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Flathead River Instream Flow Investigation Project

1. 45 where Z number of fish observed D water column depth average water column velocity bo bi 62 equation coefficients and is fitted to the surface using a least squares regression technique All of this is performed in the STATISTICA software environment Example data is provided along with examples of each required step in the process This process follows techniques described by Prewitt 1982 and Bovee 1986 PAIRED DEPTH VELOCITY DATA This procedure assumes the investigator has a complete data set of paired depth velocity observations STATISTICA allows the importation of many common formats e g MS Excel spreadsheet data The format of the new data set should be thoroughly checked after it is brought into STATISTICA Assure that the observations are aligned properly in the variables and cases columns and rows and that the correct decimal places are displayed Be careful to place labels in the variable headers since STATISTICA assigns a numeric value to text data that appears anywhere in a spreadsheet See Edit Variables Current Specs to assign variable field names decimal places etc The data must be free of missing data points gaps or unpaired depth velocity observations The data should be meticulously examined and quality controlled before starting any statistical analysis The investigator should visually inspect a simple linear plot of each variable determining w
2. 9 Figure 9 Frequency Distribution of the Residual Values eee 10 Figure 10 Normal Probability of the Residual Values eee 10 Figure 11 Plot of Observed versus Predicted Nalues AA 11 Bonneville Power Administration Technical Report May 24 2001 Miller Ecological Consultants Inc Page 1 INTRODUCTION This is a procedural manual that outlines the calculation of bivariate habitat suitability functions in the STATISTICA software environment These procedures produce a 3 dimensional frequency distribution of habitat utilization 3D Bivariate Histogram The bivariate histogram frequency data is reduced to an exponential polynomial function describing depth and velocity in habitat selection by fish This information is then used in assigning habitat suitability for use in modeling instream habitat The steps outlined here start with raw data describing habitat utilization by fish paired depth and velocity observations This raw data is used to produce a 3D Bivariate Histogram showing patterns of habitat utilization over the range of values collected for total water column depth and average water column velocity The three dimensional surface is then used in a nonlinear regression model An exponential polynomial equation is fit to the three dimensional surface by regressing the depth and velocity independent variables onto the frequency histogram surface dependent variable This equation is of the form Z exp biD
3. Pre Dam Post Dam Flathead Instream Flow Investigation Project Miller Ecological Consultants Inc Page 48 September 29 2003 Habitat time series Reach 2 Bull trout subadult night 4 500 000 4 000 000 3 500 000 3 000 000 m 2 500 000 T WU uk M n de 2 d i i D H d qt 5 A a 1 d th ft a 7 i E 1 Post Dam 2 000 000 d 1 IM b i WM I r x TE L 1 M E d 1 i LI IRAN um Ai l a T d h ab 1 1 500 000 t E d h i F VW 1 ij ie i f H NICE 98 RU 1 e 1 r MILI a i 1 NI 1 Ar I y 1 000 000 EN ir UI d mi MIL pub d d hi k 500 000 LN 1 if d i d 0 525 903 0535955555 Date Figure 43 Habitat time series Reach 2 Bull trout subadult night Page 49 Flathead Instream Flow Investigation Project September 29 2003 Miller Ecological Consultants Inc Habitat time series Reach 2 Bull trout subadult day 4 500 000 4 000 000 3 500 000 D e m e Se Post Dam 3 000 000 L a T Le 2500 000 zech 1 LJ J
4. j i 400 000 L Wa r 1 H a i i d 300 000 h i 1 LI B I 200 000 H d 1 d 100 000 0 S8 5 SS SS 5 eS Ses a SS Date Figure 33 Habitat time series Reach 1 Bull trout subadult night g g Flathead Instream Flow Investigation Project Page 39 Miller Ecological Consultants Inc September 29 2003 Habitat time series Reach 1 bull trout subadult night 1 800 000 1 600 000 1 400 000 1 200 000 1 000 000 Pre Dam Post Dam 800 000 Habitat area m2 600 000 400 000 200 000 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 Date Figure 34 Habitat time series Reach 1 Bull trout subadult night Flathead Instream Flow Investigation Project Page 40 Miller Ecological Consultants Inc September 29 2003 Habitat time series Reach 1 bull trout adult 3 000 000 2 500 000 2 000 000 1 500 000 Habitat area m2 Pre Dam Post Dam 1 000 000 500 000 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 Date Figure 35 Habitat time series Reach 1 Bull trout adult 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 Flathead Instream Flow Investigation Project Miller Ecological Consultants Inc Page 41 September 29 2003
5. Available Fields Ed Choose the Field to Create a Surface from Z Cancel Velocity Depth Subbtr1 r2w Adbtrl r2wi examplel_ example2_s Click OK 7 The program will request a search distance from each point to calculate a surface using an Inverse Distance Weighting IDW algorithm Typically this distance should be 2 5 to 3 times the average distance between points in the depth and velocity point shapefile created earlier Enter the value and click OK IDW Radial Parameters EN Enter a search distance 8 of map units for calculating the surface D Cancel 8 The program will then start interpolating a continuous surface using the species life stage suitability values from each point in the shapefile A new dialog box will pop up to allow you to modify the output grid cell size that the program will use in creating the surface See below Creating A Surface xi Please enter an Integer Cellsize The default value is 5 The units of measurement are equal to the units used in the shapefile Usually GIS Based Weighted Useable Area Modeling Manual Flathead River Prepared for Montana Fish Wildlife and Parks 10 9 15 03 Copyright MEC SSI 2003 Miller Ecological Consultants Spatial Sciences amp Imaging this will be either feet as in this example or meters Considerations in modifying this value are the units you are working in the density of data points in the shapefile and the complexi
6. Flathead Instream Flow Investigation Project Miller Ecological Consultants Inc Page 52 September 29 2003 Habitat time series Reach 3 Westslope cutthroat trout 6 000 000 5 000 000 Pre Dam Post Dam 4 000 000 3 000 000 zz 2 000 000 1 000 000 01 LOL VOL LOL VOL LOL LOL VOL VOL LOL Date Figure 47 Habitat time series Reach 3 West Slope cutthroat trout Page 53 September 29 2003 Flathead Instream Flow Investigation Project Miller Ecological Consultants Inc Annual habitat time series Reach 3 Bull trout subadult night 1 400 000 1 200 000 1 000 000 N E 800 000 5 600 000 400 000 200 000 0 r 10 DN ON st st 10 DO X e ON OG e 0 si CN e GI c Lo Ge no Ge S HI D oL ul Oo Loc o QN e CN GN ODD OT lt lt Date Figure 48 Annual habitat time series Reach 3 Bull trout subadult night Pre Dam Post Dam Flathead Instream Flow Investigation Project Miller Ecological Consultants Inc Page 54 September 29 2003 Annual habitat time series Reach 3 Bull trout sub
7. SI File Edit View Insert Format Tools Data Window Help Daw Gl 2 6 e Courier 12 B z u ex s fa 24 eil Ye Reply with Changes End Review _ M13 X 2 13 1 VLOOKUP B13 HS16 528 3 B13 VLOOKUP B13 H518 K526 4 G H J K L N Total Habitat per Site Westslope Cutthroat 18 Summer Winter BN HABTS HABTS HABTS Pre Dam 1940 1949 Dam 1993 2002 Pre Dam 1940 19 Sul her Winter Post Dam Pre Dam 201683 207924 192706 207811 1 7309 207606 177217 207474 180624 207310 181391 207313 179642 207683 185534 207774 179151 207615 185289 207446 173719 207446 170926 207433 172184 207474 171754 207669 177432 207361 178322 207191 169176 207000 168440 206827 166414 206795 172000 206522 173995 206504 181176 206677 173028 206854 Summer 233423 233313 233239 233147 233152 233357 233408 233318 233224 233224 233216 233239 233343 233457 233080 232973 232876 232858 232704 232694 232791 232891 Habitat B TERM 0 105 1 127 43 169 90 226 53 246 55 283 17 333 30 424 75 597 65 843 51 VSS Se Se Ba EE SR Wa Rn Figure 7 Example of Vlookup function for time series analysis Calculation of habitat for the site is completed for each life stage The spreadsheet is set up to calculate habitat for each species and life stage of interest The analysis
8. Annual habitat time series Reach 2 West Slope cutthroat trout summer 3 500 000 3 000 000 2 500 000 2 000 000 1 500 000 Habitat Area m2 1 000 000 500 000 0 OQ got cz OT BDA OY Ta COM as ee E S e AN e oe GE oe Date Figure 36 Annual habitat time series Reach 2 West Slope cutthroat trout summer 12 3 12 17 12 31 Pre Dam Post Dam Flathead Instream Flow Investigation Project Miller Ecological Consultants Inc Page 42 September 29 2003 Annual habitat time series Reach 2 West slope cutthroat trout winter 3 500 000 3 000 000 2 500 000 2 000 000 1 500 000 Habitat Area m2 1 000 000 500 000 0 MOM O ABORT x 0 sso eo gt 15 Uo ON cep A is EM oR PN EE e AN e oe GE o oe o e Date Figure 37 Annual habitat time series Reach 2 West Slope cutthroat trout winter 11 19 12 3 12 17 12 31 Pre Dam Post Dam Flathead Instream Flow Investigation Project Miller Ecological Consultants Inc Page 43 September 29 2003 Habitat time series Reach 2 West slope cutthroat trout summer 3 500 000 3 000 000 2 500 000 2 000 000 Pre Dam P
9. 1 250 0 000 0 000 1 250 250 9 000 1 250 750 5 000 1 250 1 250 6 000 1 250 1 750 3 000 1 250 2 250 0 000 1 250 2 750 0 000 1 750 0 000 2 000 1 750 250 23 000 1 750 750 14 000 1 750 1 250 6 000 1 750 1 750 4 000 1 750 2 250 1 000 1 750 2 750 0 000 The TOTDEPTH MEANVEL values in the 3D Surface Data Matrix must be assigned using the ranges for each of the histogram cells The midpoint value for each range will usually suffice Again knowing the distribution of the input data will highlight instances where a Bonneville Power Administration Technical Report May 24 2001 Miller Ecological Consultants Inc Page 5 different assignment strategy 15 necessary e g averages within each bin careful to assign appropriate values at the extremes of each parameter If the lowest Tot_Dep range includes data from 0 1 feet yet no fish were observed shallower than 0 8 feet then 0 75 or 1 0 would be a better value assigned to TOTDEPTH than 0 5 feet Again be careful not to create bins outside the range of the original observations Note the 3D Surface Data matrix variables are renamed to avoid confusion with the original raw data Tot Dep gt TOTDEPTH and Mean Vel gt MEANVEL Save this file once the full matrix is complete NONLINEAR USER SPECIFIED ESTIMATION The 3D Surface Data Matrix DVZTbl contains the independent variables TOTDEPTH and MEANVEL and the dependent variable 7 that are used in fitting a nonlinear re
10. ANY THIRD PARTY INCLUDING WITHOUT LIMIT LOSS OF DATA THE FOREGOING LIMITED WARRANTY IS IN LIEU OF ALL OTHER WARRANTIES EXPRESS OR IMPLIED INCLUDING BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE This agreement is the entire agreement If any provision of this agreement is held invalid the remainder of this agreement shall continue in full force and effect If you do not agree to the above terms you must discontinue any further use of this product and return to SSI MEC any material including any copies which SSI MEC has sent to you in connection with this product IF YOU DO NOT AGREE TO THE ABOVE TERMS AND CONTINUE TO USE THIS PRODUCT AND OR DO NOT RETURN THE RELATED MATERIALS WHICH SSI MEC HAS SENT TO YOU SSI MEC WILL HAVE NO OBLIGATION TO YOU WITH RESPECT TO THIS PRODUCT OR THE RELATED MATERIALS THE USE OF THIS PRODUCT AND RELATED MATERIALS WILL BE AT YOUR SOLE RISK AND YOU WILL BE LIABLE TO SSI MEC FOR THE PRICE OF THE PRODUCT AND RELATED MATERIALS GIS Based Weighted Useable Area Modeling Manual Flathead River Prepared for Montana Fish Wildlife and Parks 5 9 15 03 Copyright MEC SSI 2003 Miller Ecological Consultants Spatial Sciences amp Imaging CHAPTER 1 DIRECTORY STRUCTURE 1 Make the proper directories for this project Your root project directory should have the following directories within it reach 1 geographic data 2 Direct
11. For each flow regime assessed we conducted both hydrology and habitat time series analysis to calculate both flow and habitat statistics These values allowed a direct comparison of the changes that occur in both flow and habitat under a range of conditions These tabular data can be displayed for each flow scenario to represent the spatial habitat distributions Habitat time series uses a spreadsheet format with data arranged in columns and rows that combines the hydrology over time with the habitat use as a function of discharge These values are converted to area of habitat for the study site and then area of habitat for the reach Comparisons of change in habitat over time for each flow of interest are possible with this spreadsheet setup The steps to use the spreadsheet for analysis are as follows The habitat time series spreadsheet is arranged with data in column format Cell A1 contains the title Cell A2 contains the name of the river Cells A4 through are titles for species and life stage The species names and life stages are typed into Cells B4 B5 and B6 Figure 6 The hydrology data is placed in columns A B and C Rows 10 through 12 of those columns contain header information Column A contains the Date and Columns B and C contain the hydrology data Column B contains the baseline hydrology titled Pre dam Column contains the hydrology for the Post dam alternative To the right of the hydrology columns are a look
12. gt Bivariate Histograms This brings up the 3D Bivariate Histograms dialog box Click on Variables to bring up the Select Variables Bivariate Histogram dialog box Select the variables you wish to display e g Tot_Dep in category 1 and Mean_Vel in category 2 then click OK which returns you back to the 3D Bivariate Histograms dialog box Click OK in the 3D Bivariate Histograms dialog box to create a 3D Bivariate Histogram of the selected variables STATISTICA creates a 3D Bivariate Histogram of the selected variables see Figure 1 Figure 1 3D Bivariate Histogram of Depth Velocity Fish Frequency Bivariate Histogram Total Depth Mean Velocity Number of Fish Bonneville Power Administration Technical Report May 24 2001 Miller Ecological Consultants Inc Page 2 Depending upon the data set it may be necessary or desirable to specify the boundaries used to calculate the depth velocity matrix used to create the histogram Boundaries are analogous to the step size used while integrating Boundaries set the range of values used to sort parameters into bins while creating the histogram Allowing STATISTICA to auto calculate these boundaries is a good first step Then go back and specify boundaries and compare the histograms The desired output is a contour smooth enough to allow adequate surface fitting while maintaining a detailed and well defined gradation away from data peaks Experimentation with different boundary settings is highly
13. 424b Jbt 339b Jbt 283b Jbt 246b Jbt 226b Jbt 169b Jbt 127b _ Jbt 105b 169 _ 2 Histogram of juvbtwinni as a Surface from 169c TRES Histogram of juvbtwinni as a Surface from 169 bv 8 Value 16000 14000 12000 10000 8000 6000 4000 2000 0 Juvenile Bull Trout 169 cms 7 juvbtwinnight Juvenile Bull Trout Reach 1 amp 2 winter night Jbt 1445b Jbt 84 b Jbt 594b Jbt 424b Jbt 339b Jbt 283b Jbt 246b Jbt 226b Jbt 188b Jbt 127b _ Jbt 105b 228cms bw s e E Histogram of juvbtwinni as a Surface from 226c E3 Histogram of juvbtwinni as a Surface from 226 _ _8 9000 8000 7000 5000 5000 4000 3000 2000 1000 0 Juvenile Bull Trout 226 cms juvbtwinnight Juvenile Bull Trout Reach 1 amp 2 winter night Jbt 1445b Jbt_84ab Jbt 594b Jbt 424b Jbt 339b Jbt 283b Jbt 246b Jbt 226b Jbt 159b Jbt 127b Jbt 105b ar e e on dr bi 1 e A Histogram of juvbtwinni as a Surface from 246c Histogram of juvbtwinni as a Surface from 246cms_bv_8 Value 8000 7000 5000 5000 4000 3000 2000 1000 Juvenile Bull Trout 246 cms juvbtwinnight Juvenile Bull Trout Reach 1 amp 2 winter night Jbt 1445b Jbt 84 b Jbt 594b Jbt 424b Jbt 339b Jbt 283b Jbt 246b Jbt 226b Jbt 188b Jbt 127b Jbt 105b 283cm
14. Figure 1 Study Area for Flathead River Instream Flow Study Flathead Instream Flow Investigation Project Page 2 Miller Ecological Consultants Inc September 29 2003 Objectives There are three objectives for this study 1 Develop comprehensive spatial and tabular attribute database IFIM models to characterize physical processes in the Flathead River affected by flow from Hungry Horse Dam 2 Use IFIM models to compare the results of alternative dam operation strategies on aquatic resources Within each of three reaches calibrate IFIM submodels to describe hydraulic conditions under various flow volumes Simulate changes in physical habitat conditions at flows of interest 3 Document results in reports maps and calibrated models in user manuals Flathead Instream Flow Investigation Project Page 3 Miller Ecological Consultants Inc September 29 2003 METHODS This project used a modified application of IFIM in three reaches of the Flathead River The entire river segment downstream of Hungry Horse Dam was mapped using GIS technology and onstream ground truthing Microhabitat use by fish life stages was provided by another BPA project 9401000 and overlaid on the framework provided by this project Target species include bull trout Salvelinus confluentus and west slope cutthroat trout Oncorhynchus clarki lewisi To accomplish these goals MEC used a combination of hydraulic simulation and GIS mapping on the Flathead River
