-
https://cpw.cvlcollections.org/files/original/ecc2885744cad70c6559a3d09454f1eb.pdf
c986c5ee2617ac2f9511a94ddd67c8a3
PDF Text
Text
WaTSS User Manual
Water Temperature Summary So!ware
Version 3.0
January 2015
WaTSS Version 3!
1
�Overview!
3
Insta"ation!
4
Data preparation!
4
Running WaTSS!
5
Analysis!
5
Troubleshooting!
15
Literature cited!
18
WaTSS Version 3!
2
�User manual for WaTSS 3.0 (Water Temperature Summary Software)
Manual Version 3.0.1
January 30, 2015
Kevin B. Rogers, Aquatic Research, Colorado Parks and Wildlife, PO Box 775777, Steamboat
Springs, CO 80477, kevin.rogers@state.co.us
____________________________________________________________________________
Overview
Water temperature is perhaps the single most important environmental parameter for fish (Magnusen et al. 1979). As ectothermic organisms, ambient temperature drives survival (Dickerson
and Vinyard 1999, Bear et al. 2007, Underwood et al. 2012, Brinkman et al. 2013), behavior
(Casselman 1978, Mesing and Wicker 1986, Cook and Bergersen 1988, Rogers 1998), growth
(Selong et al. 2001, Meeuwig et al. 2004, Bear et al. 2007, Ziegler et al. 2013, Brinkman et al.
2013), and other physiological processes (Brett 1979), as well as defining the range a fish can
occupy (Dunham et al. 2003, de la Hoz Franco and Budy 2005. Recent concerns over changing
climactic conditions on fish (Ficke et al. 2007, Rahel and Olden 2007, Wenger et al. 2011, Peterson et al. 2013, Roberts et al. 2013) and its implications for persistence of threatened or endangered species has led to a proliferation of water temperature monitoring efforts (Isaak et al. 2012,
Ziegler et al. 2013b). The combination of heightened interest coupled with the availability of
relatively inexpensive and durable temperature loggers has precipitated an explosion in the use
of these devices that has spread to applied uses in fish management as well, beyond just monitoring water quality. From detecting timing of fry emergence that inform water management practices to predicting optimum timing to implement successful wild spawn operations, use of these
devices is becoming routine. While inexpensive remote temperature loggers have been available
for several decades, interpreting the resulting data has been hampered by the lack of user friendly
software. The hope is that this program can serve as a developing platform to make common
analyses of temperature data readily available to managers and researchers alike.
WaTSS Version 3!
3
�Installation
To install off the application CD to a PC running Windows 7 (other operating systems will be
similar), open the WaTSS Installer folder and double click on the setup.exe file (if extensions are
not displayed on your computer, select the larger of the two setup files). Your computer will
likely ask if it is OK to allow the program from an unknown publisher to make changes to your
computer – select yes (and enter your user name and password if it asks). The default configuration will install the program in your program folder (available from you program menu), as well
as place a shortcut on your desktop. If you are OK with that, click “Next”, then click the “Accept” radio button on the License Agreement window, then “Next” a couple of times. The program is unfortunately quite large (154 mB) so it will take a little time to install. When the installation is complete, click “Finish”. You may need to restart your computer to get the WaTSS 3.0
program to show up in your Programs menu.
To download WaTSS off the web, visit
http://cpw.state.co.us/learn/Pages/ResearchAquaticSoftware.aspx click on the software tab in the
left dropdown menu. Scroll down to the WaTSS description and click on the appropriate link.
Data preparation
This program assumes that the user has acquired thermograph data using Onset Computer Corporation’s HOBO software (Bourne, Massachusetts). Images presented in this manual come
from Version 2.7.3 of HOBOware
With the relevant data file displayed in
HOBOware, either select “Export Points
as Excel Text” in the File menu or click
on the “Export Table Data” button
In the “Export Options” window that appears, make sure the “Export to a single file” radio button is selected, the click “Export”. This should create a .csv file of the same name
WaTSS Version 3!
4
�Running WaTSS
WaTSS can be invoked by selecting the program from the START menu (PC), or double clicking
on the application (MacOSX). Once open, click the start arrow on the top left of the panel if the
program is not running already.
