Table of Contents
- Start the Animal Movements application (NPS-Alaska users will find it at
X:\GIS\Apps\AnimalMovement\10.1\AnimalMovement.exe). - Click on the Project Investigator Details button. If you do not see this button, then you are not a PI, and cannot create you own project. If you should be a PI, please contact the database administrator (regan_sarwas@nps.gov). If you want to create a project for another PI, then click on the Project List instead.
- Below the project list, click on the green add(+) button.
- If you are creating this project for another PI, then select their name in the list. The list is all the PIs that have given you permission to assist them. If the name need is not in the list, contact the PI and ask that they give you permission.
- Provide a short (less than 16 characters) code for the project. This will be used in some lists, and in database queries to identify the new project. The code is required, and must be unique.
- Provide a short but descriptive name for the project. This name will be used in most reports, and in the application to identify your project. A name is required.
- Optionally provide a Park Service Unit code and additional descriptive details.
- Click Create. If the Code you choose was not unique, you will be notified, and given a chance to select a new code.
These instructions assume you have purchased the Argos service from CLS America, and that they have allocated Argos ID numbers to you. Furthermore you will need the Program number, username, and password that they provide.
An Argos Platform is a unique Argos ID corresponding to the hardware installed on a animal tracking collar. An Argos Platform may be re-used on different collars, but will only be on one collar at a time. A refurbished collar may be given a new Argos ID. Once again, a collar can only have zero or one single Argos Platform at a given point in time. The Argos Platform is often referred to as the Argos Id of a collar. Argos Platforms are organized into an Argos Project. A project investigator is given a username and password to manage the Argos Program on the Argos website (https://argos-system.clsamerica.com).
Once given the necessary program information, the Animal Movements application can contact the Argos website and download the details on the Argos Platforms in the program. The PI can specify if the program will be automatically and regularly queried for new collar data. It is the PI's responsibility to relate the Argos Platforms to a collar. For Telonics Gen4 collars this is done automatically when the TPF file is loaded into the database.
- Start the Animal Movements application (NPS-Alaska users will find it at
X:\GIS\Apps\AnimalMovement\10.1\AnimalMovement.exe). - Click on the Project Investigator Details button. If you do not see this button, then you are not a PI, and cannot create you own Argos program. If you should be a PI, please contact the database administrator (regan_sarwas@nps.gov). If you want to create a project for another PI, then click on the Project List, select one of their projects, and then click the PI info button on the project details page.
- Click the Argos tab on the Project Investigator Details** page.
- Below the program list, click on the green add(+) button. (NOTE: if the program number is already in the list, then you "re-create" it. You must get a new program number from CLS America, or skip the program creation step and add the new platforms to the existing program.
- Provide the Program Id, Program Name, Username, and Password exactly as provided by CLS America.
- The start and end dates can also be entered, however they are purely informational and not used by the database in any automated processes.
- By checking the Active option, you are declaring your wish that this program is downloaded from the Argos website on a regular (daily) basis. If the collars in this project are not yet deployed, then you can check this option when the collars are deployed, however the website only maintains 10 days worth of data, so if you want this feature, be sure to do it with 10 days of deploying your collars.
- Click Create. If the Code you choose was not unique, you will be notified, and given a chance to select a new code.
- Select newly created program in the list, and click the info(i) button, or double click the program number/name in the program list.
- Select the Argos Platforms tab on the Argos Program Details page.
- Click the Add Missing Platforms button.
- Click the Close button(s) as necessary.
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Gen4 Datalog files (*.tdf) files can be uploaded directly to the database. The database will archive this file and use Telonics Data Convertor (TDC) software in the background to create a *.csv file that is used to create the collar fixes. Because of the binary format for the Gen3 download files (*.tfb), and because the Telonics Data Download Utility V1.41, cannot be run in the background, it is not possible to upload these files directly. If you have *.tfb files, you must first use the Telonics Data Download Utility V1.41 to create a *.csv file, and then follow the remaining instructions.
This not required to see your data, but it is good bookkeeping. By doing this, the database is able to hide any fixes that occur after the retrieval date/time. It also frees the collar up for potential redeployment on another animal.
This task is most efficiently done with deactivating old files, so the step by step instructions are in the next section.
This is not required to see your data, but it has several benefits.