15. Microsoft Excel Time Series xls SCH File Edit View Insert Format Tools Data Window Help DES rar ta Sa v e 021 Ye Reply with Change R13 X Type a question 10 B 7 u 8 4 End Review P Arial at fe M13 D 2 D51 N Westslope Cutthroat Westslope Cutthroat Summer Summer Winter Winter Summer Summer Winter HABTS HABTS HABTS HABTS HABTS HABTS HABTS Pre Dam 1940 1949 Post Dam 1993 2002 Pre Dam 1940 1943 Post Dam 1993 2002 Pre Dam 1940 1949 Post Dam 1993 2002 Pre Dam 1940 1949 F Pre Dam Post Dam Pre Dam Post Dam Pre Dam Post Dam Pre Dam 233433 201688 207924 177222 1208567 1044 034 1 076 315 r 233429 e 192706 e 20781 e 167421 1 208 336 997 539 4 075 726 r 233313 177309 207606 150573 1 207 740 917 837 1 074 665 233233 r 177217 f 207474 e 150472 1207 355 917 360 1 073 981 233147 r 180624 amp 207310 154207 1 206 878 934 994 1 073132 2277300 7 233152 ld 181391 P 207313 4 155043 1 206 905 938 366 107380 2277901 r 233357 179642 207683 153131 1 207 965 929 310 1 075 065 3984410 233408 r 185534 4 207774 r 159591 1208 230 960 413 1 075 537 370410 8 233318 r 173151 d 207615 r 152592 1 207 766 927 368 1074 712 2008888 r 233224 r 185289 r 207446 r 159322 1 207 276 959 142 1 073 840 60198 3 233224 d 173713 7 207446 d 146637 1 207 276 899 249 1 073 840 178955 7 r 233216 r 170
16. Miller Ecological Consultants Inc SPATIAL SCIENCES amp IMAGING Draft September 2003 GIS Based Weighted Useable Area Modeling Manual Flathead River Prepared for Montana Fish Wildlife and Parks 1 9 15 03 Copyright MEC SSI 2003 Miller Ecological Consultants Spatial Sciences amp Imaging Table of Contents CHAPTER 1 DIRECTORY STRUCTURE in ccsssccsscssccocsssossciccsscocssosssocdeeseesbosecenesdsvdseonctecesecdcodeocecesocssedseedsecdeseeseouss 6 CHAPTER 2 DATA PRE PROCESSING cssssccsssssscssssccecssscccssnscceessscccscssccecsssaccsessssecensceeessnaccsessseesscsacecessnaes 7 PROCESSING HYDRAULIC FLOW Data 7 CREATING see ote SLID Ee 9 CHAPTER 3 GIS BASED WEIGHTED USEABLE AREA MODELING scsssssssssssssesscccssssssersecessssseseees 9 CONDUCTING THE WEIGHTED USEABLE AREA Mopp NG 9 CHAPTER 4 HABITAT AREA MODELING RESULTG ccccccccssssssssssscsssssscssereccscsssscssecscsssssscescssesssssseess 11 GIS Based Weighted Useable Area Modeling Manual Flathead River Prepared for Montana Fish Wildlife and Parks 2 9 15 03 Copyright MEC SSI 2003 Miller Ecological Consultants Spatial Sciences amp Imaging This user manual will describe the steps MEC and SSI took to complete habitat modeling for the Flathead River Instream Flow project The procedures were created by MEC and SSI to aid personnel in processing the data for the project and to provide Montana Fish Wildlife and Parks the resu
17. Predicted Values Ej Figure 11 STG Observed versus Predicted Values Observed versus Predicted Values Observed Values Predicted Values Finding the best fit to the 3D Surface Matrix is an iterative process and generally requires multiple fine tuning attempts It is important to experiment with the order of the fitted polynomial in trying to match any particular data set The first example above used second order terms in both depth and velocity and a first order interaction term Multiple equation fitting attempts on the sample data set direct one towards a final model yielding the largest coefficient of determination R with the fewest terms This model contained depth and velocity terms expressed to the fourth order and a first order interaction term This took seven iterations of running different model equations and yielded an increase in the value from 0 64 to 0 91 The investigator should attempt to reach an R value exceeding 0 9 The investigator is encouraged to work with many different equations and settle on the one providing the best fit to the characteristics of the data set under consideration Note that Bovee 1986 cautions against the use of terms beyond second order Hanson 1988 finds the best results using higher order terms with the largest Coefficient of Determination Hanson cautions that when using models with higher order terms to evaluate the results only within the bounds of the original data This
18. User Specified Regression Function dialog box Click on the Function To Be Estimated and Loss Function button which opens the Estimated Function and Loss Function Dialog Box In the Estimated Function box you must specify the function to be used in the regression The function specified to describe the frequency distribution surface contains terms for each variable depth and velocity and one or more terms describing the interactions among the Bonneville Power Administration Technical Report May 24 2001 Miller Ecological Consultants Inc Page 6 variables The complexity of the 3D Bivariate Histogram surface number of complete peaks determines the polynomial order necessary to describe the surface A first order exponential polynomial depicts an exponential decay A second order function describes a bell shaped curve Bovee 1986 The order of the terms used and which interaction terms to include must be decided by the researcher The recommended first equation is Z exp 0 b1 v1 b2 v2 b3 v1 v2 b4 v142 65 2 2 where Z number of fish observed vl water column depth v2 average water column velocity b0 b1 b2 equation coefficients The recommended Loss Function is the program default L OBS PRED 2 where L loss OBS observed values PRED predicted values Note that STATISTICA syntax rules require TOTDEPTH and MEANVEL be entered as v1 and v2 and that multiplication and powers be sp
19. as velocity differences Flathead Instream Flow Investigation Project Page 23 Miller Ecological Consultants Inc September 29 2003 90 000 80 000 70 000 Subadult night 60 000 E Subadult day amp _ Adult 50 000 40 000 30 000 Weighted Usable Area m per km 20 000 10 000 0 100 200 300 400 500 600 700 800 900 Discharge m s Figure 16 Reach 1 Bull trout habitat versus discharge 80 000 70 000 60 000 50 000 Fall winter Summer 40 000 30 000 Weighted Usable Area gt 20 000 10 000 0 100 200 300 400 500 600 700 800 900 Discharge m s Figure 17 Reach 1 West slope cutthroat trout habitat versus discharge Flathead Instream Flow Investigation Project Page 24 Miller Ecological Consultants Inc September 29 2003 4 juvbtwinnight Juvenile Bull Trout Reach 1 amp 2 winter night Jbt 1415b Jbt 840b Jbt 5946 Jbt 424b Jbt 338b Jbt 283b Jbt 2465 Jbt 228b Jbt 188b Jbt 127b Jbt 105b 105 cms_bv s Histogram of juvbtwinni as a Surface from 105c 3 as Histogram of juvbtwinni as a Surface from 105cms_bv_8 Value 35000 30000 25000 20000 15000 10000 5000 Figure 18 Bull trout sub adult night habitat area 105 cms Reach 2 Flathead Instream Flow Investigation Pro
20. encouraged This is an excellent opportunity to perform a final quality control on the data Check the graph for outliers questionable data points and for trends and characteristics of the two variables STATISTICA allows rotation of the histogram Right mouse click anywhere on the graph select Rotate Graph Perspective Figure 2 shows the same plot rotated to afford a different view of the 3D Bivariate Histogram Print the 3D Bivariate Histogram for later comparisons by using the File pull down menu or Right mouse click anywhere on the graph This graph should be printed from at least two perspectives to obtain a full view of the surface of the histogram Figure 2 Rotated 3D Bivariate Histogram of Depth Velocity Fish Frequency Rotated Bivariate Histogram Total Depth Mean Velocity Number of Fish 24 20 16 42 gt 325 3 3 5 B lt 5 37 22525 4 7 521 2 7 1 51 gt xs E OM D MEAN VEL STATISTICA will produce a surface plot of the 3D Bivariate Histogram Right mouse click anywhere on the graph select Change General Layout then under Graph Type select Surface Plot This changes the existing 3D Bivariate Histogram to a surface plot which should also be printed from several perspectives Figure 3 shows the 3D Surface Plot of the 3D Bivariate Bonneville Power Administration Technical Report May 24 2001 Miller Ecological Consultants Inc Page 3 Histogram data The surface plot representat
21. from the South Fork confluence to the mouth of Flathead Lake as the base map for the overall analysis The technical approach is presented in the following sections General Approach The approach for assessing instream flow needs for fish utilized hydraulic analysis and habitat modeling in a modified incremental method to evaluate changes in quantity quality and distribution of habitat with changes in flow Figure 2 By collecting the hydraulic data in a manner suitable to two dimensional modeling of habitat spatial distribution of habitat was displayed with a Geographic Information System GIS and tabulations of habitat quantity and quality were related to flow levels in the river Hydraulic modeling begins with construction of a digital terrain map for the study area A survey grade Global Positioning System GPS was used to field map each study site and data points were used to construct a detailed topography map or grid of the channel Multiple data sets of water surface elevations and point velocity measurements were used to calibrate a two dimensional hydraulic model to simulate depth and direction of flow through each site Table 2 The grid of resulting flow depths and velocities is then compared to habitat preference criteria for species of interest to determine location and quality of resulting habitat Table 2 Hydraulic measurements recorded on the Flathead River above Flathead Lake Montana Discharge m s p
22. in the river This approach used a combination of georeferenced field data for each study site combined with a two dimensional hydraulic simulation of river hydraulic characteristics The hydraulic simulations were combined with habitat suitability criteria in a GIS analysis format to determine habitat area as a function of discharge Results of the analysis showed that habitat area is more available at lower discharges than higher discharges and that in comparison of the pre dam hydrology with post dam hydrology the stable pre dam baseflows provided more stable habitat than the highly variable flow regime during both summer and winter baseflow post dam periods The variability week to week and day to day under post dam conditions waters and dewaters stream margins This forces sub adult fish in particular bull trout to use less productive habitat during the night There is a distinct difference between daytime and nighttime habitat use for bull trout sub adults The marginal areas that are constantly wet and then dried provide little in productivity for lower trophic levels and consequently become unproductive for higher trophic levels especially bull trout sub adults that use those areas as flows increase A stable flow regime would be more productive than flow regimes with high variability week to week The highly variable flows likely put stress on a bull trout subadult and west slope cutthroat trout due to the additional movement required
23. initial clustering process 125 clusters were specified for the study area Once the 125 clusters were analyzed those clusters that represented true classes were kept and those that were considered confusion clusters were run through the routine again to further refine the clustering Once all of the clusters were assigned to a designated class manual editing of the classification took place to correct any misclassifications of spectrally similar features Table 5 shows the acreage for each land cover category in the study area Table 5 Land cover acreage counts 1998 classification Land Cover Category Total Acreage Developed Lands Cultivated Lands Grasslands Forest Willow Bare Lands Water Total Area Classified Developed Cultivated Grasslands Bare Lands 6 5 Urban and Rural Developed Areas Classification The urban and rural developed lands were classified separately from the rural areas to help improve the accuracy of the classification Urban structures such as concrete and rooftops are often spectrally similar to dry bare soil and exposed rock To avoid confusion between these cover types urban areas were manually delineated on the IRS data and extracted from the imagery An unsupervised classification was then performed on these areas One hundred spectral clusters were specified for the urban classification regions Clusters that represented urban areas were saved and coded appropriately Clusters that did
24. is an important constraint on the use of the modeling The original data set determines the range of application of the modeling results This process does not yield valid results outside the boundaries set by Din Dmax Vmin Vmax Results of the modeling should be interpreted and utilized only within these boundaries After printing and or saving the results of the first model return to the User Specified Regression Function dialog box Enter in the next equation used to fit the 3D Surface Data Bonneville Power Administration Technical Report May 24 2001 Miller Ecological Consultants Inc Page 11 Matrix and repeat the process Print and or save the results for comparing between different iterations The above steps are repeated until the final testing and comparisons are done and the model providing the best fit to the data is chosen Normalizing the Habitat Suitability Index The final regression equation must be normalized to provide a maximum habitat suitability index of 1 Take the maximum value N from the final model and enter it into the fitted equation as a normalizing term in front of the exponential polynomial expression This forces the maximum value equal to 1 and all other values between 0 and 1 This new equation takes the form SI exp b V b3DV b4D b45V where SI Habitat Suitability Index normalizing term D water column depth V average water column velocity bo bi
25. n bene 23 Habitat Time Sees uec t DR ER DAE HER dte eae go t a Ee be t oett dd 31 TNC cessus les UC That LE DL ML LU 60 Literature NM 61 PRORMOW aqaa cte etre tr Seas sacl sls elas E 62 List of Tables Table 1 Flathead River IFIM study Reach lengths and site lengths 1 Table 2 Hydraulic measurements recorded on the Flathead River above Flathead Lake n 4 List of Figures Figure 1 Study Area for Flathead River Instream Flow Study eese 2 Figure 2 Flow chart of data analysis for Flathead River hydraulics and aquatic habitat 5 Figure 3 Example of grid network developed from topography 9 Figure 4 Example of depth contours for Flathead River Site 2 105 9 Figure 5 Example of velocity contours Flathead River Site 2 105 CMS 10 Figure 6 Spreadsheet template for habitat time series sssssssseseeeeeeeeen 13 Figure 7 Example of Vlookup function for time series analysis 14 Figure 8 Habitat time series example for the site and reach 15 Figure 9 Observed versus predicted water surface elevations for three flows at Reach 1 17 Figure 10 Figure 11 Figure 12 Figure 13 Figure 14 Figure 15 Histogram of observed
26. not represent urban areas were coded as class zero so that categories from the rural classification would inhabit these areas when the urban and rural classifications were combined 6 7 Raster Generalization The land cover classification was generalized to remove salt and pepper from the land cover data In most original classification products very small pixel clumps which fall along category boundaries are erroneously classified In this project the single pixels and small clumps were dropped out using a clump and sieve routine and filled in by using a majority filter algorithm Clumps less than four pixels in size were eliminated and replaced with the surrounding majority class Example of Land Use Land Cover Data e ge 4 Legend Domestic E Willow Agriculture Barren rock impervious BEN Grassland Water rores Figure 2 Example of 1998 land cover classification 6 8 Simple Change Detection Simple change was defined as a change from water to another land cover class or any land cover class to water Simple change in the river channel was identified for three time periods 1978 1990 1990 1998 and 1978 1998 The river channels were digitized from the DRGs to create the 1978 channel the DOQQs to create the 1990 channel and extracted from the IRS 1C classification to create the 1998 channel An overlay technique was used to compare the river channels and identify areas of change and t
27. resource photography to determine what land use land cover was present before changes occurred at a given site This analysis produced a complex from and to change map From this information BPA can determine which land uses are most likely to be affected by river dynamics Flathead Instream Flow Investigation Project Page 6 Miller Ecological Consultants Inc September 29 2003 Topographic Mapping Each study site was surveyed with a survey grade GPS for the purpose of constructing a digital terrain model for the site The GPS provided latitude longitude and elevation of each point to an accuracy of about 0 1 foot for both horizontal and vertical resolution Horizontal stations and elevations were georeferenced to known points of origin in the vicinity of each study site A sufficient number of points were surveyed on the ground to enable construction of a digital terrain model for the study reach In the vicinity of the channel points were spaced to define channel geometry both in plan form and cross section Channel geometry points were collected up to the typical high water marks to establish ground topography for modeling high flow regimes Substrate and cover were recorded for each site along with field notes describing general stream and habitat conditions at the study site and reference photos for the area Hydraulic Data Collection Two dimensional hydraulic modeling requires channel geometry data multiple water surface elev