You will be prompted to read in a
data file. Make sure to select one
Start arrow
that has been exported from HOBOware and has the .csv extension
as described above. Make sure to
Source file
temperature units
select whether the data are in centigrade or Fahrenheit before proceeding with any analysis
Once analysis of a given file is
complete, press the red
“STOP” button. If interpreting another temperature file is desired, simply click on the start arrow again.
Analysis
Raw temperature data is presented in the upper plot (blue line).
WaTSS Version 3!
5
�The y-axis scale can be modified by clicking on the upper or
lower value and entering in a new number. Alternatively, one
can use the following tools to explore the plot in greater detail:
Clicking on the zoom tool located on the bottom
left corner of the plot allows zooming in on a portion of the trace.
Clicking this button will return to the red cursor,
so the user can directing the cursor toward regions of interest. The date and temperature located at the crosshairs of the cursor are displayed in the legend box which
makes it easy to determine timing of peak temperatures
The hand tool allows shifting the trace around if the point of interest is not displayed on the screen while zoomed in.
Individual points can be viewed incrementally by clicking the left or right diamonds for fine-scale adjustments to cursor position.
Temperature and corresponding dates associated with the cursor crosshairs can be read off the cursor legend.
Clicking the "RESET" button will return both plots to their original formatting.
Filtered temperature data is shown in the lower (green) plot
WaTSS Version 3!
6
�If more complex analyses are required, the data can be filtered with these two dropdown menus. By default, the raw
temperature data is passed from the upper to lower plot for
subsequent analysis. It is possible to view modified versions of that data using the filters as follows:
This passes the raw temperature from the top plot (blue) to the bottom graph
(green) for subsequent analysis
This pulls the daily
maxima from the raw
data and plots that for
subsequent analysis. Ignore the time
stamp on “Daily Max” as this just registers noon for the given day.
Regardless of how many points are recorded over a 24-h period, this filter
takes all temperature registered on a given calendar day (0000-2400) and
WaTSS Version 3!
7
�calculates a mean value. Ignore the time
stamp on the “Daily Average” as this just
registers noon for the given day.
This filter averages all points registered in the same 7-day period starting
with the first recording and assigning the average temperature to noon on
the fourth day in the
seven day window, then plotting the value
for consecutive weeks.
All temperatures recorded in a given month are averaged here.
Perhaps the most useful filter, this allows the user to calculate a running
average off either “Raw Data” or “Daily Max”.
If “Raw Data” is used, to get a running daily
(24-h) average from data collected hourly,
one should set the “Window” to 24 if data
was collected hourly.
Since a single “Daily Max” value represents a
daily temperature, to get a weekly running average one should enter "7" in the “Window”
box.
WaTSS Version 3!
8
�Summary statistics are then presented in the data box and results can
be toggled between English and metric units by clicking on their respective tabs. The results displayed are generated from temperature data contained between
the left (yellow) and right (orange) sliders, and
are calculated as follows:
AveTemp – This represents the average temperature between the slider bars based on the raw
data - even if the Daily Max is selected on the filter dropdown. If AveTemp from Daily
Max data is needed, export the Daily Max data to an output file, then reimport as raw data
and reanalyze.
DailyMax – This is no longer the absolute maximum temperature within the slider bars, but
rather Colorado’s state mandated maximum temperature which is the highest 2 hour running average (Todd et al. 2008). If the absolute peak reading is desired, just use the red
slider on the blue plot to identify the time and date of the highest temperature recorded.
DegDays - Whether degree days are displayed in °C or °F, both values are generated by calculating the average daily temperature, determining the number of degrees above freezing,
then summing across days incorporated between the slider bars
MWAT - This is the warmest 7-day mean of the average daily temperature (the maximum annual
value of the rolling average of mean daily water temperatures over a 7-day period; Ziegler et al. 2013b). Colorado's water quality criteria for stream temperature classify
streams where cutthroat trout occur as Cold Tier 1 (CWQCC 2012). The criteria for Cold
Tier 1 water temperature include both acute (DailyMax) and chronic (MWAT) threshold
values. The acute and chronic values for the Cold Tier 1 water temperature criteria vary
seasonally. In winter (October–May), the DailyMax threshold is 13 °C, and the
WaTSS Version 3!