- It can speed up the database. The new fixes will in most cases, hide fixes that were received by email or web services download. This effort of finding and hiding overlapping fixes is removed if the old files are first deactivated.
- It will remove any fixes that were altered in the Argos transmission. If a GPS fix that was transmitted via Argos was slightly altered in time, it will not be hidden by the new store-on-board data. It is also possible that the time is the same, but the location is different. The database considers this a conflict that requires attention (by default the last data in wins, so your store-on-board data will hide the Argos data). These errors are more common with Gen3 data.
To retrieve collars and deactivate old files, use this step-by-step procedure
- Start the Animal Movements application.
- Click on the Project Investigator Details button in the main menu. If you are not a project investigator you will not see this button and you cannot perform this task.
- Click on the Collars tab in the Project Investigator Details form.
- Double click on deployed collar that was recently retrieved. Deployed collars will list the animal it is deployed on.
- Click on the Animals tab in the Collar Details form.
- Click on the Retrieve button.
- Enter the date and time the collar was removed from the animal. The time should be local time, not GPS (UTC) time. Providing the time is optional (it defaults to 12 noon), but is recommended, as it will ensure that fixes on that day before retrieval are retained, while those after the retrieval are hidden.
- Press the Retrieve button
- Click on the Files tab in the Collar Details form.
- Select all the files that were from the deployment that was just retrieved. If this collar has only been deployed on this one animal, and if have not loaded your store-on-board data yet, then you will want to select all files. Use control-click or shift-click to select multiple files. Do not select any Inactive files. If all the selected files are Active, then the button at the bottom of the form will be labeled Deactivate, and it will be enabled.
- Click the Deactivate button
- Close the Collar Details form, and repeat at step 4 until all the collars have been retrieved.
You can bulk load an entire folder, or a selection of one or more files. While selecting a folder seems most convenient, you will need to make sure that only the files you want to load are in the folder. Any files not recognized as valid collar data files will result in an error message. In addition, if the folder contains *.tdf and the resulting *.csv files, the program will load both files. Since the database will create it's own version of the CSV file from the *.tdf file, you will redundant data in the database. I recommend loading by file, and selecting just the files you want to load.
Most likely if you are a project investigator, you have access to the Telonics Data Convertor (TDC) software to download you collars and create *.csv files from your *.tdf files. You can upload either type of file. If you upload the *.tdf file, then the application (if it can find the TDC software on your computer) or the database (otherwise) will create and upload the *.csv file, and link it to the *.tdf file. I recommended that you upload the *.tdf files for several reasons
- The *.tdf file will be archived in the database.
- The *.tdf file includes the collar parameters in effect while deployed.
- The *.tdf file could be re-processed in the future if there is some concern that it may have been processed incorrectly.
Uploaded files can be associated with a Project Investigator, or a Project. This association only determines where the file is listed in the Animal Movements application. I recommend that all files are associated with a project, unless a file contains data for multiple collars. In this case, the file should be associated with the appropriate project investigator.
Step-by-step instructions for loading multiple Gen4 store-on-board data files.
- Start the Animal Movements application.
- Click on the Project List button in the main menu.
- Double click on the project that the new collar data is for.
- Click on the Files tab in the Project Details form.
- Click the green plus sign at the bottom of the file list. If this button is greyed-out, then you cannot add files to this project. You must be the owning project investigator or an editor on the project to add files.
- Click the Browse button for File(s) on the Upload Collar Location Data form.
- In the Open dialog box, change the file type to Telonics Datalog (*.tdf)
- Select the desired files. You can select multiple files by dragging your mouse across the file names, or use control-click or shift-click to select multiple files.
- Click the Open button to close the dialog box, and proceed.
- The Upload button on the on the Upload Collar Location Data form should now be enabled.
- In the Associate file with section leave all the Collar pick list blank . This will allow the application to determine the collar from the file contents. If you are not using CTN numbers as the collar Id, then you must load the files individually and manually assign the collar id for each file.
- Click the Upload button. It may take several seconds to a minute to upload and process each file, depending on the availability of the TDC software, your network speed, the presence of active overlapping files for this collar, and the current workload on the database server. Depending on the server set up, the processing may not occur immediately, but may be schedules to occur in a batch at some later date.
- If the uploading/processing completed without errors or warnings, then the dialog box will close automatically.
