From PTAGISWiki
Discussion about ALRS Use Cases
Subject:
Re: [Fwd: Re: site codes]
From:
Thomas_Hoffman@r1.fws.gov
Date:
Fri, 19 Nov 2004 13:34:36 -0800
To:
Carter Stein <carters@psmfc.org>
Carter,
Those are questions for Kyle. He works for USGS and I don't really know
anything about his project. Sorry!
Tom
|---------+---------------------------->
| | Carter Stein |
| | <carters@psmfc.or|
| | g> |
| | |
| | 11/16/2004 12:55 |
| | PM |
| | |
|---------+---------------------------->
>------------------------------------------------------------------------------------------------------------------------------|
| |
| To: Thomas_Hoffman@fws.gov |
| cc: |
| Subject: [Fwd: Re: site codes] |
>------------------------------------------------------------------------------------------------------------------------------|
Thomas,
What is the plan for these sites? Are these recapture sites, or fixed
interrogation sites? Is this a BPA funded project?
--Carter
-------- Original Message --------
Subject: Re: site codes
Date: Tue, 16 Nov 2004 12:48:52 -0800
From: Kyle Martens <kyle_martens@usgs.gov>
To: Dave Marvin <Dave.Marvin@ptagis.org>
CC: Thomas_Hoffman@r1.fws.gov, Carter Stein <carters@ptagis.org>, Ryan Day
<rday@psmfc.org>
Dave:
I'm sorry It's been awhile, but I just got back from vacation.
This project will be looking at both anadromous fish and resident fish in
Libby, Beaver, and Gold Creeks as water diversion dams are being
reconstructed to allow better fish passage. We have been tagging bull
trout, Chinook, rainbow trout/steelhead, brook trout, and cutthroat trout.
We have one multiplexing FS-1001 reader with six antennas that Earl
Prentice installed for us that is currently downloading to a Palm pilot and
creates an int. file. The other five sites we are using Biomark's
FS2001F-ISO (cheeseblock) readers with their custom 1' x 3 ' antennas. We
are currently downloading these with your minimon program. The six antenna
system is similar to the Rattlesnake Creek site except for we are using
batteries and downloading to the palm. The Biomark units are the same as
Ian Jezorek's Hemlock lake site exce! pt we are only using one antenna
instead of two. I would really appreciate any help you have in naming
these sites.
The new sites are:
Beaver Creek:
Upper PIT tag System (six antenna system downloading to a palm)
rkm: 843.057.003
Lower unit (Biomark unit using minimon)
rkm: 843.057.001
Libby Creek:
Upper unit (Biomark unit using minimon)
rkm: 843.042.003
Lower unit (Biomark unit using minimon)
rkm: 843.042.000
Gold Creek:
Gold Creek (Biomark unit using minimon)
rkm: 843.035.009
Foggy Dew Creek (Tributary of Gold Creek) (Biomark unit using
minimon)
rkm: 843.035.009.001
South Fork Gold Creek (Tributary of Gold Creek) (Biomark unit
using minimon)
rkm: 843.035.002.002
Thanks
Kyle Martens
(509) 538-2299 ext. 238
Dave Marvin
<Dave.Marvin@ptagis.o To: Kyle Martens
rg> <kyle_martens@usgs.gov>
cc: Thomas_Hoffman@r1.fws.gov,
Carter Stein <carters@ptagis.org>, Ryan Day
11/05/2004 05:43 PM <rday@psmfc.org>
Subject: Re: site codes
Kyle:
Please accept my apologies for assuming you were requesting new site codes
for in-stream traps. I saw your references to in-stream detectors, but
thought, since you were requesting rkm codes rather than interrogation site
codes, that you were intending to provide tag release/recapture/recovery
data rather than interrogation data. Allow me to explain the difference.
The history of a PIT-tagged host fish is modeled in up to four different
event classes in the PTAGIS database. These events are generally defined
and described in the Overview section of the 2004 PIT Tag Specification
Document. Inserting or injecting a tag into a host fish and then releasing
that fish is reported in the Tag/Release event. A tagged fish can be
subsequently recaptured and re-released; this activity is reported as a
Recapture event. A tag may be recovered from a deceased or moribund host,
or a bare tag may be recovered without its host; in the PTAGIS model, this
is the termination of the tag's life history, and is reported as a
Mortality event. Tag/release, recapture, and recovery/mortality events are
all reported to PTAGIS using the Tag File structure created w! ith the P3
program. The Tag File header refers to both Tag Site and Release Site
(these values are mapped, by event context, to analogous fields associated
with individual tagging, recapture, and mortality events); these header
values are drawn from the domain of Tag and Release Site Codes in the
PTAGIS Codes Dictionary.
