Clements 2018 taxonomy update for AviSys

To install the update, please follow this doc­u­ment­ation very care­ful­ly. Read it through completely once before coming back to the beginning and actually performing the steps.

Note that you should be running AviSys Version 6.00M in order to perform the update. See how to check your AviSys version. I have no experience with what happens if you try the update on an older AviSys version. The update will deliver the 2018 taxonomy regardless of how long ago you last did a taxonomy update, but naturally the longer it has been, the more conflicts you may have to resolve.

News

Backup!

Before you even think about installing the taxonomy update, you must know how to back up your current data set. And you must know how to restore from the backup. Run a backup immediately before beginning the update. (The backup and restore procedure built-in to AviSys is simple and reliable. I use it all the time as I run backup on my laptop and restore on my desktop to keep them in synch.)

As far as I know, previous updates worked successfully for everyone who ran them. I received no reports of serious problems; many people commented on how well it worked. Nevertheless, I do not warrant that the update will work for you. This is why it is so important for you to have a backup, and know how to restore it.

One good approach that worked well for people who tried it, even if they also had a good backup, is to make a copy of your entire data folder under a new name just before performing the update. If you are dissatisfied with the results, you can just delete the updated folder and rename the copied folder back to the original name. If you are satisfied with the results, you can delete the copy of your old folder.

Not sure what I mean by data folder? Check this explanation.

If you have any custom checklists (ones that you marked yourself, manually), back them up. The update procedure does not update checklists, so after the update you will need to "Remove" all of your checklists and "Add" them back, in order to pick up any taxonomic changes. In the case of custom checklists, when you add them back, you will want to be able to mark them using your checklist backup file. If there are names in your backup file that have changed, you will get an exception file listing names that have to be corrected, similar to what you got for the main update. If you do not back up your custom checklists, they could be lost forever and you will have to recreate them from scratch. No backup procedure automatically backs up custom checklists in a way that will survive the update procedure, not the AviSys built-in backup procedure, nor any file backup technique. You must back them up one by one, using the method that is described here. Note that only custom checklists need to be backed up. You don't need to back up state or nation checklists because you'll just recreate them from the built-in data.

How many species?

This update is based on the 2018 Clements spreadsheet which has 10585 species. Of those, 114 are marked extinct (10471 not extinct), and like Jerry, with some exceptions I excluded all species that Clements designates as extinct. As in past updates, extinct species that are on the ABA checklist are included. These are the four extinct species in the ABA continental area (Labrador Duck, Great Auk, Passenger Pigeon, and Carolina Parakeet) plus 24 extinct Hawaiian species. Thus, this update has 10471+4+24 = 10499 world species. Note that there are other species on the ABA checklist such as Ivory-billed Woodpecker and Bachman's Warbler that may be extinct, but are not so designated by the Clements checklist.

The N.A. mode checklist has 1012 species. The N.A. mode checklist is constrained to continue to be a North American checklist; there is no way to integrate Hawaii into it. Thus, it can no longer match the ABA checklist, but does match the ABA checklist for the continental area. For guidance on how to display the new ABA checklist, see The new ABA checklist.

The built-in state checklists are updated with eBird data through 17 August 2018.

Summary of taxonomic changes

You will very likely have to do a little bit of research to learn how to resolve some taxonomic changes. You should be able to find everything you need in the summary of taxonomic changes. (Seriously, read this link! It will save you time.)

Built-in checklists

The taxonomic update also provides updates to the built-in state and province checklists. Also, the nation checklist addon is available as a separate download.

Preparation for update

First download and run the file AviSys Clements 2018 Taxonomy.exe.

Download AviSys Clements 2018 Taxonomy.exe

Anti-virus warnings. It is likely that your anti-virus program will put up warnings when you try to run the program, for the simple reason that this is a program that it hasn't seen before, and is not in its database. Anti-virus programs are always suspicious about such programs and put up warnings even though they have no idea about what's in it. You can run the program safely. If you want to be super-cautious, you can have your anti-virus scan the program file before you run it.

When you run AviSys Clements 2018 Taxonomy.exe, click the Unzip button on the window that comes up. This will create a sub-folder, also named AviSys Clements 2018 Taxonomy, in the same folder where you downloaded the .exe file. Click OK and then Close, and open the new AviSys Clements 2018 Taxonomy folder.

You will find two subfolders, named For Data folder and For Main folder. In For Data folder, you will find four files, named MASTER.UPD, NEWNAMES11.AVI, WLDCODE.AVI, and WORLDSEL.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.