28. up table with regression coefficients and functions for the weighted usable area for juvenile and adults of the species The headers denote discharge Q habitat and the A and B terms for the functions The cells contain the formulas Flathead Instream Flow Investigation Project Page 12 Miller Ecological Consultants Inc September 29 2003 that calculate the A terms The discharge and habitat values are generated in the GIS Base habitat model and copied or typed into the cells The data for the blocks should start in cells of the time series spreadsheet contained in the distribution CD The habitat for the site for each flow is analyzed by date and flow regime The rows must be identical for the correct analysis The habitat calculations are based on a Vlookup formula contained in cells R12 12 and higher Figure 7 Microsoft Excel Time Series xls H File Edit Insert Format Tools Data Window DE Boe El ERR A 10 amp 4 i ta ta a ud E o Ye Reply with Changes End Review g Al fe HABITAT TIME SERIES 1 B D E H 1 K HABITAT TIME SERIES Site Length km 3 4 2 Flathead River Reach 1 Reach Length km 17 6 3 4 SPECIES Westslope Cutthroat 5 LIFE STG Summer 6 LIFE STG Winter 7 LIFE STG 8 3 Hydrology Hydrology 10 WITH WITH eaten Pre Dam 1940 1949 Post Dam 1993 2002 12 Date Q lt Q m s Summer Winter 13
29. vele Ur 1 000 000 A P RU E ah LE e e lt 800 000 5 5 600 000 Post Dam i 4 400 000 200 000 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 Date Figure 51 Habitat time series Reach 3 Bull trout subadult night Flathead Instream Flow Investigation Project Miller Ecological Consultants Inc Page 57 September 29 2003 Habitat time series Reach 3 Bull trout subadult day 14 000 000 12 000 000 10 000 000 Gi 8 000 000 5 Post Dam 5 6 000 000 4 000 000 2 000 000 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 Date Figure 52 Habitat time series Reach 3 Bull trout subadult day Flathead Instream Flow Investigation Project Page 58 Miller Ecological Consultants Inc September 29 2003 Habitat time series Reach 3 Bull trout adult 10 000 000 9 000 000 8 000 000 7 000 000 6 000 000 Pre Dam 5 000 000 Post Dam Habitat area m2 4 000 000 3 000 000 2 000 000 1 000 000 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 Date Figure 53 Habitat time series Reach 3 Bull trout adult Flathead Instream
30. 0 1 920 1 120 12 FE AWIT 936 9 000 2 000 00 2 400 2 420 13 AWIT 550 93 000 P 2 400 1400 1 190 1 170 14 RB ADULT 352 9 000 Sot 3 200 1 500 1120 1 050 1t RE ADULT 9 000 POE 2 4 00 Ban CH Bonneville Power Administration Technical Report May 24 2001 Miller Ecological Consultants Inc Page 14 2 Produce simple Line Plots of variables and quality control the data Graph1 STG Line Plot Line Plot BPAHabData lt MEAN VEL 3 Produce 3D Bivariate Histogram Bivariate Histogram Total Depth Mean Velocity Number of Fish Bonneville Power Administration Technical Report May 24 2001 Page 15 Miller Ecological Consultants Inc 4 Plot the Rotated 3D Bivariate Histogram Rotated Bivariate Histogram Total Depth Mean Velocity Number or Fish 24 20 16 42 3 5 EJ 3 3 5 g 2 3 amp 2 2 5 5 4 ES 7 1 51 CC fe S d c A ge tern eee ME re MEAN VEL 5 Produce the 3D Surface and Rotated 3D Surface Plots of the 3D Bivariate Histogram Bivariate Histogram Total Depth Mean Velocity Numbre of Fish Bonneville Power Administration Technical Report May 24 2001 Miller Ecological Consultants Inc Page 16 6 Edit the 3D Bivariate Histogram graph data matrix Graph Data for Graph11 Bivariate Histogram Bivariate Histogram BPAHabData2 sta 18v 159c 7 C
31. 0 1200 1400 1600 Discharge m s Figure 24 Reach 3 Bull trout habitat versus discharge 200 000 180 000 160 000 140 000 120 000 100 000 80 000 60 000 Weighted Usable Area m per km 40 000 20 000 0 0 200 400 600 800 1000 1200 1400 1600 Discharge m s Figure 25 Reach 3 West slope cutthroat habitat versus discharge Flathead Instream Flow Investigation Project Page 30 Miller Ecological Consultants Inc September 29 2003 Habitat Time Series Habitat time series analysis used ten year and annual hydrology The hydrology for west slope cutthroat trout was divided into summer and winter seasons The response of habitat to flow is similar to the flow regime change between the pre dam and post dam conditions Pre dam conditions for summer shows that the habitat increased sharply after runoff and was stable in the summer baseflow period Post dam conditions show that the response of habitat to flow is slower and also is much more variable in the summer baseflow period Figure 26 Winter baseflows for west slope cutthroat trout show that the winter pre dam period was very stable with a relatively high amount of habitat area and that current conditions have much more variable habitats over time Figure 27 The ten year time series also show that the variability and magnitude of habitat response continues over time from what was calculated in the annual hydrograph series Figures
32. 00 Pre Dam Post Dam 200 000 VOL 101 VOL VOL VOL VOL VOL VOL Date Figure 29 Habitat time series Reach 1 West slope cutthroat trout winter VOL VOL Wv Flathead Instream Flow Investigation Project Miller Ecological Consultants Inc Page 35 September 29 2003 Annual habitat time series bull trout subadult night 1 000 000 900 000 800 000 700 000 600 000 500 000 Habitat area m2 400 000 300 000 200 000 100 000 1 1 1 15 1 29 2 12 2 26 3 12 3 26 4 9 4 23 5 7 5 21 6 4 6 18 7 2 7 16 7 30 8 13 Date Figure 30 Annual habitat time series bull trout subadult night 8 27 9 10 9 24 10 8 10 22 11 5 11 19 12 3 12 17 12 31 Pre Dam Post Dam Flathead Instream Flow Investigation Project Miller Ecological Consultants Inc Page 36 September 29 2003 Annual habitat time series Bull trout sub adult day 1 400 000 1 200 000 Y 1 000 000 a N 800 000 3 600 000 I 400 000 200 000 0 OQ o Q o x pe amp X EN ep 2 e El e E cL 4 x Ed oco oL co e oe 5 e Or e SS Date Figure 31 Annual habitat time ser
33. 1 Jan 63 1 157 6 1 1 M 2 Jan 62 4 164 7 1 1 Summer 15 3 Jan 611 178 2 1 1 16 4 Jan 50 3 178 3 1 1 17 5 Jan 59 3 1751 1 1 18 53 3 1744 13 7 Jan 516 176 0 20 8 Jan 622 170 6 127 43 21 3 612 176 5 169 90 22 10 50 1 170 8 226 53 23 1t Jan 50 1 1815 246 55 24 12 50 0 184 1 28317 25 13 60 3 182 3 339 80 26 14 Jan 615 183 3 424 75 27 15 62 7 1781 597 65 28 16 Jan 58 5 177 2 849 51 29 17 57 3 185 7 30 18 Jan 56 3 186 4 31 13 56 1 188 2 32 20 544 183 1 33 21 Jan 54 3 181 2 34 22 Jan 553 174 6 35 23 Jan 56 4 176 6 36 24 Jan 57 6 182 9 37 25 Jan 572 1842 Winter 38 26 Jan 55 8 177 2 39 27 Jan 55 5 175 8 40 28 Jan 55 3 174 0 23 55 1 1724 197778 197773 0 42 30 Jan 554 166 0 214692 197777 9 43 31 54 3 172 9 218272 391915 3 44 1 Feb 54 8 173 6 160400 1188 362287 9 45 2 Feb 54 3 180 3 33108 442 193350 5 46 Feb 546 1786 84248 j 2495 6 47 4 Feb 55 2 174 2 37132 180 148355 6 48 5 Feb 55 9 167 8 86888 144 136008 0 43 amp Feb 56 0 153 2 74608 31 8083 39 50 7 Feb 55 4 158 0 69120 48 37785 2 51 8 Feb 55 6 176 8 57040 Arak ec Figure 6 Spreadsheet template for habitat time series Flathead Instream Flow Investigation Project Page 13 Miller Ecological Consultants Inc September 29 2003 Microsoft Excel Time Series xls
34. 28 and 29 The baseflow period is much more variable than during the post dam conditions than the pre dam conditions and habitat values for pre dam can be higher at times than the post dam period Bull trout sub adults show a very similar response to flow for day and night Although the nighttime suitability criteria for bull trout sub adults shows that the total amount of habitat in pre dam conditions was higher during the winter baseflows than currently exist Also there is more stability during the pre dam conditions during summer and winter baseflows than exist for both bull trout sub adult nighttime and daytime criteria Figures 30 and 31 Bull trout adult habitat in reach 1 shows a similar stability during the pre dam baseflow conditions and much more variability during the post dam baseflow conditions Figures 32 and 33 Habitat characteristics for reach 2 are similar to those shown for reach 1 with west slope cutthroat trout having more variability in baseflow conditions post dam than pre dam The curve habitat area during runoff in summer periods show that there is very little difference between the reach 2 conditions pre and post dam There is a distinct difference for winter west slope cutthroat trout habitat showing both less habitat and more variability in the habitat on a daily basis in the post dam condition than was shown in the pre dam condition Figures 34 and 35 The analysis of the ten year time series again shows west slope cut
35. 3 Wim 246 Wim 226 v Wie 169 _ Ww 427 _ mim 105 4 168cms flow shp e Q Histogram of wctriwin as a Surface from 169cm IET TE o S COR LAG o Histogram of wctrlwin as a Surface from 159cms flow 8 Value Figure 21 West slope cutthroat trout habitat area 169 cms Reach 2 Flathead Instream Flow Investigation Project Page 28 Miller Ecological Consultants Inc September 29 2003 200 000 180 000 160 000 Subadult night Subadult day 120 000 lt Adult 140 000 100 000 80 000 60 000 Weighted Usable Area 40 000 20 000 0 200 400 600 800 1000 1200 1400 1600 Discharge m s Figure 22 Reach 2 Bull Trout Habitat versus discharge 180 000 160 000 140 000 120 000 Fall winter 100 000 Summer 80 000 60 000 Weighted Usable Area gt per km 40 000 20 000 0 200 400 600 800 1000 1200 1400 1600 Discharge m s Figure 23 Reach 2 Westslope cutthroat trout habitat versus discharge Flathead Instream Flow Investigation Project Page 29 Miller Ecological Consultants Inc September 29 2003 250 000 200 000 Subadult night Subadult day 150 000 amp _ Adult 100 000 Weighted Usable Area gt 50 000 x 0 200 400 600 800 100
36. 314 Bonneville Power Administration Technical Report May 24 2001 Miller Ecological Consultants Inc Page 18 Print the Fitted 3D Function and Rotated 3D Function graphs Frequency Distribution Residuals No of obs Sc pg q J a Expected 0 3 5 3 0 2 5 210 1 5 210 05 0005 10 15 2 25 30 36 41 Normal Bonneville Power Administration Technical Report May 24 2001 Miller Ecological Consultants Inc Page 19 Print the Normal Probability of the Residual Values 27 Figure 10 576 Normal Probability Plot of Residuals Normal Probability Plot of Residuals Expected Normal Value 3 5 2 0 0 5 1 0 25 40 Residuals Print the plot of Observed versus Predicted Values Figure 11 STG Observed versus Predicted Yalues OF Xx Observed versus Predicted Values 26 22 18 14 10 Observed Values 2 2 6 10 14 18 22 Predicted Values Bonneville Power Administration Technical Report May 24 2001 Miller Ecological Consultants Inc Page 20 11 Test models to find the best fit to the data Formulate the final regression equation based iterations of the model testing 12 Normalize the final equation to produce the Habitat Suitability Index SI I N exp b D b3DV b4D 65 where SI Habitat Suitability Index N normalizing term D water column depth V average water column velocity bo bi 62 equation
37. 326 r 207433 e 143575 1 207 236 884 792 1 073 763 144344 0 233239 e 172184 207474 144954 1207 355 831306 1073 381 142587 4 4 233343 r 171754 r 207668 144483 1 207 925 889 082 1 074 995 1728753 r 233457 r 177432 r 207861 r 150708 1208 482 918 472 1 075 985 00 4 233080 r 178322 207191 14 151684 1 206 534 323 073 4 072 519 23 r 232973 r 169176 r 207000 r 141657 1 205 978 875 737 1071523 30 r 232876 e 168440 r 206827 e 140849 1 205 474 871 324 4 070 634 r nee E a 4 66 6 A 4020 Figure 8 Habitat time series example for the site and reach Flathead Instream Flow Investigation Project Page 15 Miller Ecological Consultants Inc September 29 2003 RESULTS The results presented here provide the details of the instream flow analysis for the Flathead River reaches 1 2 and 3 A more comprehensive data set is included in the distribution compact disk CD with the Arcview projects files that contain all simulations for all species and life stages at each site Those data present the visual results of the analysis as well as provide grid files for additional analysis in GIS as needed by BPA and Montana Fish Wildlife and Parks Model Calibration The hydraulic models were calibrated to both water surface and water velocity to insure an accurate representation of the measured flows for each study site Water surface elevations from the simulations accurately represent measured f
38. 5 y Post dam discharge 1993 2002 5 E d a 1000 0 D 4 i P 500 0 i Figure 13 Hydrology time series Reach 3 Flathead Instream Flow Investigation Project Page 20 Miller Ecological Consultants Inc September 29 2003 1400 0 1200 0 1000 0 800 0 Post Dam Pre Dam 600 0 Discharge m s 400 0 200 0 0 0 VY eO oD AA o Ab vi AL oD a dh WD ok uo dl uo LY 9 qe d Date Figure 14 Average Discharge Reaches 1 and 2 Flathead Instream Flow Investigation Project Page 21 Miller Ecological Consultants Inc September 29 2003 1400 1200 1000 Pre Dam Post Dam 800 On E a 2 amp 600 5 lt 400 200 0 m m 5 E gt 2 8 en en 5 5 gt 3 D eee fe SS ee ee Soo e r dL OE Guy Er Date Figure 15 Average discharge Reach 3 Flathead Instream Flow Investigation Project Page 22 September 29 2003 Miller Ecological Consultants Inc Habitat Simulations Habitat for all three reaches was simulated using the combination of two dimensional hydraulic model and GIS weighted useable area model to generate weighted useable area in m per kilometer for each of the t
39. 62 equation coefficients This is the input equation for the habitat suitability modeling These steps are repeated for each species and life stage to develop a series of equations for habitat suitability These equations with the data sets will be passed to Miller Ecological Consultants Inc for use in the Flathead River instream flow study Bonneville Power Administration Technical Report May 24 2001 Miller Ecological Consultants Inc Page 12 LITERATURE CITED Bovee K D 1986 Development and Evaluation of Habitat Suitability Criteria for Use in the Instream Flow Incremental Methodology Instream Flow Information Paper No 21 Instream Flow and Aquatic Systems Group National Ecology Center U S Fish and Wildlife Service Biological Report 86 7 235pp Hanson D F 1988 Investigations into the use of bivariate habitat suitability functions in application of the PHABSIM model In Bovee K D and J R Zuboy ed Proceedings of a Workshop on the Development and Evaluation of Habitat Suitability Criteria 1988 Fish and Wildlife Service U S Department of the Interior Biological Report 88 11 407 Prewitt C G 1982 The Effect of Depth Velocity Correlations on Aquatic Physical Habitat Usability Estimates Ph D Dissertation submitted to Department of Fishery and Wildlife Biology Colorado State University 83pp Bonneville Power Administration Technical Report May 24 2001 Miller Ecological Consultants Inc
40. Directories OK 9 1 demo geographic example_1025cfs csv Es d example 1245cfs csv example 1591cfs csv gt wuamfl 1 example 2218c s csv demo example 3334cfs csv Ger geographic data example 334cfs csv List Files of Type Drives Comma Delimited Files csv z d 2 You can select one or more csv files for processing Each file selected will be generated as shapefile with the same filename prefix The shapefiles will also be loaded into the active view document in ArcView GIS Based Weighted Useable Area Modeling Manual Flathead River Prepared for Montana Fish Wildlife and Parks 8 9 15 03 OCopyright MEC SSI 2003 Miller Ecological Consultants Spatial Sciences amp Imaging CHAPTER 3 GIS BASED WEIGHTED USEABLE AREA MODELING Conducting the Weighted Useable Area Modeling 1 sure that you have at least one fish species life stage equation name heq and species life stage min max value statement name hmm in the heq directory You will also need at least one flow shapefile in the geographic data directory We will be using the 339 cfs shapefile in this example 2 Bring the 339 cfs shapefile up in the View document Click on the HSM Equations and Surface Modeling button This will start up a series of input dialog boxes to set up the modeling 3 The first dialog box allows you to select the flow that you want to model Hydrauli
41. ECTION ANALYSIS DRAFT FINAL REPORT September 10 2003 Provided to Bonneville Power Administration Montana Fish Wildlife amp Parks 905 NE 11 Ave 490 North Meridian Portland OR 97232 Kalispell MT 59901 Ron Morinaka Brian Marotz Miller Ecological Consultants Inc 1401 Riverside Avenue Suite 3 Fort Collins CO 80524 William J Miller Provided by Spatial Sciences amp Imaging 1113 Stoney Hill Drive Suite B Fort Collins CO 80524 Copyright 2000 Revised August 2003 1 0 Introduction This report describes the land cover classification and change detection analysis work completed for Bonneville Power Administration BPA in conjunction with Montana Fish Wildlife and Parks MFW amp P as part of the Flathead River Instream Flow Investigation Project The land cover classification was derived from a spatially enhanced multispectral IRS 1C image acquired in 1998 Historic river channels were delineated from data acquired at three different time periods spanning 20 years to help identify and monitor changes in the river channel Changes occurring between 1990 and 1998 were mapped in greater detail identifying the type from to of land use land cover change 2 0 Project Area The Flathead River stretches approximately 42 miles through the Flathead Valley in northwest Montana The valley consists of fertile agriculture land and timber and is bound by the Swan Mountain Range to the East The study area encompasses th