9
�MWAT=9 °C. In Summer (June–September), the threshold for DailyMax is 21.7 °C and
an MWAT=17 °C.
MWMT – This is the warmest 7-day mean of the maximum daily stream temperature (Roberts et
al. 2013), and is used to determine if streams are cool enough for fish survival. In cutthroat trout, Roberts et al. (2013) used an MWMT=26 °C as the temperature beyond
which Colorado River Cutthroat Trout could not survive.
M30AT – The maximum 30 day average temperature is the most relevant metric for growth and
recruitment in fish (Roberts et al. 2013), and describes the average temperature of the
warmest month. Growth in cutthroat trout is maximized between 9-18 °C, peaking
around 15 °C (Bear et al. 2007, Brandt 2009, Ziegler et al. 2013) and 13.8 °C in mountain
whitefish (Brinkman et al. 2013). This metric is similar to the mean July temperature
metric used by Harig and Fausch (2002) to evaluate translocation success in cutthroat
trout. This study, and those by Coleman and Fausch (2007a, 2007b) suggest that an
M30AT<8 °C will result in no recruitment, and that M30AT>9 °C is required for robust
recruitment to occur.
WaTSS Version 3!
10
�The same calculations are possible using only the maximum daily temperatures if desired by selecting "Daily Max" on the left hand filter (Filter). This represents an alternative approach to
calculating metrics like the maximum weekly maximum temperature (MWMT) that has the
benefit of depicting when that MWMT occurred.
The MWMT can be derived by setting the left filter to "Daily Max",
then selecting "Running Average" on the right filter followed by "7"
days. The orange slider was moved to the peak (77.4 °F), allowing the
date (June 24th) and temperature to be displayed in the cursor legend
near the bottom right
WaTSS Version 3!
11
�An approximation of the average weekly average temperature (AWAT) can be calculated similarly. Inspecting the input file shows that temperature data was collected hourly. A running average with a window of 168 points (7 days * 24 hrs) shows that the weekly estimates reached
their 68.1 °F peak the week surrounding July 2nd.
Technically, the AWAT should be calculated as the 7 day running average on average daily temperatures. That can be achieved by exporting the average daily temperatures
, then reading that back in and calculating the 7 day running
average.
WaTSS Version 3!
12
�Exporting data
By pressing the the “Export” button, WaTSS will export an ASCII text file in the format shown
below that can be read back into WaTSS. Output data is restricted to what lies between the slider
bars. Data is filtered as per the “Filter” and “Averaging” dropdown menus, and reflects what is
shown in the lower plot. Filtered temperatures are exported along with a median date and time.
If you are trying to import temperature data from other sources, it must adhere to the above data
structure (similar to that exported by the HOBO software). Specifically, the file must be in ASCII format (export as “plain text” from any text editing software), and must have two header
lines that are ignored by WaTSS. The file should be in comma delimited format with the first
column being the reading number, the second being the date and time stamp as shown below
which must include seconds with a single space before and after the time stamp, followed by the
temperature in either Celsius or Fahrenheit.
WaTSS Version 3!
13
�Desiccation
During dry years, it is possible that a logger will become exposed and begin logging air temperatures rather than stream temperatures. This obviously
will compromise the integrity of the data and should be
screened for. Although often more subtle than the example shown here, zooming in can reveal a more jagged
profile uncharacteristic of stream temperatures that tend to
be more buffered.
Sedimentation
In an effort to keep a logger from recording air temperatures, we may place them in deep depositional areas where they can become buried.
Although this might not change mean temperature values much, it can dramatically alter the
diel temperature fluctuations experienced by the
logger and therefore values like the Daily Max
or MWMT. It is important to select sites where
the logger will be scoured clean rather than buried.
WaTSS Version 3!
14
�Troubleshooting
✓ You are running the application on a Windows 7 platform and the fonts on the plot legends are
so large they no longer fit in the defined space.
➡ Check your Display setting in your computer’s Control Panel. For some reason, Microsoft
decided inflating text by 125% as default would be a good thing. Setting this back to 100%
should solve the problem. Let me know if it too small to read on your screen and I will try
to find a better fix.
