Taxonomy update for AviSys (2016)—Fix 1

I have created a taxonomy update for AviSys incorporating the 2016 Clements updates. To install it, please follow this documentation very carefully.

News

Now available, Update Fix 1. You should do the entire update procedure for Fix 1, even if you installed the original update (it will go very easily the second time). For the benefit of those who have installed the original update, read what is new in Fix 1.

24 Oct 2016: Enhanced World bandcodes. Read more.

25 Oct 2016: Nation Checklist Add-On available.

26 Nov 2016: Nation Checklist Add-On updated. Read more.

First download and run the file AviSys Clements 2016 Taxonomy Fix1.exe.

Download AviSys Clements 2016 Taxonomy Fix1.exe

When you run AviSys Clements 2016 Taxonomy Fix1.exe, click the Unzip button on the window that comes up. This will create a sub-folder, also named AviSys Clements 2016 Taxonomy Fix1, in the same folder where you downloaded the .exe file. Click OK and then Close, and open the new AviSys Clements 2016 Taxonomy Fix1 folder.

You will find two subfolders, named For Data folder and For Main folder. In For Data folder, you will find two files, one named MASTER.UPD, and one named NEWNAMES11.AVI. In For Main folder, you will find nine files, all with extension .AVI. (Note: if you use the Windows option “Hide extensions for known file types”, you will see all of the .AVI files as just names without an extension. That's ok.) Only AviSys knows what to do with these files; Windows cannot open any of them correctly, so do not even try clicking on them. Strange (although harmless) results will occur if you do. The .AVI extension has a special meaning in Windows, but AviSys uses it with a different meaning.

These files go to different places, so pay careful attention to getting them in the right place. The folder names make this easy: copy all of the files in For Main folder to your main AviSys folder, and all of the files in For Data folder to your data folder (each data folder, if you have more than one). Your main AviSys folder might be named C:\AVI6, if it is, then your AviSys data folder will be named something similar to C:\AVI6\KENT.

For the nine .AVI files that go to your main AviSys folder, you should already have old copies of all of these files in that folder; if you don't find them, you are looking in the wrong folder. You'll be replacing all of them, so be sure you have them backed up. Note: The AviSys backup procedure does not back up files in the main folder, so make your own backup copies manually. One easy backup would be just to rename the files. If you are sure that you are all backed up and ready to go, you can go ahead and copy these files to your main AviSys folder before running the update; or you can wait and copy them after you have run the update and verified its success.

Here is what all these files do:

AviSys data folder, e.g., C:\AVI6\KENT
MASTER.UPDThe taxonomy and state checklist update
NEWNAMES11.AVIProvides simple 1-to-1 renames that don't involve splits or lumps
AviSys main folder, e.g., C:\AVI6
SSDATA.AVIThe subspecies data
BANDCODE.AVI
BANDSEL.AVI
Four-letter band codes for N.A. mode (which are completely separate from band codes for World mode). Note: BANDCODE.AVI can be in either your main folder (recommended) or your data folder. Put the new one wherever you had your old one. If you have it in both places, the one in the main folder will be used. Only put it in your data folder if you want to customize it for different data sets.
Alias.avi
Alpha.avi
Famfile.avi
Jump tables for N.A. mode
Walias.avi
Wfam.avi
Wfam2.avi
Jump tables for World mode

This update is based on the 2016 Clements spreadsheet which has 10514 species. Of those, 109 are marked extinct, and like Jerry, I excluded all extinct species except for the four that are on the ABA list, or in other words I excluded 105 species. 10514–105 = 10409 which is the number of species in this update. (By extinct species, I mean species that are designated extinct on the Clements list. There are a couple of species such as Ivory-billed Woodpecker and Bachman's Warbler that you might think are extinct but are not so designated by the Clements list.) The N.A. list matches the July 2016 edition of the ABA checklist (v7.9.0) and contains 993 species.

Backup!

Before you even think about installing the taxonomy update, you must backup your current data set. And you must know how to restore from the backup. (Restoring is simple and reliable. I do it all the time to keep my desktop in synch with my laptop.)

Also, beware that installing the taxonomy update probably will empty or delete all of your checklists (the exact outcome seems to be unpredictable). In any case, you will want to remove and re-add any built-in state checklists that you are using, in order to pick up the new versions. If you have custom checklists, you must make backups ahead of time that you can restore later. If you do not backup your custom checklists, they could be lost forever and you will have to recreate them from scratch.

Dry run!

Besides having your known good data backed up, I strongly recommend that you create a second copy of your data to use for a dry run. Take a few minutes now and read how to create a test data set.

Random observations

Now that you are set up to do your dry run, here are some considerations.

Brass Tacks

Ok, here are the actual installation steps. Because I strongly advise doing a dry run first, these steps refer to the dry run test data set that you created. Once you decide to go ahead for real, the steps are the same except for the name of the data set. If you have done an update before, this should all look familiar to you..