42. Flow Investigation Project Page 59 Miller Ecological Consultants Inc September 29 2003 CONCLUSIONS The habitat simulations for the Flathead River show that under the current hydrology there is much more variability in habitat on a weekly and daily basis during the baseflow period through pre dam There are times when flows change from 105 cms to 169 cms in winter baseflows and extensive areas of channel margins are wet and then dried The habitat suitability criteria show that bull trout move into those shoreline areas at night most likely to feed Muhlfeld et al 2003 Areas that are recently inundated have not had time to recolonize with benthic invertebrates Dewatering of shoreline areas likely impacts bull trout sub adults in foraging behavior as well as the benthic productivity of those areas Benthic invertebrates provide food for higher trophic levels such as west slope cutthroat trout Fluctuations during summer periods from 10 000 to 20 000 cfs also have impacts to channel margins Similar impacts to invertebrates can occur which may require movement to find suitable foraging habitat by sub adult and juvenile life stages of bull trout and west slope cutthroat trout The flow regimes with more stable baseflows whether those flows are at 3 500 or 6 000 cfs will likely be more productive for the system than flow regimes with high variability week to week and day to day in the operation of the reservoir Summer flows with increased flow
43. Investigation Project Page 7 Miller Ecological Consultants Inc September 29 2003 suitability criteria This method of substrate categorization can be adapted to most of the usual substrate codes in the existing habitat suitability criteria Cover was visually estimated by percentage The following cover types were used Velocity Refuge any instream object that provides a velocity refuge for the species of interest This could include objects such as boulders root wads large woody debris or other such objects Visual Isolation any object that provides visual isolation for the species of interest such as overhanging vegetation undercut banks or other such items Combination Cover any cover that provides both velocity refuge and visual isolation This could be any combination of the cover items listed above or a single cover object such as a downfall that provides both velocity refuge and visual isolation No Cover absence of cover will also be noted The full set of data was recorded at one flow Table 2 Repeat measurements of water surface elevations were taken at low and high flows During these measurements water surface elevations were surveyed at each study site These stage discharge measurements provided the data necessary for model calibration and for extending the range of hydraulic simulations Two Dimensional Hydraulic Modeling Two dimensional hydraulic modeling was accomplished in the Surface water Modeling System
44. Page 13 APPENDIX A Step by Step Sequence 1 Import data and make necessary formatting adjustments Le Jala BRA data lest ae Site 160 B DES SPECIES L TEXPHAB TOT DEPFISH VELFISH VEL 34717 1 RB ADULT 910 5 GLIDE 4 1 1 1 PILIVATY ADULT 914 5 GLIDE d 1 1 1 3 RE 915 5 GLIDE al 2 1 2 CATCH d ADULT 416 5 GLIDE 3 2 2 b RB 17 8 GLIE 2 1 1 1 E RE ADULT 313 3 GLIDE 1 2 TESS T RE aDOLT 925 9 GLIDE z 1 2 2 amp ADULT 926 a GLIDE 2 1 2 2 An 9 PP ADULT aji 3 GLIDE 1 1 3 i 10 RE ADULT 333 5 GLIDE Z 1 Z 2 12 11 RE 334 GLIDE 2 1 2 1 13 iz RE 936 5 GLIDE z 1 i 2 14 13 RE ADULT 950 9 Pat 2 1 i 1 14 RB ADILT 252 5 Poo 2 1 1 Vay 000 1 RB ADULT 9 1 500 1 480 1 290 RE ADULT 14 9 000 GLIDE 1 800 1000 1110 1 080 _ ADULT 315 93 000 GLIDE 7 600 1500 1 480 1 720 4 FE ADUIT 916 9 000 GLIDE 2 800 1 200 1 540 2 080 RB ADULT 517 9 000 1 900 500 1 100 HE ADULT 9519 9 000 GLIDE 1 0800 1000 1 670 10 RE ADULT 325 9 000 GLIDE 1 600 1 000 1 690 2 110 ADUIT 9 000 GLIDE 2 100 1 400 1 880 2 220 E RB ADULT 331 9 000 GLIIE 1 200 00 1 590 1 720 L BP ADILT 533 GLIDE 1 000 00 1 700 1 gab 11 RE ADULT aa 9 00 GLIDE 2 300 1 20
45. SMS using the Corps of Engineers RMA2 model This model was developed specifically to look at two dimensional velocity vectors in river systems and is capable of handling element 1 grid cell wetting and drying as flows are increased or decreased This model operates on a grid developed from the digital terrain model for each study site and output can be linked to GIS models for analysis and display of habitat availability Appendix B The 2 D model uses the georeferenced field data collected from each study site Data inputs include maps of site topography substrate and flow impediments a stage discharge relationship at the downstream end of the site and calibration and validation data throughout the reach Model calibration and validation data consist of depth and velocity measurements taken at know flow rates and locations in the study site usually at points upstream of impediments along one or more cross sections and scattered throughout the reach The GPS survey data is used to develop a grid system to represent the stream geometry Figure 3 This mesh is combined with the hydraulic data to simulate water depths and velocities for a range of flow conditions Figures 4 and 5 Flathead Instream Flow Investigation Project Page 8 Miller Ecological Consultants Inc September 29 2003 velocity mag 11800 000 2 01 Figure 3 Example of grid network developed from topography data Figure 4 Example of depth contours for F
46. Satellite Imagery Imagery from the Indian Remote Sensing Satellite IRS 1C was acquired to produce the 1998 land cover classification Since the IRS satellite has multiple sensors on board it was possible to obtain both a 20 meter mutlispectral image LISS channel and a 5 meter panchromatic PAN channel image that were acquired at the same time The two images were then merged together to create a single image that combined the spectral resolution from the LISS HI product with the higher spatial resolution of the PAN product This spatially enhanced multispectral image allowed SSI to map the land cover and changes at a larger scale Table 2 IRS bands used for classification Wavelength um Wavelength nominal 0 52 0 59 Green 0 62 0 68 Red 0 77 0 86 Near infrared 0 5 0 75 Panchromatic Table 3 IRS imagery specifications Scene Date Scene ID Size Notes 249 034 9 6 98 99103037 01 70x70 km 1C Panchromatic 249 034 9 6 98 99103037 01 141x141 km 1C LISS 3 4band multi spectral 4 2 USDA Forest Service Resource Photography Aerial photography was acquired from the USDA Forest Service at a scale of 1 15 840 These natural color photographs were flown during 1997 and 1998 The aerial photographs provided ground reference information for the land cover classification and also served as a basemap for classifying channel characteristics during fieldwork Twenty five 10x10 photographs were required for full coverage of the study a
47. This report has been modified to facilitate web viewing Landscape pages were rotated and blank non text pages were removed To download a copy of this report ready for printing click here Flathead River Instream Flow Investigation Project Final Report 1996 2003 KS8RKLSAAAA 00006358 1 September 2003 This Document should be cited as follows Bonneville Power Administration P O Box 3621 Portland Oregon 97208 This report was funded by the Bonneville Power Administration BPA U S Department of Energy as part of BPA s program to protect mitigate and enhance fish and wildlife affected by the development and operation of hydroelectric facilities on the Columbia River and its tributaries The views in this report are the author s and do not necessarily represent the views of BPA Final Report Flathead River Instream Flow Investigation Project Project No 1995 025 00 Submitted to Bonneville Power Administration 905 NE 11 Avenue Portlane H MILLER ECOLOGICAL CONSULTANTS INC EXECUTIVE SUMMARY A modified Instream Flow Incremental Methodology IFIM approach was used on the mainstem Flathead River from the South Fork Flathead River downstream to Flathead Lake The objective of this study was to quantify changes in habitat for the target fish species bull trout Salvelinus confluentus and west slope cutthroat trout Oncorhynchus clarki lewisi as a function of discharge
48. Wildlife and Parks Kalispell MT Submitted by Miller Ecological Consultants Inc 1113 Stoney Hill Drive Suite A Fort Collins CO 80525 May 24 2001 MILLER ECOLOGICAL TS CONSULTANTS INC Table of Contents IntrGduCtiOI aa pated eee tel ase ie all 1 Paired Depth Velocity 1 Creating the 3D Bivariate Histogram 2 Creatine the 31D Surtace Data Matix saree sic 4 Nonlinear User Specified Estimation ease 6 Specifying the Input and 6 Running the Regression and Evaluating the Model P 7 Normalizing the Habitat Suitability Index 12 Taterature GCE EE 13 ee EE 14 List of Figures Figure 1 3D Bivariate Histogram of Depth Velocity Fish Frequency eese 2 Figure 2 Rotated 3D Bivariate Histogram of Depth Velocity Fish Frequency 3 Figure 3 3D Surface Plot of the Bivariate Histogram Data 4 Figure 4 Graph Data Matrix from the 3D Bivariate Hietogeram 5 Figure 5 Sample portion of the 3D Surface Data Matrix DVZTDbI eee 5 Figure 6 Parameter Estimates coefficients for the regression equation eese 8 Figure 7 Graph of the Fitted 3D Function and Observed Values 9 Figure 8 Rotated Graph of the Fitted 3D Function and Observed Values
49. a software environment Report prepared for Bonneville Power Administration and Montana Fish Wildlife and Parks Muhlfed 2002 Bivariate habitat suitability functions for native fishes in the Upper Flathead River Montana Montana Fish Wildlife amp Parks Kalispell Montana Muhlfeld C C S Glutting Hunt D Daniels and Marotz 2003 Winter diel habitat use and movement by subadult bull trout in the Upper Flathead River Montana North American Journal of Fisheries Management 23 163 171 Trihey E W and D L Wegner 1981 Field data collection procedures for use with the Physical Habitat Simulation System of the Instream Flow Group Cooperative Instream Flow Service Group Fort Collins Colorado Flathead Instream Flow Investigation Project Page 61 Miller Ecological Consultants Inc September 29 2003 ACKNOWLEDGEMENTS We thank those individuals and organizations that helped support this project In particular personnel from Montana Fish Wildlife amp Parks including Clint Muhlfeld and Brian Marotz and their staff that developed the habitat suitability information Thanks also to Bonneville Power Administration for technical and administrative support on this project Flathead Instream Flow Investigation Project Page 62 Miller Ecological Consultants Inc September 29 2003 APPENDIX LAND USE LAND COVER ANALYSIS FLATHEAD RIVER INSTREAM FLOW INVESTIGATION LAND COVER CLASSIFICATION AND CHANGE DET
50. abitat Flathead Instream Flow Investigation Project Page 5 Miller Ecological Consultants Inc September 29 2003 Habitat modeling thus requires information on fish utilization of certain depths and velocities of flow in addition to utilization of certain substrate cover and other channel conditions The habitat suitability functions are then used as a filter against the grid of depth and velocity values predicted by the hydraulic model to estimate suitability of habitat in each grid cell at the site The area of grid cells with suitable habitat are then summed to obtain total usable area for a given streamflow level BPA requested that a geographic information system GIS be developed to provide these functions for the project Hydraulic data was measured in a manner compatible with both standard and modified IFIM techniques River gradient and flow was measured using standard surveying techniques Channel morphology was measured using a boat mounted GPS hydroacoustic system to develop detailed river topography maps and digital terrain maps that could be incorporated in GIS These maps were developed for two mile subreaches of each of the three main reaches A total of six miles of digital terrain mapping was conducted on the river The digital terrain maps were linked to above water surveys to the high water mark at each of the two mile reaches to establish ground topography for higher flow regimes for the modeling effort Substrate and
51. adult day 8 000 000 7 000 000 6 000 000 5 000 000 4 000 000 Habitat area m2 3 000 000 2 000 000 1 000 000 0 10 DN ON DORK TY st DN e DN E E 0 e DN rn Ge S Hi Ge Ko 0 0 Oo Date Figure 49 Annual habitat time series Reach 3 Bull trout subadult day 10 8 10 22 11 5 11 19 12 3 12 17 12 31 Pre Dam Post Dam Flathead Instream Flow Investigation Project Miller Ecological Consultants Inc Page 55 September 29 2003 Annual habitat time series Reach 3 trout Adult 5 000 000 4 500 000 4 000 000 3 500 000 3 000 000 2 500 000 Habitat Area m2 2 000 000 1 500 000 1 000 000 500 000 1 1 1 15 1 29 2 12 2 26 3 12 3 26 4 9 4 23 5 7 5 21 6 4 6 18 7 2 7 16 7 30 8 13 Date Figure 50 Annual habitat time series Reach 3 Bull trout adult 8 27 9 10 9 24 10 8 10 22 11 5 11 19 12 3 12 17 12 31 Pre Dam Post Dam Flathead Instream Flow Investigation Project Miller Ecological Consultants Inc Page 56 September 29 2003 1 600 000 Habitat time series Reach 3 Bull trout subadult night a Del 1 400 000 LT 1 200 000 31 i slg uS 1 8
52. ae Reaches 1 2 Reach 3 Measurement 2 9 August 1999 246 56 257 10 Bed topography water surface elevations velocity profiles substrate mapping 20 June 2000 594 65 624 88 Water surface elevations 3 7 January 2001 105 17 108 15 Water surface elevations Note Reported discharge for Reaches 1 and 2 are from USGS gaging station 12363000 Flathead River at Columbia Falls MT Discharge for Reach 3 is the combined flow reported from USGS gaging stations 12363000 12366000 Whitefish River near Kalispell MT and 12365000 Stillwater River near Whitefish MT Flathead Instream Flow Investigation Project Page 4 Miller Ecological Consultants Inc September 29 2003 Field Data Channel Topography Water Surface d Hydraulic Elevations Modeling Output depth and velocity pairings for individual nodes Velocity GIS Profile Framework Output Quantified Habitat Suitability representation of suitable dosi habitat for a range of A Analysis measured flows Fish Data Output Regression equation Depth Velocity for suitability data E E GIS Time Series Framework Analysis Output Quantified habitat suitability for non measured flows and flows significant to the determination of future management of the system Hydrology Figure 2 Flow chart of data analysis for Flathead River hydraulics and aquatic h
53. and predicted water velocities for 246 55 cms at Reach 1 18 Water surface elevations at a range of discharges for Site 1 Flathead River 18 Hydrology time senes Reaches 1 and 2 21342 deoa dt ie as editum eat 19 Hydrology time series Reach 3 adus atrio teme iisi eiae 20 Average Discharge Reaches 1 and 2 eie dae tenete idunt ede ese tian 2 Average discharge Reach EE 22 Flathead Instream Flow Investigation Project Page i Miller Ecological Consultants Inc September 29 2003 Figure 16 Reach 1 Bull trout habitat versus discharge 24 Figure 17 Reach 1 West slope cutthroat trout habitat versus discharge 24 Figure 18 Bull trout sub adult night habitat area 105 cms Reach 2 25 Figure 19 Bull trout sub adult night habitat area 169 cms Reach 2 26 Figure 20 West slope cutthroat trout habitat area 105 cms Reach 2 27 Figure 21 West slope cutthroat trout habitat area 169 cms Reach 2 28 Figure 22 Reach 2 Bull Trout Habitat versus discharge 29 Figure 23 Reach 2 Westslope cutthroat trout habitat versus discharge 29 Figure 24 Reach 3 Bull trout habitat versus discharge 30 Figure 25 Reach 3 West slop
54. ange 1937 1978 from land surface to water from water to land surface 1937 1990 from land surface to water from water to land surface 1937 1998 from land surface to water from water to land surface As opposed to the more recent river change detection conducting this simple change analysis revealed a very high magnitude of change in the Flathead River since 1937 Multiple areas exist where the shift in the main channel is 300 to 400 feet and in some cases is over 1 000 feet in the upper reaches of the river study area Changes are equally dramatic in the braided area east and south east of Kalispell In the lower reaches of the river affected by Flathead Lake changes are less pronounced but still visible in multiple areas See Figures 3 and 4 for examples of this change 11 Example Channel Change 1937 1998 IRS 1C Panchromatic image used as a backdrop Legend 1998 Channel 1937 Channel ee ee ee 0 5 0 5 1 Kilometers Figure 3 Example of 1937 1998 change Example Channel Change 1937 1998 IRS 1C Panchromatic image used as backdrop Legend 1998 Channel 1937 Channel 0 5 0 5 1 Scale Kilometers Figure 4 Example of 1937 1998 change 13 6 9 Detailed Change Analysis Areas identified as change during the 1990 1998 time period were processed at a larger scale and in greater detail to produce the Detailed Change Analysis layer The DOQQs aerial photographs ground trut