Important: Most of these files that you will be copying are replacements for files that you already have. When Windows asks you how you want to handle the copy, be sure to select the option "Replace the file in the destination". Do not choose an option to retain the old copies.

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
WLDCODE.AVI
WORLDSEL.AVI
Four-letter band codes for World mode. See Enhanced AviSys world bandcode files for more about these files.
AviSys main folder, e.g., C:\AVI6
SSDATA.AVIThe subspecies data
BANDCODE.AVI
BANDSEL.AVI
Four-letter band codes for N.A. mode.
Alias.avi
Alpha.avi
Famfile.avi
Jump tables for N.A. mode
Walias.avi
Wfam.avi
Wfam2.avi
Jump tables for World mode

Installation steps

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

    Suggestion: If you use band codes for finding species, I suggest that you do not copy the new band code files until after you have resolved conflicts. Otherwise there may not be a band code available for finding an old name that you need to change. The band code files are WLDCODE.AVI and WORLDSEL.AVI in the data folder, and BANDCODE.AVI and BANDSEL.AVI in the data file.

    For each of the .AVI files, you should find that you already have an old copy; if you don't find them, you are looking in the wrong folders. 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. When you are sure that you are all backed up and ready to go, delete the old files (unless you renamed them instead) and copy the new replacements. Careful! Don't delete all of the AVI files, only the ones that I have listed here.

  2. Run AviSys, making sure that you are in the data set that you wish to update. If you decide to install to a test data set rather than your default data set, remember that AviSys starts in your default data set every time you start it, so each time you restart AviSys, you have to manually switch to the data set that you are working in. (Speaking from experience, you will forget this.)
  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 do not have the file MASTER.UPD in your AviSys data folder for this data set, this choice will be grayed-out (not clickable).
    Launch update
  5. This is your last chance to stop and create a backup if you still haven't done it. If you are ready, click Start.
    Start update
  6. If you are really ready, click Yes.
    Confirm backup
  7. 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 after the first run.
    New names prompt
  8. 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
  9. Click yes, you do want to view the file.
    View exception file
  10. 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.

    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. (Seriously, read this link! It will save you time.)

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

    Just in case you might have to start over on the update for some unexpected reason, keep a record of the changes that you make, so that it will be easier to repeat them.

  11. After you have resolved all exceptions, restart at step 2, and try again. Or, if you were lucky and didn't have any exceptions, just keep going here.

  12. If there are no exceptions, you will get this result. Click ok.
    First success message
  13. 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
  14. When the update is complete, AviSys shuts down and you will need to restart it. While it is shutdown, if you deferred moving the band code files to their destinations, do that now.
    Shutdown notice
  15. When you restart, you will get two more prompts like this, for which there is nothing to do but click OK. It doesn't actually take long on today's computers.
    Update notice
    Subspecies rebuild notice
  16. Restore your checklists. If you have any checklists defined, remove all of them and add them back. This is the only way that checklists will pick up taxonomic changes. For custom checklists, remove them and restore them from your backups. AviSys will provide you with an exception list if you need to adjust for any taxonomic changes. For built-in state checklists, just remove them and add them back using the built-in checklists. If you use the optional nation checklist addon, replace your RANGES.LST file with a fresh download from the nation checklist addon page.

    If you find that your checklist sighting markers are not correct after restoring checklists, run “Set Checklist Markers” to fix them.

    Set Checklist Markers
  17. Congratulations, you should be good to go! Verify that you have 10499 species in World Mode and 1012 species in N.A. Mode. I've noticed that when I first restart AviSys, it may not show the correct number of species in N.A. mode. If doesn't show 1012 species, close AviSys and restart again.

Appendix

Extinct Hawaiian species that are on the ABA checklist

If you prefer not to have these species included, you can simply delete them after you finish the update.

Laysan Rail
Hawaiian Rail
Amaui
Oahu Oo
Kauai Oo
Bishop's Oo
Hawaii Oo
Kioea
Kakawahie
Kona Grosbeak
Lesser Koa-Finch
Greater Koa-Finch
Ula-ai-hawane
Laysan Honeycreeper
Hawaii Mamo
Black Mamo
Lanai Hookbill
Oahu Nukupuu
Lesser Akialoa
Kauai Akialoa
Oahu Akialoa
Maui-nui Akialoa
Greater Amakihi
Oahu Akepa

AviSys Memorial Page

Questions or comments?