✓ The file you select gives you an error message and
fails to load.
➡ The format of your input file is different than
what is produced by HOBOware, and cannot be
read by the program. Open the file in a word
processor like Microsoft Word and select “show
non-printing characters”. Bring up another file
that you know works fine (or one of the demo files
installed with your program in your Programs
WaTSS Version 3!
15
�Files (x86) folder) and compare the two for differences. Files can be modified easily in
Excel and saved in the .csv format for import into WaTSS.
✓ Values in the data box are not changing when the sliders are moved?
➡ Check to confirm that the program is running (that the run arrow in the top left of the application (Page 5) is black.
✓ Why does filtering not affect the calculated values of MWAT, MWMT, or A30AT?
➡ These are specifically defined, and would be called something else if they were calculated
with Daily Max data.
➡ If for some reason you need to calculate any of the metrics in the data box with filtered
data, create a new input file on filtered data by clicking the Export button, the reanalyze
that file.
✓ Why is the DailyMax value is a little less that the peak of the diel cycle registered on the plots
or the highest value for a given day in the Input File pane?
➡ This is by design as the DailyMax reflects Colorado’s state water quality standard which is
the highest 2-hr average (Todd et al. 2008).
➡ If the absolute peak temperature is required, simply zoom in to the area of interest on the
blue plot and move the red cross-hairs to the maximum recorded temperature and read that
temperature and date from the plot legend.
✓ Zoomed out, the blue plot looks normal, but zooming in reveals an unexpected thermal profile.
➡ The plot on the left is the result of importing a file that logged temperature using a 24-hr
clock (Military) while by default, the program is anticipating a 12-hr clock and an AM or
PM. The plot on the right is the result of importing a 12-hr clock data (HOBOware default)
when WaTSS is expecting military format.
WaTSS Version 3!
16
�➡ Check the raw input data on the right of the screen or in a word processor and see if the
exported file uses a 24 hr clock or AM/PM. Make sure your Time Units toggle is in the appropriate position. The toggle has to be selected prior to running the program for it to work.
➡ If you are still having trouble, you can go back in to HOBOware and export a new .csv file after changing the export
preferences to output in the AM/PM format.
➡ Another workaround provided by Jim White if you don’t have
HOBOware on your computer: open the .csv file in Excel and
highlight the date:time field. Change the field format to
Date:Time and select the AM/PM format and save (still in the
.csv format).
WaTSS Version 3!
17
�Literature cited
Bear, E. A., T. E. McMahon, and A. V. Zale. 2007. Comparative thermal requirements of
Westslope cutthroat trout and rainbow trout: implications for species interactions and development of thermal protection standards. Transactions of the American Fisheries Society 136:1113-1121.
Brandt, M. M. 2009. Optimal starter diets and culture conditions for Colorado River Cutthroat
Trout (Oncorhynchus clarkii pleuriticus). Master's thesis. Colorado State University, Fort
Collins.
Brett, J. R. 1979. Ten environmental factors and growth. Fish Physiology 8:599-675.
Brinkman, S. F., H. J. Crockett, and K. B. Rogers. 2013. Upper thermal tolerance of mountain
whitefish (Prosopium williamsoni) eggs and fry. Transactions of the American Fisheries
Society 142:824-831.
Casselman, J. M. 1978. Effects of environmental factors on growth, survival, activity, and exploitation of northern pike. Pages 114-128 in R. D. Kendall, editor. Selected coolwater
fishes of North America. American Fisheries Society, Special Publication 11, Washington
D.C.
Coleman, M. A., and K. D. Fausch. 2007a. Cold summer temperature limits recruitment of Age0 cutthroat trout in high-elevation Colorado streams. Transactions of the American Fisheries Society 136:1231-1244.
Coleman, M. A., and K. D. Fausch. 2007b. Cold summer temperature regimes cause a recruitment bottleneck in Age-0 Colorado River cutthroat trout reared in laboratory streams.
Transactions of the American Fisheries Society 136:639-654.
Cook, M. F., and E. P. Bergersen. 1988. Movements, habitat selection, and activity periods of
northern pike in Eleven Mile Reservoir, Colorado. Transactions of the American Fisheries
Society 117:495-502.