55. as 10 Histogram of juvbtwinni as a Surface from 594cms bv 8 Value 8000 7000 5000 5000 4000 3000 2000 1000 0 01 L10 1 0 2 0 2 0 3 103 04 0 4 0 5 0 5 og B8o5 07 Wu og Woo oo Woo in Juvenile Bull Trout 594 cms Z2 juvbtwinnight Juvenile Bull Trout Reach 1 amp 2 winter night Jbt1a45b gt Jbt_84ab Jbt 584b Jbt 424b Jbt 339b Jbt 283b Jbt 246b Jbt 226b Jbt 169b Jbt 127b Jbt 105b ai aen 1 Does m e ZS 3 2 Histogram of juvbtwinni as a Surface from 849c Histogram of juvbtwinni as a Surface from 849cms bv 8 Value 4500 4000 3500 3000 2500 2000 1500 1000 500 0 Juvenile Bull Trout 849 cms 2 juvybtwinnight Juvenile Bull Trout Reach 1 amp 2 winter night Jt 1415b Jbt _ Jbt 584b _ Jbt 424b chs _ Jbt 330b Jbt 283b 4bt 248b E 1 Jbt 226b Jbt 159b Jbt 127b Jbt 105b 1415cms bw Histogram of juybtwinni as a Surface from 1415 EG Histogram of juvbtwinni as a Surface from 1415cms bv 8 Value Juvenile Bull Trout 1415 cms APPENDIX C BIVARIATE SUITABILITY METHODOLOGY TECHNICAL REPORT CALCULATION OF BIVARIATE HABITAT SUITABILITY FUNCTIONS IN THE STATISTICA SOFTWARE ENVIRONMENT Submitted to Bonneville Power Administration P O Box 3621 Portland OR 97208 Contract No 00000537 00001 and Montana Fish
56. ation data sets and multiple velocity data sets Thus the specific hydraulic data collected at each site includes stream bed elevations mean column velocity at selected locations multiple collections at each habitat type visual estimates of dominant and subdominant substrate size and percent embeddedness and percent cover All hydraulic data were georeferenced for inclusion in the digital terrain model of the site and the associated GIS data base The following procedures were used to obtain the necessary data Stream Bed Elevations The survey grade GPS was used to collect stream bed elevations as described above Above water points also were surveyed using standard techniques and georeferenced for linkage to GIS Water Velocities At a selected number of locations within each study site water velocity was measured for use in hydraulic model calibration Multiple measurements were taken in each specific site for use in model calibration Substrate Composition Substrate composition was visually estimated at each site for all habitats Substrate was denoted for the following categories Aquatic vegetation Silt Sand Small gravel 0 25 1 0 inch Large Gravel gt 1 0 3 0 inch Cobble gt 3 0 10 0 inch Boulder gt 10 0 inch Bedrock The substrate was categorized by dominant and subdominant size class The substrate classification system was modified to provide the information required for the habitat Flathead Instream Flow
57. ations these components are used for simulation of usable habitat The geo referenced hydraulic data sets are imported into Arcview and combined with habitat suitability data for the analysis The habitat suitability equations are combined with the geo referenced output from the hydraulic data sets and habitat suitabilities are calculated based on the depth and velocity at each point within the site Habitat maps are created and tabular data sets produced that are used in the habitat time series A detailed description of the analytical steps is provided in the software manual Appendix B The combination of hydraulics and habitat are repeated at each study site for all flows of interest and for all species and life stages The habitat areas for each flow for each species are extracted from the GIS output and either copied or typed into the time series spreadsheet to conduct the habitat time series Habitat versus Discharge Modeling Habitat suitability modeling for each species of interest is accomplished in an Arcview GIS analysis Appendix B The Arcview instream habitat model relies on inputs from both the 2 D hydraulic modeling and the habitat suitability criteria described above These inputs are Flathead Instream Flow Investigation Project Page 11 Miller Ecological Consultants Inc September 29 2003 provided in the form of data layers within the GIS and parameters for spatial queries Data layers corresponding to flow depths and veloc
58. bitat depth and velocity Recommended next steps for this contract include 1 Map and quantify area of habitat types in the 1937 river channel Compare to area of habitat mapped by MEC in 1998 2 Summarize the habitat from each species life stage through all flows to identify best habitat locations through the range of flows 3 Assess high value habitats in 2 above for risk of modification due to dam operations looking at flow velocities and substrate Develop mitigation plans based on results 4 Build a comprehensive GIS plan framework and processes to collect analyze and map ongoing management and investigations into this reach of the Flathead River SSI feels fortunate to be a part of the Flathead Instream Flow Investigation Project and would like to thank everyone that has assisted our staff throughout this portion of the project 19 11 0 References ERDAS 1995 Field Guide Third Edition Atlanta Georgia Lillisand T M and R W Kiefer 1994 Remote Sensing and Image Interpretation Third Edition John Wiley amp Sons Lunetta R S and C D Elvidge 1998 Remote Sensing Change Detection Evironmental Monitoring Methods and Applications Ann Arbor Press 20 APPENDIX B GIS WEIGHTED USABLE AREA MODEL Miller Ecological Consultants Spatial Sciences amp Imaging GIS based Weighted Useable Area Model Software User Manual Bonneville Power Administration Flathead River Instream Flow Investigation
59. bitat component Study Area The study area includes the Flathead River from the South Fork confluence downstream to the river mouth on Flathead Lake Montana The river was divided into three reaches The first reach begins at the South Fork confluence and extends downstream 17 6 km in mostly homogeneous habitat with some island complexes The second reach was the braided reach and depositional area from the end of Segment 1 downstream to the end of the braided section The third reach extends from the lower end of the braided section to the mouth of Flathead Lake and is characterized by low gradient and seasonal backwater effects from the lake impounded by Kerr Dam Figure 1 A study site was selected in each reach to represent the physical characteristics of the reach Each study site was more than 3 km in length Table 1 Table 1 Flathead River IFIM study Reach lengths and site lengths Reach Total Length km Site Length km 1 17 6 3 4 2 19 2 3 9 3 31 6 3 7 Flathead Instream Flow Investigation Project Page 1 Miller Ecological Consultants Inc September 29 2003 2 Middle PE Flathead River Nort Fork Fla head River Dm NS Le J 5 2 S Y La lt MILLER ECOLOGICAL 3 CONSULTANTS N e WING INCA Legend ment 2 Highway N Water Feature Town Meters E 2000 0 2000 4000 d 8 Eu e
60. c Surface Modeling Select the Reach Master Shapefile 339cm CS flo NES h h p Select the flow and click OK 4 The program will then search the heq directory to find all species life stage equations If it finds an equation that has not been run for that flow shapefile it will list the equation as in the box below The HSM Equation examplel species lifestage 1 57 54017026 2 718282 1 141814 4 83317 7 depth 4 i 3 476033 velocity 4 0 1908487 depth velocity 1 738853 depth 2 4 073766 velocity 2 0 156164 depth 3 10 2655 velocity 3 If it does not find a new equation it will move on to step 6 5 Click OK The program will then query the shapefile dbf file and select only those values for processing that are within the minimum and maximum ranges of depth and velocity for the species life GIS Based Weighted Useable Area Modeling Manual Flathead River Prepared for Montana Fish Wildlife and Parks 9 9 15 03 Copyright MEC SSI 2003 Miller Ecological Consultants Spatial Sciences amp Imaging stage using the name hmm file It will then process the Depth and Velocity data to produce a new fish species life stage field in the shapefile dbf 6 After it completes step 5 the program will ask which species life stage that you want to further process for a surface and create the output files In this case we want to use the example field in the list See below
61. coefficients 13 Repeat these steps for each species and life stage to develop a series of equations for habitat suitability B Quality Control Measures Quality control of the calculation of bivariate habitat suitability functions using the above process requires at a minimum that Montana Fish Wildlife and Parks return to Miller Ecological Consultants Inc copies of the following for each species and life stage analyzed DAG Boundary values for the input Depth Velocity observations Dmax Vmin V max 3D Bivariate Histogram and Rotated 3D Bivariate Histogram plots 3D Surface and Rotated 3D Surface plots of the 3D Bivariate Histogram 3D Surface Data Matrix DVZ table Description of the Model Inputs used in fitting an equation to the DVZ table Evaluation of the Model Fit for the final equation including Model equation Parameter estimates and R value Graph of the Fitted 3D Function Rotated graph of the Fitted 3D Function Plot of the Frequency Distribution of Residual Values Normal Probability Plot of the Residuals Plot of Observed versus Predicted Values Habitat Suitability Index SI Normalizing term used to set maximum habitat suitability index 1 0 Bonneville Power Administration Technical Report May 24 2001 Miller Ecological Consultants Inc Page 21 Miller Ecological Consultants Inc 1113 Stoney Hill Drive Suite A Fort Collins Colorado 80525 970 224 4505
62. cover data was collected using visual or tactile methods to determine sediment at cross sections established for the IFIM modeling Habitat suitability was developed concurrently in BPA Project 9401000 The data from that project Muhlfeld 2002 was used as input to the habitat model for the IFIM analysis River hydrology for determining flow scenarios and flow operations was calculated using existing hydrology from USGS records for the Flathead River and Hungry Horse Dam A flow time series was constructed using approximately ten years of daily flow data and incorporating that into a spreadsheet for flow comparison alternatives Flow comparisons were made for both flow scenarios The specific methods for the project are listed below River Channel Change Analysis and Land Use Land Cover Mapping The main objectives of this portion of the project were 1 Identify areas of the Flathead River channel that are dynamically changing and 2 Map land use and land cover along the river A detailed description of the land use land cover mapping is provided in Appendix A This task involved processing the river channel and land use land cover data to produce deliverable products The old and new river channel GIS layers were overlain to produce a layer that identifies all of the areas where the river course has shifted between the two time periods This simple change layer highlights the most dynamic reaches of the river A second analysis utilized historical
63. dicted water surface elevations for three flows at Reach 1 Flathead Instream Flow Investigation Project Page 17 Miller Ecological Consultants Inc September 29 2003 E Predicted O Observed Number of Observations Mean Column Velocity m s Figure 10 Histogram of observed and predicted water velocities for 246 55 cms at Reach 1 Cross Section 10 File Options Help Fiver RIVERA x each Reach 1 River Sta s x BPA Reach One Plan Imported Plan 02 2 5 1 1 5 104 k 5 920 En ELE T Elevation 910 40 20 D 20 40 50 80 100 12 ating fond Figure 11 Water surface elevations at a range of discharges for Site 1 Flathead River Flathead Instream Flow Investigation Project Page 18 Miller Ecological Consultants Inc September 29 2003 Hydrology time series Reaches 1 and 2 3000 0 2500 0 2000 0 T gt 1500 0 Pre dam 1940 49 S s Post dam 1993 2002 5 2 1000 0 500 0 0 0 Figure 12 Hydrology time series Reaches 1 and 2 Flathead Instream Flow Investigation Project Page 19 Miller Ecological Consultants Inc September 29 2003 Hydrology Time series Reach 3 3000 0 2500 0 2000 0 E gt 1500 0 Pre dam discharge 1940 49
64. e Flathead River from the confluence of the South Fork of the Flathead River near Columbia Falls south to the Flathead Lake inlet It was determined at the project initiation meeting that land cover would be mapped within one half mile of the furthest outlying river channel Figure 1 Flathead River Study Area 0 x Montana Kalispell 3 0 Classification Scheme It was determined during the project initiation meeting between MFW amp P and SSI that the following land cover classes would be mapped for the study area Classes mapped at a larger scale were facilitated through the collection of data during two days of fieldwork Channel characteristics such as erosive banks and stabilized banks were captured in vector format because of their linear nature The vectors were coded by height as shown below in Table 1 See Appendix A for class definitions Table 1 Final Land Cover classification scheme Class Format Mapping Source Scale Domestic raster 1 24 000 IRS 1C Imagery Agriculture raster 1 24 000 IRS 1C Imagery Grasslands raster 1 24 000 IRS 1C Imagery Forest raster 1 24 000 IRS 1C Imagery Willow raster 1 12 000 IRS 1C Imagery Bare rocky lands raster 1 24 000 IRS 1C Imagery Water raster 1 24 000 IRS 1C Imagery Steep highly erosive banks vector 1 12 000 Field work lt 5 feet 6 10 feet gt 10 feet Stabilized banks vector Field work Automobiles Rock Rip Rap Cobbles 4 0 Data Used 4 1 IRS
65. e cutthroat habitat versus 30 Figure 26 Annual habitat time series Reach 1 West slope cutthroat summer 32 Figure 27 Annual habitat time series Reach 1 West slope cutthroat trout winter 33 Figure 28 Habitat time series Reach 1 West slope cutthroat trout 34 Figure 29 Habitat time series Reach 1 West slope cutthroat trout winter 35 Figure 30 Annual habitat time series bull trout subadult night 36 Figure 31 Annual habitat time series Bullt rout subadult day 37 Figure 32 Annual habitat time series Reach 1 Bull trout adult sss 38 Figure 33 Habitat time series Reach 1 Bull trout subadult night esses 39 Figure 34 Habitat time series Reach 1 Bull trout subadult night esses 40 Figure 35 Habitat time series Reach 1 Bull trout adult eene 41 Figure 36 Annual habitat time series Reach 2 West Slope cutthroat trout summer 42 Figure 37 Annual habitat time series Reach 2 West Slope cutthroat trout winter 43 Figure 38 Habitat time series Reach 2 West Slope cutthroat trout summer 44 Figure 39 Habitat time series Reach 2 West Slope cutthroat trout wimter sss 45 Figure 40 Annual habitat time series Reach 2 Bull tr
66. ecified with the and operators See the STATISTICA manual sections for General Syntax Conventions Regression Equations Loss Function for the proper syntax if another loss function is desired Next click OK to return to the User Specified Regression Function dialog box There should be no missing data so just click OK Running the Regression and Evaluating the Model Fit The Regression Model dialog box opens and displays the model number of parameters equation coefficients loss function dependent and independent variables missing data strategy and number of valid cases rows in the data matrix The recommended Estimation Method is the default Quasi Newton Hanson 1988 Bovee 1986 This is a reliable and fast estimation subroutine and works well with most datasets Make sure these inputs are correct then click OK STATISTICA begins the regression calculations and displays its progress in the Parameter Estimation dialog box The number of iterations performed loss and coefficient values are shown and if successful the message Parameter Estimation Process Converged appears in the bottom of the box If the estimation does not initially converge try several more attempts continue If the parameter estimation process will not converge try specifying different orders of the depth and velocity terms and different usually less interaction terms If the estimation process still does not converge repeat these adjustments using a diff
67. ed to collect ground control points for rectification No irregularities were encountered during the rectification process and a RMS error of less than 0 5 was attained for both of the satellite scenes 6 3 Ground Truth Data Collection Fieldwork was required to collect data that was not discernable on the satellite imagery and also to provide additional ground truth for areas adjacent to the river channel for the 1998 classification A piloted boat was provided by MFW amp P for two days to allow two image analysts from SSI to map channel features and adjacent land uses and land cover Natural color aerial photography printed at 1 15 840 scale was used as a basemap for mapping features such as eroded banks stabilized banks and willows These data were then digitized to create a digital georeferenced data set that could be used to enhance the land cover classification derived from the IRS image Table 5 shows the data created from the fieldwork completed in July 1999 Table 5 Data Collected During Field Work Feature Class Erosive Bank lt 5 feet 6 10 feet gt 10 feet Stabilized Bank Automobiles Rock Rip Rap Cobbles Willows Willows 6 4 Classification The enhanced IRS data was processed using an ISODATA clustering routine which groups the image into spectral clusters The number of spectral clusters output by the ISODATA routine is specified by the image analyst and depends on the spectral variability of the data For the