- The uploaded files should appear at the top of the files list in the Project Details form. To see the derived *.csv files, click on the Show Derived check box. If there are no derived files (they will be colored brown to match the Show Derived check box text, then the server has scheduled the processing for later. At NPS, batch processing occurs every 10 minutes, if it was unable to be performed immediately for some reason.
The title of this section is mis-named. The source location data in the database is never deleted or altered.
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There is no way to change the time or location of a fix. Nor should you. You cannot add an ad-hoc location. All fix data must come from the raw collar data. This ensures a defensible dataset. You can however decide that some location data is bad, and eliminate this from display and analysis. These hidden locations are available for review, and can be un-hidden if your assessment of the data changes in the future.
If you notice locations on the map that are before or after the collar was deployed on the animal, Then you need to edit the deployment dates in the Database application.
Similarly if you think some locations may be missing from the map, you can increase the deployment range to show locations that may be hidden.
Fixes that are outside the deployment dates are not shown in the invalid locations layer, they can only be displayed/hidden by editing the deployment dates.
If an animal slips a collar, or a collar releases prematurely, this should be treated as a retrieved collar to remove the locations of the stationary collar no longer on the animal. Since you are not 'retrieval date' in the deployment is not the date you actually retrieved the collar, you may want to make a note in the collar table remarks section for future reference.
Identifying mortalities, and hiding the locations of the stationary collar is covered in the Mortalities section.
There may be a tool to put in geographic coordinates that define the extreme boundaries of your project area. Any locations that occur outside those bounds will automatically be hidden. This is easy to do in the database, and can be problematic in ArcMap. There is a current limitation in ArcMap when you zoom out too far (so that more than one hemisphere is displayed - easy to do in Alaska, where anything above 90 degrees north is in the other hemisphere). In this case, the database returns no locations, so you cannot see the data to hide the bogus locations.
This database feature will be coming soon.
There are primarily two was to identify bad locations in ArcMap.
- Visual Review. Some bad fixes are visually obvious when reviewing the movement vectors. These will show up as a spike from and immediately returning to a cluster of locations.
By reviewing the attributes (speed, duration, and distance) in the movement vectors table to identify suspect locations. this is easiest to do if you first define a definition query on the locations and movement layers to limit the data to just one animal.
- In ArcMap, right click on the Movement Vectors layer and select Open Attributes
- Right click on either the speed, duration, or distance column and sort. High speeds, short durations, or large distances are all the result of suspect locations.
- When you identify a movement vector that is suspect, note the start and ending time.
- Open the attribute table for the location data.
- Scroll to the locations at the start and end time.
- Select each location, starting two locations before the suspect vector, and proceeding to two locations after the suspect vector, and watch the animals progress on the map. In this way, it is usually quite easy to identify which end of the vector is the bad location.
- Use the ArcMap Selection tool to select the unwanted location(s).
- Click the paw print icon (Edit Location Status tool).
- Click the Yes to hide the selected locations.
If you turn on the invalid locations layer, you will see these points have been removed from the valid locations/vectors layers and added to the invalid locations layer. If you want to re-activate them, select the points in the invalid locations layer, click the paw print, and then select No to un-hide these locations.
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Dead animals should be identified so that the locations after the animal died are removed from the data set used for analysis, particularly home range analysis.
This is done in ArcMap. More to come.
- Click on Project List
- Double click your project
- In the middle list, double click the animal that died
- In the Animal Details window, click edit, then check the box next to Date of Death
- Correct the date, then click Save.
If you refresh the view in ArcMap, it should draw with the corrected data.
Close the windows (If you close the first window, it will close all the others), and your done.
- Open ArcMap, and make sure that the Animal Movements Add-In is loaded. If you select Customize->Add-In Manager... from the ArcMap menu, you should see the following:
If not, make sure that you have X:GISAddins10.1 specified as the Add-Ins folder in the Options tab.
- Select Customize->Customize Mode... from the ArcMap menu.
- Click the Commands tab
- Scroll down to the NPS Alaska Category.
- Find the Edit Location Status Command (paw print icon)
- Click on the paw icon, and drag it over an existing toolbar (I like to use the Alaska Pak toolbar), and drop it. The icon should now be on the toolbar.
- Close the Customize window.