  1. If you have not already copied MASTER.UPD and NEWNAMES11.AVI to your data folder, do so now. You want to copy them to your AviSys data folder, which for the dry run is your DRYRUN folder, and which for the real update will be your personal data folder. (Each of them if you have more than one.) I suggest not putting them in your personal folder until you are actually ready to update, to prevent absent-mindedly starting the update when you don't mean to. (Just so you know, once you run the update, these files are never needed again, so they get deleted. This is normal.)
  2. Run AviSys, making sure that you are in the data set that you wish to update (e.g., DRYRUN). Remember that every time you start AviSys, it starts in your default data set so each time you have to manually switch to DRYRUN.
  3. Switch to World Mode.
  4. You should notice that in the Utilities menu, the choice “Update Master Checklist (from update file)” is clickable. Click on it. If you have not placed the file MASTER.UPD in your AviSys data folder for this data set, this choice will not be clickable. This is a good reason not to copy MASTER.UPD to your real data folder until you are ready to use it—you won't be able to click it absent-mindedly.
    Launch update
  5. If you are really ready, click Start.
    Start update

    If this is your real data set, this is your last chance to stop and create a backup if you still haven't done it.

    With the dry run data set, no worries, click Yes.

    Confirm backup
  6. Click Yes to this prompt. It provides automatic name changes for one-to-one renames that don't involve splits or lumps. Note: These renames are done on the first pass regardless of whether the entire update succeeds or not. Thus, you will only see this prompt on the first try. If you have to rerun the update, this prompt is not repeated.
    New names prompt
  7. Your first attempt to update may well abort due to exceptions that AviSys cannot resolve. This is not unusual. Click OK.

    Abort due to exceptions

    Yes, you do want to view the file.

    View exception file
  8. Here is what Jerry had to say about this:

    YOUR INVOLVEMENT REQUIRED

    It would have been nice to provide a taxonomy update that, with the push of a button, updates your entire master list and all sightings. Sadly, that CAN'T POSSIBLY happen. It would require AviSys to change your sighting records without your involvement --- that's simply too horribly dangerous. AviSys has no idea which species you actually saw; only you know that. So you will be involved with sighting records that need to be changed because of this update --- AviSys simply keeps you informed of what is going on in the process and makes it as easy as possible. HOWEVER, in this release, virtually all one-on-one English name changes are done automatically by AviSys, and you NEVER have to deal with Latin name changes in any case.

  9. In short, if you have observations of a species whose name has disappeared from the taxonomy because of a split or lump, AviSys has no way of knowing what other species your observations of that species should be reassigned to. These are the cases that are listed as exceptions in the UPDEXCEP.TXT file, and you must resolve them manually before attempting the update again.

    For your reference, here is a summary of possible exceptions.

    One example: If you have observations of Western Scrub-Jay, that will be flagged as an exception because there is no longer a Western Scrub-Jay in the taxonomy. You will need to rename Western Scrub-Jay to either California Scrub-Jay or Woodhouse's Scrub-Jay, whichever you have most observations of. If you have seen both species, you can go back after the update and separate them out.

    Keep a record of the changes that you make in your test data set, because you will need to make the same changes again when you do the update for real!

  10. After you have resolved all exceptions, go back to step 4 and click “Update Master Checklist (from update file)” again. Or, if you were lucky and didn't have any exceptions, just keep going here.

  11. If there are no exceptions, you will get this result. Click ok.
    First success message
  12. It is my observation that AviSys goes ahead and converts your data regardless of which button you click here. It's safest to click Yes.

    Ready to convert prompt
  13. When the update is complete, AviSys shuts down and you will need to restart it.
    Shutdown notice
  14. Remember that each time you start AviSys, it begins in the default data set. If you are doing the dry run, you will need to switch to the DRYRUN data set. If this is your real update, no worries here.
    Restart
  15. You will get a series of prompts like this, for which there is nothing to do but click OK.
    Update notice
  16. Rebuild the world bandcode files. This gives you four-letter bandcodes that work when you are in World Mode. Note that world bandcodes are completely separate from N.A. bandcodes.
    Rebuild world band codes
  17. If you have not yet copied the nine updated .AVI files to your main AviSys folder, copy them now, as described at the top of this document. Then restart AviSys.
  18. If you did not copy SSDATA.AVI to your main AviSys folder before running the update, then reload the SSDATA.AVI data by clicking “Reindex Subspecies Data”.
    Reindex Subspecies Data
  19. Confirm successful installation of subspecies data by checking that California Scrub-Jay and Woodhouse's Scrub-Jay each have subspecies listed.
  20. Restore your checklists. When you open the checklist menu, you might find that your checklists are gone, or you may see that the names of all your checklists are there, but the checklists are empty. If you are lucky, you might find that your checklists are intact. The exact outcome seems to be unpredictable. Regardless, if you are using any built-in state checklists, remove them and re-add them to pick up the new versions. If your custom checklists are not intact, restore them from backups. Regardless, if any of them contain species affected by taxonomy change, you will have to re-mark the correct species. Sometimes after restoring checklists you might find that your sighting markers are not correct; run “Set Checklist Markers” to fix this.
    Set Checklist Markers
  21. Congratulations, you should be good to go!
  22. When you are done with the DRYRUN dataset, you can simply delete its entire folder. AviSys will simply forget about it if it's gone. Important: Just be sure that you don't have the data set open in AviSys at the time you delete it. AviSys gets extremely unhappy if a data set disappears while it's in use.

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Questions or comments?