68. erent Estimation Method Click OK when the Parameter Estimation Process is complete Bonneville Power Administration Technical Report May 24 2001 Miller Ecological Consultants Inc Page 7 The Results dialog box is opened From here the investigator can review many different displays of the resulting fit of the equation The Parameter Estimates Fitted 3D Function and Observed Values and Distribution of Residuals are a recommended minimum for reviewing the results see Figures 6 through 9 It is quite helpful to print the Fitted 3D Function and Observed Values graph and Parameter Estimates showing R and Variance Explained WO values for later comparisons Observe the Coefficient of Determination R and values assigned to the Equation Coefficients parameters The Coefficient of Determination evaluates how well the values predicted by the model matched the actual values The Equation Coefficients offer insight to the relative importance of each term in the equation If an Equation Coefficient approaches 0 then consider omitting that term in the next running of the model The Normal Probability Plot of Residuals and Predicted vs Observed Values plot are also useful for comparisons between different model runs see Figures 10 and 11 Click OK to complete this regression and return to the User Specified Regression Function dialog box Note that some functions are too complex and cannot be printed within the Results dialog box These functi
69. ermit this program to be used on more than one computer at any one time This license is not for sale and it may not be assigned or sublicensed to anyone else Title and copyrights to the program and the accompanying documentation and any copies remain with SSI MEC If you do not comply with any of the above restrictions this license will terminate you will be liable to SSI MEC for damages or losses caused by your non compliance and SSI MEC will be entitled to a court order which will require you to comply LIMITED WARRANTY AND DISCLAIMER If within 30 days from your first use of this product you are not satisfied with it for any reason you should stop using it and notify SSI MEC If you return to SSI MEC any materials that SSI MEC has sent to you in connection with the product SSI MEC will at your option either refund your purchase price or replace the product and related materials SSI MEC S LIABILITY IS LIMITED TO THE REPLACEMENT OF THE PRODUCT AND RELATED MATERIALS OR THE REFUND OF THE PURCHASE PRICE THIS IS THE ENTIRE LIABILITY OF GIS Based Weighted Useable Area Modeling Manual Flathead River Prepared for Montana Fish Wildlife and Parks 4 9 15 03 Copyright MEC SSI 2003 Miller Ecological Consultants Spatial Sciences amp Imaging SSI MEC AND IS YOUR EXCLUSIVE REMEDY SSI MEC SHALL NOT BE LIABLE FOR ANY OTHER DAMAGES OR LOSSES INCLUDING DIRECT INDIRECT SPECIAL INCIDENTAL OR CONSEQUENTIAL DAMAGES OR LOSS OF PROFITS TO YOU OR
70. et The details of the habitat time series are presented in the Instream Flow Project Report GIS Based Weighted Useable Area Modeling Manual Flathead River Prepared for Montana Fish Wildlife and Parks 13 9 15 03 Copyright MEC SSI 2003 Appendix Example GIS output from Weighted Useable Area Model Site 2 Juvenile Bull Trout juvbtwinnight Juvenile Bull Trout Reach 1 amp 2 winter night Jbt 1415b Jbt 849 Jbt 594b Jbt 424b Jbt 339b Jbt 283b Jbt 246b Jbt 226b Jbt 189b Jbt 127b Jbt 105b MEC pores qa Cos a C 105 bw s 2 Histogram of juvbtwinni as a Surface from 105c Histogram of Juvbtwinni as a Surface from 105cms bw 8 Value 35000 30000 25000 20000 15000 10000 5000 0 Juvenile Bull Trout 105 cms juvbtwinnight Juvenile Bull Trout Reach 1 amp 2 winter night Jbt 1445b Jbt_84ab J0 h59 Jbt_424b Jbt 339b Jbt 283b Jbt 248b Jbt 226b E xp AC ARE b s n Jbt 189b w Jbt 127b _ Jbt 105b 127 cms_bv s 2 Histogram of juybtwinni as a Surface from 127cms_ ES Histogram of juvbtwinni as a Surface from 127cms bv 25000 20000 15000 10000 5000 Il gt 064 001 0 2 0 2 0 3 0 3 0 4 0 4 0 5 0 5 0 5 07 Wu og Woo oo Woo in Juvenile Bull Trout 127 cms 5 juvbtwinnight Juvenile Bull Trout Reach 1 amp 2 winter night Jbt1a45b gt Jbt_84ab Jbt 594b Jbt
71. gression model The investigator must specify this model in the Nonlinear Estimation module An exponential polynomial equation is fit to the three dimensional surface by regressing the independent depth and velocity variables onto the dependent variable histogram frequency surface This equation is of the form Z exp bo biD b4D b45V where Z number of fish observed D water column depth V average water column velocity bo bi 62 equation coefficients and is fitted to the surface using a least squares regression technique Prewitt 1982 Bovee 1986 The results are displayed in several ways which are analyzed to test the fit of the equation Hanson 1988 Once a final equation is chosen the data are normalized to provide a maximum output value of 1 Specifying the Input and Model To begin the regression of depth and velocity on the Z surface click on the STATISTICA Module Switcher gt Nonlinear Estimation and click the Switch To button The Nonlinear Estimation Panel will open Click cancel on the Nonlinear Estimation Dialog Box From the pull down menus select File gt Open Data which brings up the Open Data File Dialog Box Select the previously saved 3D Surface Data Matrix e g DVZTbl and click Open This opens the data file created in the previous section within the Nonlinear Estimation Panel From the pull down menus select Analysis gt User specified regression which opens the
72. h Fork Flathead River downstream to Flathead Lake to determine changes in habitat availability for fish in the Flathead River as a function of changes in river flow The goal of this study was to provide the physical framework for assessing changes in physical habitat in the river as a function of flow for the species of interest and provide the tool for decision makers to assess tradeoffs in river management scenarios The basis for this GIS approach comes from the Instream Flow Incremental Methodology and is patterned after Bovee 1982 Bovee et al 1998 We used the components of physical hydraulic simulations habitat suitability data and the GIS analysis tool to develop habitat versus discharge functions for the Flathead River Components needed for this methodology include habitat use information for the species of interest physical geometry and hydraulics information of geo referenced physical data collected at each study site Data included bed topography bathymetry depth velocity substrate cover and water surface elevations These data provide the physical framework for habitat analysis These physical data are then placed into a two dimensional hydraulic simulation where the field data is used to construct the model data sets Models are calibrated for measured flows and hydraulics simulated for the flows of interest All output is geo referenced for each study site and the hydraulic simulations for each study site are passed to the ha
73. h data and the 1998 IRS land cover classification were used to create this layer which identifies the from and to classes of change A spatial model was developed to further classify the type of change identified in the results of the simple change analysis Areas that had changed from water in 1990 to a class other than water in 1998 were coded using the values of the1998 land cover classification as the to class Since there was not any land cover established for the 1990 data beyond the water class areas that had changed from a land cover class other than water had to be manually interpreted from the 1990 DOQQ data The results produced a detailed from and to change analysis layer mapped at approximately 1 12 000 scale Table 6 shows the from and to classes and amounts identified for each class Table 6 Results of the Detail Change Detection Analysis Change Type Acres pru UE 14 Example of Detail Change Detection Data IRS 1C Panchromatic image used as a backdrop Legend No change Water to grass P Agriculture to water Water to forest Grassland to water Water to barren 7 Forest to water Water to willow Barren to water Figure 5 Example of detailed change detection analysis 15 6 9 Classification Accuracy Assessment After completion of the 1998 IRS classification accuracy assessment was performed This task was accomplished by analyzing 100 randomly selec
74. he general type of change Table 6 shows amount of change identified Table 6 Results of the Simple Change Detection Analysis Simple Change 1978 1990 from land surface to water from water to land surface 1978 1998 from land surface to water from water to land surface 1990 1998 from land surface to water from water to land surface The simple change analysis was extended to include the time span between 1937 38 and 1978 1990 and 1998 Black and white aerial photos were acquired from federal archives of the Agricultural Stabilization and Conservation Service Twenty seven photos from three dates of acquisition were available to make up the composite image for the Flathead River The dates are 8 16 1937 8 29 1937 and 5 21 1938 The recorded flow of the river for each date were 2 910 cfs 2 200 cfs and 26 100 cfs respectively The four photos from the high flow date of 5 21 1938 covered an east west strip approximately midway between the upper and lower ends of the study area The photos were scanned rectified to the project coordinate system and mosaiced into one seamless image Within the mosaicing process steps were taken to minimize the area used from the high flow date photos 10 The river channel was digitized and converted to a raster image file for processing The results of each date comparison are shown in Table 7 below Table 7 Results of the Simple Change Detection Analysis 1937 1978 1990 1998 Simple Ch
75. hich if any outlying or questionable data points should be removed The researcher should become familiar with each data set and know the range of values mean standard deviation and distribution characteristics before progressing to any regression analysis Bonneville Power Administration Technical Report May 24 2001 Miller Ecological Consultants Inc Page 1 Record the boundary values from the depth and velocity observations Dmin Dmax Vmin V max These boundaries set the range over which the habitat suitability functions can be applied since the functions are fit within these bounds and are not representative outside the scope of the input data It is recommended that all data be plotted and visually inspected again after the depth velocity matrix is complete CREATING THE 3D BIVARIATE HISTOGRAM The goal of data processing is to reduce raw frequency data down to an easily interpreted graphical display This represents the behavioral response of a species with respect to environmental parameters Bovee 1986 The 3D Bivariate Histogram takes observations of water depth and velocity in habitat utilization by fish and displays the frequency of use for each combination of these variables The graphical display of these behavioral observations serves as the basis for the regression analysis From the STATISTICA Basic Statistics module open import the desired data file From the Graphs pull down menu select Stats 3D Sequential Graphs
76. hree reaches Species with several life stages have similar patterns of weighted useable area discharge functions in reach 1 Bull trout habitat versus discharge shows a similar relationship with the highest weighted useable area occurring at the lower flows and value of weighted useable area being reduced at higher flows for both day and night usage and for adults Figure 16 West slope cutthroat trout for fall and winter criteria and summer show a similar relationship with the highest weighted useable area at the lower flow conditions Figure 17 Both of these species show that the useable habitat area is more widely distributed through the channel at the lower flow conditions than they are at the high flow conditions This is likely a result of the increased velocities that occur as flows increase with most of the habitat occurring along the lower velocity margins of the river and around the islands rather than in the main channel Figures 18 through 21 The reduction in suitable near shore habitat is particularly important for bull trout subadults Muhlfeld 2003 reports a distinct difference in diel habitat use by subadult bull trout The shallow habitat near the river shorelines is used at night by subadult bull trout The quality of this habitat is higher when the river is stable for longer periods several weeks and benthic productivity can increase Habitat areas for both bull trout and west slope cutthroat trout for reach 2 shows similar res
77. ies Bullt rout subadult day Pre Dam Post Dam Flathead Instream Flow Investigation Project Miller Ecological Consultants Inc Page 37 September 29 2003 Annual habitat time series Reach 1 Bull trout adult 1 600 000 1 400 000 1 200 000 1 000 000 lt 800 000 Pe 2 600 000 400 000 200 000 0 OQ tc x pe ot e qe XL SE QU x o5 XS aS Gi el e oe 5 e e Or e eA Date Figure 32 Annual habitat time series Reach 1 Bull trout adult 12 31 Pre Dam Post Dam Flathead Instream Flow Investigation Project Miller Ecological Consultants Inc Page 38 September 29 2003 Habitat time series Reach 1 Bull trout subadult night 1 000 000 H Li T KI H wll 900 000 v HEAT EY N H n jM vil Pi P H Wa Al d 1 H H j Bb oc i I af 800 000 Mi B H db H M i L a d 1 i U MS 2 da IA d 700 000 td jh nn ah AJ H I E T d 1 l ii 1 i M L T LIE ih RM 600 000 k utl g wheel Pe WW i d gouge H d A n 500 000 4 uL d d E d
78. ion makes a useful point of comparison as the curve fitting results in Nonlinear Regression are displayed similarly Figure 3 3D Surface Plot of the Bivariate Histogram Data Bivariate Histogram Total Depth Mean Velocity Number of Fish z gt gt lt RS Tu aS CREATING THE 3D SURFACE DATA MATRIX The Nonlinear Estimation process uses a matrix containing the observations of depth and velocity independent variables and frequency dependent variable from the 3D Bivariate Histogram The Nonlinear Estimation process will analyze each depth bin against each velocity bin and use the corresponding frequency Z value to calculate regression coefficients for the exponential polynomial Therefore each permutation of depth and velocity bins along with the corresponding frequency Z value must be set up in the 3D Surface Data Matrix Create a new data file for the 3D Surface Data Matrix using the File pull down menu File gt Open other gt New data STATISTICA prompts you to name this new file e g DVZTbI then click Save This brings up the new blank data file that must now be sized to accommodate the Graph Data from the 3D Bivariate Histogram The number of cells in the histogram determines the size of the new data file In the example provided the histogram contains 7 ranges for values of both Tot Dep and for Mean Vel i e both data sets are grouped into 7 bins Note that a square matrix is not necessary This
79. is case it was sometimes challenging to separate the boundary between trees and water using the IRS imagery The Barren class showed slight confusion with several of the other classes This confusion seems to represent the natural intermixing of the Barren class with Willow Agriculture and Grassland The willows were found mainly on rocky substrates within the channel and intermixed with the Barren class which represented the rocks Confusion with the Agriculture class and Grassland class appeared to be a result of the spectral reflectance of the soil being stronger than the spectral reflectance of the sparse vegetation 7 2 Change Detection Analysis The Simple Change data created accurate representations of the dynamic river channel over the span of twenty years Differences in water levels may have contributed to false change identification The 1990 data had a flow level that was 7 5 times the flow during the acquisition of the 1998 IRS imagery Although certain types of change may have been influenced by the difference in water levels true changes in the channel s extent were detected The Detail Change went a step further to identify exactly what types of changes had occurred during the 1990 1998 time period This process required manual interpretation of the historic land cover present in the 1990 DOQQ data where change was identified A portion of the areas identified in the Simple Change layer were not identified further if there was
80. ities are provided by the 2 D hydraulic modeling Specific habitat criteria developed from the suitability analyses described above are then used to conduct GIS queries In this way the amount of area within the study site that matches a particular species habitat use can be determined for a specified flow rate Multiple layers of usable habitat were generated corresponding to each species life stage and flow of interest The analysis can be output as a 2D map and linked to a GIS base map or plotted as hard copy for visual presentation of the results Summation of total habitat for each species and simulated flow results in a habitat flow relationship by species that becomes input for the habitat time series analysis Habitat Time Series The actual habitat experienced by the fish in any river depends on the flow regime of the river The development of habitat conditions over a period of time is an integral part of the comparison of flow regimes Habitat time series is the decision point in IFIM Bovee 1982 Habitat time series analysis requires the following data total usable habitat for each species and life stage at each flow of interest preferably over a range from normal high to low flow hydrology data for current conditions usually weekly or daily flow for a range of water years and hydrology for the proposed operation for the same dates as the current conditions MEC conducted time series evaluations on several different flow regimes