CWQCC (Colorado Water Quality Control Commission). 2012. Regulation 31—The basic
standards and methodologies for surface water: Denver, Colo., Colorado Department of
Public Health and the Environment.
de la Hoz Franco, E. A., and P. Budy. 2005. Effects of biotic and abiotic factors on the distribution of trout and salmon along a longitudinal stream gradient. Environmental Biology of
Fishes 72:379–391.
WaTSS Version 3!
18
�Dickerson, B. R., and G. L. Vinyard. 1999. Effects of high chronic temperatures and diel temperature cycles on the survival and growth of Lahontan Cutthroat Trout. Transactions of
the American Fisheries Society 128: 516–521.
Dunham, J., R. Schroeter, and B. Rieman. 2003. Influence of maximum water temperature on
occurrence of Lahontan Cutthroat Trout within streams. North American Journal of Fisheries Management 23:1042–1049.
Ficke, A. D., C. A. Myrick, and L. J. Hansen. 2007. Potential impacts of global climate change
on freshwater fisheries. Reviews in Fish Biology and Fisheries 17: 581–613.
Harig, A. L., and K. D. Fausch. 2002. Minimum habitat requirements for establishing translocated cutthroat trout populations. Ecological Applications 12:535-551.
Isaak, D. J., C. C. Muhlfeld, A. S. Todd, R. Al-Chokhachy, J. Roberts, J. L. Kershner, K. D.
Fausch, S. W. Hostetler. 2012. The past as prelude to the future for understanding 21stcentury climate effects on Rocky Mountain trout.
Magnuson, J. J., L. B. Crowder, and P. A. Medvick. 1979. Temperature as an ecological resource. American Zoologist 19:331-343.
Meeuwig, M. H., J. B. Dunham, J. P. Hayes, and G. L. Vinyard. 2004. Ef-fects of constant and
cyclical thermal regimes on growth and feeding of juvenile Cutthroat Trout of variable
sizes. Ecology of Freshwater Fish 13: 208–216.
Mesing, C. L., and A. M. Wicker. 1986. Home range, spawning migrations, and homing of
radio-tagged Florida largemouth bass in two central Florida lakes. Transactions of the
American Fisheries Society 115:286-295.
Peterson, D. P., S. J. Wenger , B. E. Rieman and D. J. Isaak. 2013. Linking climate change and
fish conservation efforts using spatially explicit decision support tools. Fisheries
38:112-127.
Rahel, F. J., and J. D. Olden. 2007. Assessing the effects of climate change on aquatic invasive
species. Conservation Biology 22:521-533.
Roberts, J. J., K. D. Fausch, D. P. Peterson, and M. B. Hooten. 2013. Fragmentation and thermal risks from climate change interact to affect persistence of native trout in the Colorado
River basin. Global Change Biology 19:1383-1398.
Rogers, K. B. 1998. Habitat use by largemouth bass and northern pike on the Rocky Mountain
Arsenal, Colorado. Doctoral dissertation. Colorado State University, Fort Collins.
WaTSS Version 3!
19
�Rogers, K. B., and G. C. White. 2007. Analysis of movement and habitat use from telemetry
data. M. Brown and C. Guy, editors. Analysis and interpretation of freshwater fisheries
data. American Fisheries Society, Bethesda, Maryland. Available online at
http://cpw.state.co.us/learn/Pages/ResearchAquaticSoftware.aspx
Selong, J. H., T. E. McMahon, A. V. Zale, and F. T. Barrows. 2001. Effect of temperature on
growth and survival of Bull Trout, with application of an improved method for determining thermal tolerance in fishes. Transactions of the American Fisheries Society
130:1026–1037.
Todd, A.S., M. A. Coleman, A. M. Konowal, M. K. May, M.K., S. Johnson, N. K. M. Vieira, and
J. F. Saunders. 2008. Development of new water temperature criteria to protect Colorado's fisheries. Fisheries 33:433–443.
Underwood, Z. E., C. A. Myrick, and K. B. Rogers. 2012. Effect of acclimation temperature
and the upper thermal tolerance of Colorado River cutthroat trout Oncorhynchus clarkii
pleuriticus. Journal of Fish Biology 80:2420-2433.
