level geolocation, etc.
 
  Satellite telemetry presumes surfacing events, to allow an instrument to obtain a GPS or Argos network location of a tagged individual. These surfacings are often monitored in near-realtime with a high degree of position error, and paths can be reprocessed and corrected post-deployment using light level geolocation, state-space modelling, or other emerging techniques. 
 
- For satellite telemetry, tracks are not published automatically by OTN, but on a case-by-case basis. A method for publishing satellite-based animal telemetry data that conforms to the ETN/OTN standard above as an Occurrence Core archive is explained here: https://github.com/tdwg/dwc-for-biologging/wiki/Movebank-GPS-data . The R package `movepub` implements this method and its SQL algorithm is also browsable on GitHub for those adapting it to use outside of R. https://github.com/inbo/movepub/blob/main/inst/sql/dwc_occurrence.sql 
+ For satellite telemetry, tracks are not published automatically by OTN, but on a case-by-case basis. A method for publishing satellite-based animal telemetry data that conforms to the ETN/OTN standard above as an Occurrence Core archive is explained here: <https://github.com/tdwg/dwc-for-biologging/wiki/Movebank-GPS-data>. The R package `movepub` implements this method and its SQL algorithm is also browsable on GitHub for those adapting it to use outside of R. <https://github.com/inbo/movepub/blob/main/inst/sql/dwc_occurrence.sql>
+
+ In the case of working with the [IOOS Animal Telemetry Network](https://atn.ioos.us/) for satellite telemetry data, tracks will be automatically archived at NOAA's [National Centers for Environmental Information](https://www.ncei.noaa.gov/) and published to [OBIS-USA](https://obis.org/node/b7c47783-a020-4173-b390-7b57c4fa1426), as identified by the scientist in the registration system. The mapping between the [ATN's netCDF archival format](https://ioos.github.io/ioos-atn-data/) submitted to NCEI and the Darwin Core format is currently being discussed in this [issue](https://github.com/ioos/bio_data_guide/issues/145).
 
 
 ### Multiple-method tagging of animals
@@ -84,7 +121,7 @@ Sometimes, stranger setups like animals-as-listening-stations or animals collect
 
 If you want to publish animal telemetry data to OBIS and GBIF, OTN is a thematic OBIS node for animal telemetry and we are able to help you do that. Providing your data to OTN augments it with other potential detections that may have occurred outside your owned listening stations, quality controls the aggregated results, and produces the archive using the QCed metadata and data that you and your collaborators have provided to OTN. These archives are then automatically updated whenever new data or metadata are supplied that extends your project's dataset. It's the best way to guarantee there will be an accurate record of your study animals in OBIS now and into the future.
 
-Supplying acoustic or satellite data to OTN or one of its Nodes can be done via our templates at https://members.oceantrack.org/data/data-collection/ . Reporting the project metadata provides the information necessary to fulfill the EML metadata, and the Tag/Instrument metadata along with the detection files are the sources of the DwC archive's Event and Occurrence and eMoF data.
+Supplying acoustic or satellite data to OTN or one of its Nodes can be done via our templates at <https://members.oceantrack.org/data/data-collection/>. Reporting the project metadata provides the information necessary to fulfill the EML metadata, and the Tag/Instrument metadata along with the detection files are the sources of the DwC archive's Event and Occurrence and eMoF data.
 
 Telemetry for satellite tagged animals can be provided as-is, with an indication of whether it is raw or post-processed.