81. ject Page 25 Miller Ecological Consultants Inc September 29 2003 5 juvbtwinnight Juvenile Bull Trout Reach 1 amp 2 winter night Jbt 1445b Jbt_84ab Jbt 504b Jbt 424b Jbt 330b Jbt 283b Jbt 246b Jbt 226b Jbt 160b Jbt 127b Jbt 105b S ems bus Histogram of juvbtwinni as a Surface from 169c DKG Wis Histogram of juvbtwinni as a Surface from 169 8 16000 14000 12000 10000 8000 5000 4000 2000 Figure 19 Bull trout sub adult night habitat area 169 cms Reach 2 Flathead Instream Flow Investigation Project Miller Ecological Consultants Inc Page 26 September 29 2003 5 wctilwin West Slope Cutthroat Reach 1 winter day Wim 1445 Wie _848 594 im 424 Ww 339 Ww 283 Wim 246 W tw 226 Ww 169 Wim 127 ww 105 4 105cms flow shp mj E B ml m El El Histogram of wctrlwin as a Surface from 105cm Histogram of wctrlwin as a Surface from 105cms flow 8 Value 0 0 0 1 10 1 0 2 E10 2 0 3 Elo 3 0 4 El0 4 0 5 0 5 og Bo5 07 Wo og Woo 0 3 Figure 20 West slope cutthroat trout habitat area 105 cms Reach 2 Flathead Instream Flow Investigation Project Miller Ecological Consultants Inc Page 27 September 29 2003 wetriwin West Slope Cutthroat Reach 1 winter day Wie _1415 tw 849 594 Wim _424 Wim 339 Wie 28
82. lathead River Site 2 105 cms Flathead Instream Flow Investigation Project Page 9 Miller Ecological Consultants Inc September 29 2003 R2 105 All O 10000 000 Figure 5 Example of velocity contours Flathead River Site 2 105 cms Habitat Suitability Curves Species habitat suitability criteria are required for the habitat analysis The recommended approach is to develop site specific criteria for each species and life stage of interest Habitat suitability criteria that accurately reflect the habitat requirements of the species of interest are essential to conducting meaningful and defensible instream flow analyses The curves used in this study will fit that criterion Site specific curves were developed for the study by Muhlfeld 2002 Calculation of habitat suitability criteria for a two dimensional hydraulic model requires use of a bivariate analysis of depth velocity paired data to calculate fish preference for depth and velocity in the stream reach An analysis approach was developed by Miller Ecological 2001 Appendix C for this suitability criteria A bivariate statistical analysis was used to develop habitat suitability criteria for each species with sufficient data This analysis first plotted bivariate histograms then converted those Flathead Instream Flow Investigation Project Page 10 Miller Ecological Consultants Inc September 29 2003 to 3 dimensional surface and finally computed a polyn
83. lows for low mid and high flow ranges Figure 9 Water velocities were measured at mid flow for all three study sites A comparison of measured water velocity to predicted shows that the predicted velocities in general match measured water velocities with a slight underprediction Figure 10 Habitat suitability data were applied for west slope cutthroat trout for reach 1 and 2 summer and winter curves and west slope cutthroat trout year round for reach 3 Muhlfeld 2002 In addition bull trout sub adult criteria for day and bull trout sub adult criteria for night were applied to sites 1 2 and 3 Bull trout adult data were applied to reaches 1 2 and 3 The only diel comparison was made for sub adult bull trout in reaches 1 and 2 Model hydraulics show that both depths and velocities vary as expected for each of the sites and reaches See distribution CD There is a significant difference between the wetted channel width for the 105 cms and the 169 cms values in riffle areas Fluctuations in riffles between these two flows can reach approximately 40 meters Figure 11 Hydrology time series was generated for pre dam and post dam conditions to compare the unregulated and regulated system The main differences in the hydrology are shown in the winter baseflow period where post dam flows are highly variable and in the reduction of peak flows during certain conditions especially during peak snowmelt runoffs Historically pre dam conditions had su
84. lt S I 2 000 000 i G L L 1 500 000 ui EE 1 000 000 500 000 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 Date Figure 44 Habitat time series Reach 2 Bull trout subadult day 4 1 10 1 4 1 10 1 4 1 10 1 4 1 Flathead Instream Flow Investigation Project Miller Ecological Consultants Inc Page 50 September 29 2003 Habitat time series Reach 2 Bull trout adult 3 500 000 Pre Dam Post Dam 3 000 000 1 i T i i 1 1 2 500 000 e H E L i y L 2 000 000 1 4 5 5 1 500 000 i X 1 000 000 500 000 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 Date Figure 45 Habitat time series Reach 2 Bull trout adult 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 Flathead Instream Flow Investigation Project Miller Ecological Consultants Inc Page 51 September 29 2003 Annual habitat time series West slope cutthroat trout 6 000 000 5 000 000 4 000 000 3 000 000 Habitat area m2 2 000 000 1 000 000 1 1 1 15 1 29 2 12 2 26 3 12 3 26 4 9 4 23 5 7 5 21 6 4 6 18 7 2 7 16 7 30 8 13 8 27 9 10 Date Figure 46 Annual habitat time series West Slope cutthroat trout 9 24 10 8 10 22 11 5 11 19 12 3 12 17 12 31 Pre Dam Post Dam
85. lts of this analysis These procedures and software routines have been developed from standard IFIM procedures with field survey and GIS data While this procedure is not specific to this data or project the equations or data used may need to be modified to accommodate other fish species life cycles or other project requirements This report will discuss raster and vector GIS data processing The GIS work uses ArcView and ESRI Spatial Analyst processes modules and terms The vector processing terms coverage theme and shapefile are used interchangeably Note on filename conventions Several different file formats are used in this procedure You will use ArcView shapefiles and grid raster files ASCII and comma delimited text files and Microsoft Excel files They will all be referred to by their root coverage name Approved systems required for processing Software 1 ArcView 3 2a 2 Spatial Analyst extension Hardware 1 PC Workstations 256 Mbytes RAM and at least 250 Mbytes swap space Enough available disk space for your project 2 Networked printer 3 Tape Backup System Notes Terms This manual was written with the assumption that the reader or user is proficient with ESRI s ArcView Spatial Analyst Microsoft Windows environments and GIS concepts and PC hardware For more detailed information on specific processes or software use please refer to the software manuals or manufacturers online help sys
86. magnitudes late summer may be just as disruptive as the smaller fluctuations that occur in the winter period Fluctuations in the summer with the higher discharges may be more disruptive to younger life stages which have less ability to move about the channel and are required to move more often to find better habitat An illustration of that was shown in the overlay maps with the 105cms and 169cms values that show that the habitat areas change substantially when flows change The results of this study can be used by Montana Fish Wildlife and Parks for incorporation into flow recommendations for the Flathead River The data presented here can incorporate operational constraints for both the thermal regime and spatial variability of habitat within the Flathead River Flathead Instream Flow Investigation Project Page 60 Miller Ecological Consultants Inc September 29 2003 LITERATURE CITED Bovee K D 1982 A guide to stream habitat analysis using the Instream Flow Incremental Methodology Instream Flow Information Paper 12 U S Fish and Wildlife Service FWS OBS 82 26 Bovee K D 1989 Determination of reach lengths and weighting factors using Habitat Mapping data PHABSIM Technical Note 48 Unpublished U S Fish and Wildlife Service Fort Collins CO Bovee K D B L Lamb J M Bartholow C B Stalnaker J Taylor and J Henriksen 1998 Stream habitat analysis using the Instream Flow Incremental Methodology U S Geological Sur
87. mmer Flathead Instream Flow Investigation Project Page 32 Miller Ecological Consultants Inc September 29 2003 Annual habitat time series Reach 1 West slope cutthroat trout winter 1 200 000 1 000 000 800 000 x E S 5 i PreD 5 600 000 REIS vU 5 5 H 400 000 200 000 0 x 10 O N Pr D Q TWA OO v OQ oco Uoc o xD Xo Wn XO Le 5 ee a XO Date Figure 27 Annual habitat time series Reach 1 West slope cutthroat trout winter Flathead Instream Flow Investigation Project Page 33 Miller Ecological Consultants Inc September 29 2003 Habitat time series Reach 1 West slope cutthroat trout summer 1 400 000 1 200 000 TN I 1 000 000 1 i i Vi I 800 000 8 9 A Pre Dam lt 1 Post Dam 5 5 600 000 400 000 200 000 0 1 01 Ur 1 01 Ur 1 01 Ur 1 01 Ur 1 01 Ur 1 01 Ur 1 01 Ur 1 01 Ur 1 01 Ur 1 01 Ur Date Figure 28 Habitat time series Reach 1 West slope cutthroat trout summer Flathead Instream Flow Investigation Project Page 34 Miller Ecological Consultants Inc September 29 2003 Habitat time series Reach 1 West slope cutthroat trout winter 1 200 000 1 000 000 800 000 ee e SC 600 000 Habitat Area m2 1 1 400 0
88. mmer peak flows during snowmelt of over 2 000 cms and very stable but lower baseflows Current post dam conditions show that the baseflow period can vary by as much 200cms or more and that peak flows are generally less than 1 500 cms Figure 12 There is a similar representation of high hydrology for reach 3 The difference between hydrology in reach 3 and reaches 1 and 2 is the additional inflow from the White Fish and Stillwater rivers that enter the Flathead at the upstream end of reach 3 Figure 13 Average annual hydrology were developed from the 1940 49 pre dam data and the 1993 2002 post dam hydrology These annual hydrographs allow the comparison of baseflow and peak flow conditions to show the differences between those two seasonal characateristics Figures 14 and 15 The baseflow period is much more variable in the post dam hydrology and peak flows truncated when compared with the pre dam hydrology showing very stable baseflows and higher peak flows Flathead Instream Flow Investigation Project Page 16 Miller Ecological Consultants Inc September 29 2003 105 17 m s Water Surface Elevation 246 55 m s Predicted Observed Water Surface Elevation m 916 5 916 915 5 594 65 2 5 920 5 920 919 5 Water Surface Elevation 2 0 1 2 3 4 5 6 Continuity Line Figure 9 Observed versus pre
89. not substantial evidence in the data that true change had 17 occurred Some of these uncharacterized areas were influenced by tree canopies and shadows that extended into the river channel due to the off nadir look angle inherent in the DOQQ data The types of detailed changes identified can be divided into two broader categories for comparison purposes change from Water in 1990 and change to Water in 1998 Approximately 30 000 acres of land cover fell into from Water while only 3 300 acres were classified as to Water The large amount of land cover identified as from Water is due to the increased flow of water in the 1990 data Those areas classified as to Water are more indicative of true change representing a loss of landmass due to erosion 8 0 Deliverables The following products were delivered for the Flathead River 1937 river channel in Shapefile format 1978 river channel in Shapefile format 1990 river channel in Shapefile format 1998 river channel in Shapefile format 1978 1990 simple channel change in Shapefile format 1978 1998 simple channel change in Shapefile format 1990 1998 simple channel change in Shapefile format 1998 land cover classification in Shapefile format 1990 1998 From and to change analysis file in Shapefile format 1999 channel characteristics derived from fieldwork in Shapefile format Metadata for the above Shapefiles IRS sa
90. ntinuous surface by extrapolating between points using Inverse Distance Weighting algorithm This distance and the grid cell size are selected by the operator 4 Calculates total habitat within the 0 1 0 range in 1 increments Creates bar chart showing the distribution of the habitat per increment 5 Creates a permanent ESRI GRID file of the habitat This process is discussed in more detail in Appendix WUAM User Manual 16 7 0 Results Analysis 7 1 Land Cover Classification The land cover classification derived from the enhanced IRS 1C imagery proved to be an accurate representation of the river channel and the adjacent lands providing an overall classification accuracy of 91 Due to spectral similarities between Agriculture lands and Grasslands many of the Agriculture lands were delineated manually Grasslands were recoded to agriculture if the land use pattern indicated agricultural practices were being applied Since these classes were very similar in the spectral response it was not unexpected to see some Grassland and Agriculture confusion in the accuracy assessment table Water and Forest classes did extremely well in the accuracy table Deep clear water and coniferous forests are spectrally similar and are often confused with each other Some confusion of this nature had to be edited out but the amount was minimal Some Forest may be confused with water where coniferous trees are growing next to the river In th
91. omial expression to compute suitability values that replicate the 3 D surface GIS Model The basis for this GIS approach comes from the Instream Flow Incremental Methodology and is patterned after Bovee 1982 Bovee et al 1998 We used the components of physical hydraulic simulations habitat suitability data and the GIS analysis tool to develop habitat use information The original concept for this approach was presented in Miller Ecological Consultants Inc and SAIC 2000 The current application of the GIS approach included a time series analysis of habitat based on flow scenarios in the Flathead Components needed for this methodology include habitat use information for the species of interest physical geometry and hydraulics information of geo referenced physical data collected at each study site Data included bed topography bathymetry depth velocity substrate cover and water surface elevations These data provide the physical framework for habitat analysis These physical data are then placed into a two dimensional hydraulic simulation where the field data is used to construct the model data sets Models are calibrated for measured flows and hydraulics simulated for the flows of interest All output is geo referenced for each study site and the hydraulic simulations for each study site are passed to the habitat component GIS Based Weighted Usable Area Model After pre processing data for habitat suitability and hydraulic simul
92. ons can be copied into the 3D XYZ Graphs Select Graphs gt 3D XYZ Graphs gt Surface Plots In the 3D Surface Plots dialog box assign the variables in the proper order and select Custom Function and enter the fitted equation and coefficients These variables must be entered as x y z in the Custom Function Figure 6 Parameter Estimates coefficients for the regression equation Bonneville Power Administration Technical Report May 24 2001 Miller Ecological Consultants Inc Page 8 Figure 7 Graph of the Fitted 3D Function and Observed Values Use the same commands to rotate the Graph of the Fitted 3D Function and Observed Values as in the 3D Bivariate Histogram section This allows the researcher to view all aspects of the goodness of fit accomplished in the estimation process see Figure 8 Figure 8 Rotated Graph of the Fitted 3D Function and Observed Values Bonneville Power Administration Technical Report May 24 2001 Miller Ecological Consultants Inc Page 9 Figure 9 Frequency Distribution of the Residual Values Figure 9 5 Frequency Distribution Residuals Frequency Distribution Residuals 14 S P 6 0 Ul d SE Figure 10 Normal Probability of the Residual Values Expected Normal Value Residuals Bonneville Power Administration Technical Report May 24 2001 Miller Ecological Consultants Inc Page 10 Figure 11 Plot of Observed versus
93. ormat click the Convert to GRID button 4 This will make a ESRI GRID file and replicate the suitability categories of the original file The program will ask if you want to add the GRID file as a theme to the current view Click Yes UM 5 The graphic below shows the results GIS Based Weighted Useable Area Modeling Manual Flathead River Prepared for Montana Fish Wildlife and Parks 12 9 15 03 Copyright MEC SSI 2003 Miller Ecological Consultants Spatial Sciences amp Imaging 6 The summary csv looks like this ICLASS LABEL COUNT CellSize Area 1017 25425 935 23375 550 13750 280 7000 169 4225 134 3350 58 1450 42 1050 32 800 10 0 9 1 0 12 300 5 5 5 5 5 5 5 5 5 5 H example1_s Flow 339cms_ flow shp _ 1 Draw AutoShapes N w 4 5 A bii ae EE Definitions Class Label the class category of habitat suitability Count the number of pixels or raster cells represented in the class category CellSize the number 5 means the pixels are 5 by 5 or 25 sq ft in area Area total area of the class category in sq ft The area calculations listed in the example above are used in the habitat time series analysis The values in column E are summed to provide the total habitat for the site for each flow modeled The total habitat and discharge are either typed or copied into the appropriate location in the habitat time series spreadshe