Wenger, S. J., D. J. Isaak, C. H. Luce, H. M. Neville, K. D. Fausch, J. B. Dunham, D. C. Dauwalter, M. K. Young, M. M. Elsner, B. E. Rieman, A. F. Hamlet, and J. E. Williams.
2011. Flow regime, temperature, and biotic interactions drive differential declines of
trout species under climate change. Proceedings of the National Academy of Sciences
108:14175-14180.
Zeigler, M. P., S. F. Brinkman, C. A. Caldwell, A. S. Todd, M. S. Recsetar, S. A. Bonar. 2013.
Upper thermal tolerances of Rio Grande cutthroat trout under constant and fluctuating
temperatures. Transactions of the American Fisheries Society 142:1395-1405.
Zeigler, M.P., A. S. Todd, and C. A. Caldwell. 2013b. Water temperature and baseflow discharge of streams throughout the range of Rio Grande cutthroat trout in Colorado and
New Mexico—2010 and 2011: U.S. Geological Survey Open-File Report 2013–1051, 18
p., http://pubs.usgs.gov/of/2013/1051/.
WaTSS Version 3!
20
�
Dublin Core
The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/.
Title
A name given to the resource
Reports
Text
A resource consisting primarily of words for reading. Examples include books, letters, dissertations, poems, newspapers, articles, archives of mailing lists. Note that facsimiles or images of texts are still of the genre Text.
Dublin Core
The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/.
Title
A name given to the resource
WaTSS user manual: water temperature summary software
Description
An account of the resource
Water temperature is perhaps the single most important environmental parameter for fish (Magnusen et al. 1979). As ectothermic organisms, ambient temperature drives survival (Dickerson and Vinyard 1999, Bear et al. 2007, Underwood et al. 2012, Brinkman et al. 2013), behavior<br />(Casselman 1978, Mesing and Wicker 1986, Cook and Bergersen 1988, Rogers 1998), growth (Selong et al. 2001, Meeuwig et al. 2004, Bear et al. 2007, Ziegler et al. 2013, Brinkman et al. 2013), and other physiological processes (Brett 1979), as well as defining the range a fish can occupy (Dunham et al. 2003, de la Hoz Franco and Budy 2005. Recent concerns over changing climactic conditions on fish (Ficke et al. 2007, Rahel and Olden 2007, Wenger et al. 2011, Peterson et al. 2013, Roberts et al. 2013) and its implications for persistence of threatened or endangered species has led to a proliferation of water temperature monitoring efforts (Isaak et al. 2012, Ziegler et al. 2013b). The combination of heightened interest coupled with the availability of relatively inexpensive and durable temperature loggers has precipitated an explosion in the use of these devices that has spread to applied uses in fish management as well, beyond just monitoring water quality. From detecting timing of fry emergence that inform water management practices to predicting optimum timing to implement successful wild spawn operations, use of these devices is becoming routine. While inexpensive remote temperature loggers have been available for several decades, interpreting the resulting data has been hampered by the lack of user friendly software. The hope is that this program can serve as a developing platform to make common analyses of temperature data readily available to managers and researchers alike.
Creator
An entity primarily responsible for making the resource
Rogers, Kevin B.
Subject
The topic of the resource
Water temperature
WaTSS 3.0 (water temperature summary software)
Extent
The size or duration of the resource.
20 pages
Date Created
Date of creation of the resource.
2015-01-30
Rights
Information about rights held in and over the resource
<a href="http://rightsstatements.org/vocab/InC-NC/1.0/" target="_blank" rel="noreferrer noopener">In Copyright - Non-Commercial Use Permitted</a>
Type
The nature or genre of the resource
Text
Format
The file format, physical medium, or dimensions of the resource
application/pdf
Language
A language of the resource
English
Bibliographic Citation
A bibliographic reference for the resource. Recommended practice is to include sufficient bibliographic detail to identify the resource as unambiguously as possible.
<a href="https://cpw.state.co.us/learn/Pages/ResearchAquaticSoftware.aspx" target="_blank" rel="noreferrer noopener">https://cpw.state.co.us/learn/Pages/ResearchAquaticSoftware.aspx</a>