The fourth event class in the PTAGIS tag history model is the "passive
detection" or "interrogation" event. Interrogation events occur when fish
swim through or past a fixed antenna deployed within a fishway or, more
recently, a waterway. A timestamp is automatically associated with this
event. An interrogation record also includes an antenna (coil) ID coil,
and possibly a separate transceiver ID code. Interrogation sites are not
explicitly referenced to a geographic location or waterway, and their site
codes are not part of the domain of the Tag and Release Sites, but are
included in a separate Interrogation Site Codes domain. Interrogation data
are generally reported to PTAGIS in data files created using the MiniMon
program. The three-character int! errogation site code is incorporated
directly into each data file. PTAGIS does not accept interrogation data
from sites not defined in this domain, and rejects data records from coils
at those sites that have not previously been identified and configured in a
suite of internal PTAGIS database tables.
Historically, interrogation events were associated with the passive,
unattended, detection of PIT-tagged fish, while recapture records provided
a method to insert a morphological and physiological observation into the
life history of a previously-tagged fish, along with the date and location
of that recapture. In the last few years, especially, this distinction has
blurred, and we now regularly receive Tag Data files containing recapture
records that simply document the detection of one or more tags at a given
location on a specified date. In these cases, the researchers prefer not
to establish, maintain, and audit interrogation site configurations within
the PTAGIS database. The data are generally collected using FS-1001
transceivers and the MiniMon software; the interrogation data files are
then transformed and the data are written (or appended) to recapture
records in a P3 Tag File. (Or, the data are date-stamped and stored to the
FS-2001F reader, ! and the data are downloaded directly into a P3 Tag
File.)
This is the approach I recommend for your project, especially if your
detection data are documenting the migration of anadromous salmonids into
or out of the Methow River watershed. You can use the MiniMon software (or
similar application) to time-stamp your detection events, and monitor the
equipment operations, if you are using FS-1001 transceivers or their
equivalents, but the data will be reported to PTAGIS in P3 files.
Regardless of how the interrogation data are initially collected, or how
they are captured into a P3 Tag File, the individual recapture dates can be
obtained, reformatted, and documented programmatically with a minimum of
effort.
If the purpose of your study is to track the movement of resident fish and
record multiple detections of those fish over an extended period of time,
and you wish to share that information with PTAGIS community within the
Columbia Basin, then you will need to report your data in the native
MiniMon files. Please contact me if this is the case, so we can discuss
the possible interrogation site code(s) that would be appropriate for your
application. It will be that code (or those codes) that you then present
to Tom for his approval and submittal to PTAGIS.
Again, I apologize for any confusion my previous email may have generated.
I hope this clarifies the types and attributes of the various PTAGIS event
classes, and our expectations regarding the format and content of the data
files associated with those events. Please don't hesitate to write or call
(503.595.3100) if you have any further questions.
Best regards,
Dave Marvin
Kyle Martens wrote:
Hi everyone,
These site are not traps, but instream PIT-tag antennas. I expect the
project to go on in the foreseeable future and to maintain the readers as
long as funding allows. I think I need to have a point site to send in
time-stamped files. South Fork of Gold Creek enters Gold Creek at 2 rkms
and my PIT tag reader is placed about 2 rkms up from the mouth. So I think
I have the rkms right. I hope this clears everything up.
Kyle Martens
Thomas_Hoffman@r
1.fws.gov To: Dave Marvin <Dave.Marvin@ptagis.org>
cc: Carter Stein <carters@ptagis.org>,
11/03/2004 01:26 Kyle Martens <kyle_martens@usgs.gov>, Ryan Day
PM <rday@psmfc.org>
Subject: Re: site codes
Hi Dave!
The naming conventions are my mistake...sorry about that! The definitions
you provided look fine to me. Kyle will have to get back to you about the
problems with the rkms. Let me know if I need to do anything else.
Tom
|---------+---------------------------->
| | Dave Marvin |
| | <Dave.Marvin@ptag|
| | is.org> |
| | |
| | 11/03/2004 11:39 |
| | AM |
| | |
|---------+---------------------------->
>>------------------------------------------------------------------------------------------------------------------------------|
|
|
| To: Thomas_Hoffman@fws.gov, Kyle Martens
<kyle_martens@usgs.gov> |
| cc: Carter Stein <carters@ptagis.org>, Ryan Day
<rday@psmfc.org> |
| Subject: Re: site codes
|
>>------------------------------------------------------------------------------------------------------------------------------|
Hi Tom and Kyle:
Given that the PTAGIS database currently contains almost 20 years of
mark/recapture/interrogation data, and that we expect our geographic site
definitions to remain constant and consistent for all data records, in all
years, we therefore consider any instream structure (especially fish traps)
not created by Mother Nature or the Corps of Engineers to be "ephemeral",
and not to be referenced as a point site. Unless your trap (or weir)
locations are "permanent" monitoring locations (as opposed to "research"
locations with a finite lifetime) I recommend that you submit
Tag/Recapture/Mortality from referencing the existing stream name code
(GOLD2C, LIBBYC, BEAV2C, etc.) and using the River KM values you've noted
below to distinguish between your trap sites. You can further identify
your segregated data sets by using unique site labels in the "Transect"
field of the Tag File header, and by separate references in the "Session
Message" field of the Tag File.
If in fact your sites are "permanent" installations that will be operated
annually for the foreseeable future at these given locations, then, at
Tom's discretion and direction, we will add point release site definitions
to the PTAGIS data dictionary. The site codes you have proposed are not
acceptable, however, as they contravene the site naming conventions
detailed in Section IV.J.1 of the 2004 PIT Tag Specification Document by
utilizing stream or river names as fish trap designators. Your valid site
codes will end in "TRP" or "T".
Regardless of how you reference these sites, we will apparently need to
added definitions for South Fork Gold Creek (GOLDSF) and Foggy Dew Creek
(FOGGDC) to the PTAGIS RKM Site Code Dictionary. Tom, please let me know
if these proposed site codes are acceptable. Please verify the RKM of
"843.035.009.001" as the mouth of Foggy Dew Creek. The RKM of
"843.035.002.002" for the mouth of South Fork Gold Creek is incorrect;
please let me know if you meant "843.035.009.002". And note that the
4th-order HUC for all of the Methow subbasin is "17020008"; the "17020002"
value you have associated with all of your definitions in the Gold Creek
drainage is incorrect.
As always, you can contact me or any of the PTAGIS staff with questions
regarding this or any other PTAGIS issue.
Best Regards,
Dave Marvin
Thomas_Hoffman@r1.fws.gov wrote:
Hey Dave!
Here is a request from Kyle. Hold off on the GOLD3C for now. I
asked him
if it is a modification or a new site. If there are any problems
with the
rest, please let me know. I didn't know if the sites are named
upstream to
down or vice versa. So, I went with down to up (for no apparent
reason).
I'll get back to you on the GOLD3C site. Thanks!
Tom
----- Forwarded by Thomas Hoffman/CRFO/R1/FWS/DOI on 11/03/2004 09:29
AM
-----
|---------+---------------------------->
| | "Kyle Martens" |
| | <kyle_martens@usg|
| | s.gov> |
| | |
| | 10/29/2004 01:50 |
| | PM |
| | |
|---------+---------------------------->
>>------------------------------------------------------------------------------------------------------------------------------|
|
|
| To: Thomas_Hoffman@fws.gov
|
| cc:
|
| Subject: Re: site codes
|
>>------------------------------------------------------------------------------------------------------------------------------|
Hi Tom,
I have recently installed six PIT-tag interrogation sites in the
Lower
Methow River subwatershed. I would like to register these new sites
in
Ptagis as point sites. Let me know if you have any other questions.
The new sites are:
Beaver Creek: BEAV4C
Upper PIT tag System
HUC: 17020008
rkm: 843.057.003
Lower unit BEAV3C
HUC:17020008
rkm: 843.057.001
Libby Creek: LIBB3C
Upper unit
HUC: 17020008
rkm: 843.042.003
Lower unit LIBB2C
HUC: 17020008
rkm: 843.042.000
Gold Creek: GOLD3C
Gold Creek
HUC: 17020002
rkm: 843.035.009
Foggy Dew Creek (Tributary of Gold Creek) FOGGYC
HUC: 17020002
rkm: 843.035.009.001
South Fork Gold Creek (Tributary of Gold Creek) GOLDSC
HUC: 17020002
rkm: 843.035.002.002
Thanks for your help.
Kyle martens
Thomas_Hoffman@r1.fws.gov
To:
dave.marvin@ptagis.org
09/27/2004 04:30 PM cc:
kyle_martens@usgs.gov
Subject: site
codes
Het Dave!
Here are some site codes requested by Kyle Martens. The question I
have is
that there already is a Gold Creek (GOLDC). If my choice of another
site
code for a different Gold Creek isn't correct, please let me know and
I
will change it.
Here is the info that Kyle sent:
Beaver Creek: BEAVEC
rkm: 843.057
HUC: 17020008
Libby Creek: LIBBYC
rkm: 843.042
HUC: 17020008
Gold Creek: GOLDCR
rkm: 843.035
HUC: 17020008
These are all tributaries to the Methow River. Again, if there is
any
missing data, please let me know and I will get you whatever you
need.
Thanks!
Tom
(See attached file: carters.vcf)
carters.vcf
Content-Type:
application/octet-stream
Content-Encoding:
base64