94. ory definitions and Contents river reach n heq hat misc geographic data time series grids Contains nested project directories for the river being modeled This may be the river name i e flathead Contains all the reach specific directories and files including equations geographic data and miscellaneous files used to model the reach Contains all species lifecycle equations Contains all modeling results in csv format Contains program icons legends and other misc files Contains all geographic data files including shapefiles and comma delimited files Contains the time series data created from the modeling Data is in xls format Contains all grids created for the reach Note the path to the grid directory must not contain any subdirectory names longer then eight characters GIS Based Weighted Useable Area Modeling Manual Flathead River Prepared for Montana Fish Wildlife and Parks 6 9 15 03 Copyright MEC SSI 2003 Miller Ecological Consultants Spatial Sciences amp Imaging CHAPTER 2 DATA PRE PROCESSING Processing Hydraulic Flow Data 1 Load the hydraulic data on to your computer hard disk This should be an MS Excel spreadsheet if it represents just one flow or a workbook if it contains multiple flows Typically the name of the file refers to the flow it represents so a file representing a hydraulic flow of 805 cfs would be named 805cfs xls See below X Mic
95. ost Dam 1 500 000 Habitat Area m2 1 000 000 500 000 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 Date Figure 38 Habitat time series Reach 2 West Slope cutthroat trout summer 10 1 4 1 10 1 4 1 Flathead Instream Flow Investigation Project Miller Ecological Consultants Inc Page 44 September 29 2003 Habitat time series Reach 2 West slope cutthroat trout winter 3 500 000 3 000 000 2 500 000 vi d y Th 2 000 000 18 d 8 i Pre D E nh ud duod 5 Ti 3 ost Dam 5 1 500 000 T 1 1 1 000 000 500 000 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 10 1 4 1 Date Figure 39 Habitat time series Reach 2 West Slope cutthroat trout winter Flathead Instream Flow Investigation Project Page 45 Miller Ecological Consultants Inc September 29 2003 Annual habitat time series Reach 2 Bull trout subadult night 4 000 000 3 500 000 3 000 000 2 500 000 2 000 000 Habitat Area m2 1 500 000 1 000 000 500 000 0 e ODN e GN Oo OA o Fl OO st gt e QN e e QN c e e e OG e e CN E LT OO LOO x C a5 C w LIF m LOO E E SZ EN NN te oO 0 Date Figure 40 Annual habitat
96. out subadult 46 Figure 41 Annual habitat time series Reach 2 Bull trout subadult day 47 Figure 42 Annual habitat time series Reach 2 Bull trout adult sess 48 Figure 43 Habitat time series Reach 2 Bull trout subadult night esses 49 Figure 44 Habitat time series Reach 2 Bull trout subadult dan 50 Figure 45 Habitat time series Reach 2 Bull trout adult eere 51 Figure 46 Annual habitat time series West Slope cutthroat frout 52 Figure 47 Habitat time series Reach 3 West Slope cutthroat out 53 Figure 48 Annual habitat time series Reach 3 Bull trout subadult night 54 Figure 49 Annual habitat time series Reach 3 Bull trout subadult day 55 Figure 50 Annual habitat time series Reach 3 Bull trout 56 Figure 51 Habitat time series Reach 3 Bull trout subadult night sss 24 Figure 52 Habitat time series Reach 3 Bull trout subadult day 58 Figure 53 Habitat time series Reach 3 Bull trout 59 Flathead Instream Flow Investigation Project Page ii Miller Ecological Consultants Inc September 29 2003 INTRODUCTION Bonneville Power Administration BPA requested studies on the Flathead River from the Sout
97. ponse of weighted useable area to discharge with the higher values at the lower discharges There is a difference between reach 1 and reach 2 in the response shape of the curves showing that there is a difference between those two reaches for hydraulic conditions The curve that is most different in reach 2 from those in reach 1 is sub adult night bull trout Figure 22 and the fall and winter west slope cutthroat trout curves Figure 23 Reach 3 is hydraulically controlled by the water surface elevation of Flathead Lake and therefore there is very little change with discharge to the amount or the shape of the weighted useable area criteria curve for bull trout In general it appears to be a scaling factor of where that habitat is located based on depth of the water and current velocity In general there is very little difference between the amount of habitat for each life stage at high or low flow as those response curves are very flat There is a difference in absolute value for weighted useable area between the different life stages of sub adult night sub adult day and adult bull trout Figure 24 West slope cutthroat trout in contrast has a distinct relationship between discharge and weighted useable area in reach 3 Figure 25 As with the upper two reaches the habitat is greatest at the lower flow range and then declines in the upper flow ranges There is substantial decline in reach 3 response which may be due to depth differences as well
98. rea A diagram showing the coverage can be found in Appendix B 4 3 Digital Orthophoto Quarter Quads Digital Orthophoto Quarter Quads DOQQs were acquired and used as the data source for interpreting the 1990 river channel and detailing the change that occurred between 1990 and 1998 These panchromatic aerial photos are scanned at 1 meter spatial resolution and orthogonally rectified to remove any displacement caused by relief or camera distortions The aerial photos were flown during the month of July 1990 and 1991 A list of the DOQQs that cover the study area can be found in Appendix C 4 4 Digital Raster Graphics Digital Raster Graphics DRGs were used as the data source for interpreting the earliest river channel A DRG is a standard USGS 7 5 minute topographic map scanned at a resolution of 2 8 meters and output to a georeferenced TIF file The majority of the DRGs used for the study area were originally produced during the 1950s and photo updated in 1978 A list of the DRGs used can be found in Appendix D 5 0 Flow Levels Mapping the extent of the river from aerial photographs and satellite imagery involved interpreting the boundary between water and land within the river channel Since the Hungry Horse Dam impacts the flow of the Flathead River the dynamic flow levels of the river influence the channel boundaries Daily flow levels were obtained from the USGS gauging station located at Columbia Falls which lies on the upper por
99. reate the 3D Surface Data Matrix DVZTbI Data DVZTBL STA 3v 4 E3 m 1 m E FE 2 5 1 000 1 750 0 0 1 000 2 250 0 0 1 000 2 750 0 1 250 0 000 0 9 1 250 250 9 10 1 250 750 5 11 1 250 1 250 6 12 1 250 1 750 3 13 1 250 2 250 0 14 1 250 2 750 0 Bonneville Power Administration Technical Report May 24 2001 Miller Ecological Consultants Inc Page 17 8 Specify the Input Nonlinear Estimation Model and the Loss Function Z exp 0 b1 v1 b2 v2 b3 v1 v2 b4 v1 2 b5 v2 2 where Z Z DVZTbl number of fish observed vl TOTDEPTH from DVZTbI water column depth v2 MEANVEL from average water column velocity b0 b1 b2 equation coefficients L OBS PRED 2 where L loss OBS observed values PRED predicted values 9 Assign check Model settings and Run the Regression Model Model equation parameters equation coefficients loss function variables Missing data valid cases estimation method Convergence of the Parameter Estimation Process 10 Evaluating the Model Fit Print the Parameter Estimates Loss and Variance results LEG emt bite birim a biyi Coetinan ee Z less 0 mI Joes 3D 6837 Be SESS 91 0125 EI Be L Pik SREL D IE 33 3868 17 583855 E 16 4
100. requires a 3 X 49 sized 3D Surface Data Matrix one column each for the depth velocity and frequency values and 49 rows for each of the possible combinations of depth velocity bins 7 X 7 The file can be resized using the Edit pull down menu Edit gt Variables Cases gt Add Delete or use Right mouse click anywhere on the file and select Modify Variables Cases gt Add Delete Bonneville Power Administration Technical Report May 24 2001 Miller Ecological Consultants Inc Page 4 fill the 3D Surface Data Matrix return to the histogram and use the Layouts pull down menu and select Edit Data or Right mouse click anywhere on the 3D Bivariate Histogram and select Edit Graph Data This opens the Graph Data file displaying the frequency Z values within each bin cell of the histogram see Figure 4 The bins along the y axis of the histogram e g Mean_Vel bins are displayed in the Graph Data as the variables columns The bins along the x axis of the histogram e g Tot_Dep bins are displayed in the Graph Data as the cases rows Use the Z values shown to fill in the Z data column in the 3D Surface Data Matrix e g DVZTbl The first 21 rows of a sample DVZ Table are shown in Figure 5 Figure 4 Graph Data Matrix from the 3D Bivariate Histogram Figure 5 Sample portion of the 3D Surface Data Matrix 1 000 1 000 1 000 750 2 000 1 000 1 250 1 000 1 000 1 750 0 000 1 000 2 250 0 000 1 000 2 750 0 000
101. requires that the formula be copied into the appropriate number of rows that correspond to every row containing hydrology in Columns B and C There are corresponding formulas in columns R S T and U to calculate the total habitat for the reach The amount of habitat for the site is multiplied by the reach distance to compute total habitat for the reach Figure 8 Again the number of rows corresponds to the number of hydrology data points This spreadsheet can also be used to graphically display the data to compare habitat over time This identifies the information visually to give the capability of displaying where changes occur in habitat over time with the proposed flow regimes Those results are presented in the next section The GIS based model calculated habitat from geo referenced hydraulic data and habitat suitability indices The resulting values calculate habitat time series using the included spreadsheet The habitat time series relies on formulas in specific cells to calculate habitat Flathead Instream Flow Investigation Project Page 14 Miller Ecological Consultants Inc September 29 2003 values over time The user is cautioned to keep the data in the same cells as those in the example sheet An experienced spreadsheet user can customize the example sheet for any number of species and dates for hydrology In our experience it is best to limit each spreadsheet to no more than four hydrology data sets and four life stages
102. rosoft Excel example_334cfs cs 5 File Edit View Insert Format Tools Data Window Help E eT BBS wr 2 473782 1241553 4725 293 0 0 1473758 1241552 4724482 1 42 0 43 1473765 1241548 4724 319 zaf 0 4 1473773 1241543 4724 485 2 69 0 36 1473780 1241541 4724 356 2 68 0 47 1473786 1241539 4724 234 2 7 0 571 1473794 1241536 4724 083 2 57 0 64 1473801 1241533 4724 2 26 0 71 1473819 1241528 4724 1 76 0 71 1473826 1241526 4724 1 54 0 7 2 Once the data has been loaded QC the data Quality Control Verify that the xls spreadsheet has data columns and names for x 2 velocity and depth in that order in the first row of the table If there is any other data above these delete it 3 Save this xls file as a comma delimited csv file of the same name Use the File Save As option in Excel If the file is a workbook save each tabbed spreadsheet as a separate csv file Save the files to the geographic data subdirectory Creating Shapefiles 1 To create shapefiles click the Create shapefiles button xr This will pop up a dialog box that will allow you to navigate to the geographic data subdirectory See below GIS Based Weighted Useable Area Modeling Manual Flathead River Prepared for Montana Fish Wildlife and Parks 7 9 15 03 Copyright MEC SSI 2003 Miller Ecological Consultants Spatial Sciences amp Imaging Choose a Comma Delimited File to turn into point based shapefile File Name
103. s bw s DS Ee Un Log bi Wie Histogram of juvbtwinni as a Surface 283c E3 Histogram of juvbtwinni as a Surface from 283cms bv 8S Value 7000 5000 5000 4000 3000 2000 1000 Juvenile Bull Trout 283 cms 7 juvbtwinnight Juvenile Bull Trout Reach 1 amp 2 winter night Jbt 1415b Jbt 84 b Jbt 504b Jbt 424b Jbt 339b Jbt 283b Jbt 248b Jbt 226b Jbt 188b Jbt 127b Jbt 105b 339 bw s Histogram of juvbtwinni as a Surface from 339cm ign Pics por na Dia ES er We Histogram of juvbtwinni as a Surface from 339cms bv 8 Value 7000 5000 5000 4000 3000 2000 1000 0 Juvenile Bull Trout 339 cms juvbtwinnight Juvenile Bull Trout Reach 1 amp 2 winter night Jbt 1415b Jbt_84ab Jbt 504b Jbt 424b Jbt 339b Jbt 283b Jbt 246b Jbt 226b Jbt 188b Jbt 127b ja es PR aen n Done rios pe Jbt 105b Sens cave 2 Histogram of juvbtwinni as a Surface from 424c _ m Histogram of juvbtwinni as a Surface from 424cms 8 Value 7000 5000 5000 4000 3000 2000 1000 Juvenile Bull Trout 424 cms 7 juvbtey night Juvenile Bull Trout Reach 1 amp 2 winter night Jbt 14455 Jbt_84ab Jbt 504b Jbt 424b Jbt 330b Jbt 283b Jbt 246b Jbt 226b Jbt 160b Jbt 127b Jbt 105b Us DG 2 Histogram of juvbtwinni
104. ted assessment points within the classification At least 10 accuracy assessment sites for each class were obtained The number of accuracy assessment sites assigned to each information class was roughly proportional to the abundance of that category in the classification Accuracy assessment sites were coded based on the land cover type present in the aerial photography where coverage was available and the IRS image in other areas All of the accuracy assessment sites were compared with the classification to determine an overall accuracy for a classification unit In addition accuracy figures were calculated for each class Appendix F shows the accuracy assessment tables 6 10 Weighted Useable Area Habitat Analysis Together MEC and SSI developed an automated GIS based software script to analyze weighted useable area for fish habitat and produce graphic and tabular output quantifying the results These software routines run on ESRI s ArcView 3 x platform with Spatial Analyst The software script is called WUAM for Weighted Useable Area Modeling The software produces the weighted useable area through the following process 1 Builds point shapefile from tabular csv file produced by MEC hydraulic modeling containing x y elevation depth and velocity 2 Applies operator selected fish species life stage equation and minimum maximum valid values for depth and velocity to produce habitat value at each point in the shapefile 3 Creates co
105. tellite imagery 1937 historical air photo mosaic 00008 DRGs Preliminary report Final report 9 0 Hardware and Software Two Pentium PCs were used for image processing Both systems were equipped with dual Pentium Pro 200 processors 128 megabytes of RAM and 11 gigabyte hard drives The system used for vector processing was a Pentium Pro 200 with 132 megabytes of RAM and six gigabytes of disk space All systems were running Windows NT version 4 0 18 ERDAS Imagine software version 8 3 1 was used for image processing and ARC INFO version 7 2 1 was used for vector manipulation Both software packages were developed for the NT operating system Microsoft Word was used for word processing and Excel was utilized for mathematical operations 10 0 Conclusion and Recommendations This portion of the Flathead River Instream Flow Investigation Project has provided many insights into the dynamic characteristics of this river system while providing a solid baseline for future studies and data development The next step is to transform this two dimensional data set into three dimensions Three reaches of the Flathead River each representing unique channel characteristics have been identified Detailed channel topography has been generated for each of these reaches and will be used for three dimensional visualization A spatial model will also be developed to identify species habitat suitability based on river characteristics such as ha
106. tems All references to software and function are copyright of the respective manufacturer Use of this manual and the GIS based Weighted Useable Area Modeling software constitutes acceptance of the GIS WUAM End User License Agreement GIS Based Weighted Useable Area Modeling Manual Flathead River Prepared for Montana Fish Wildlife and Parks 3 9 15 03 Copyright MEC SSI 2003 Miller Ecological Consultants Spatial Sciences amp Imaging GIS based Weighted Useable Area Modeling Software License Agreement SOFTWARE LICENSE AGREEMENT Spatial Sciences amp Imaging Miller Ecological Consultants Inc SSI MEC grants you a non exclusive license to use this copy of the program and user manual subject to the following terms and the proprietary notices labels or marks on the program and the accompanying documentation You may 1 Use this program only on any one computer at any one time 2 Make a copy of the program in machine readable form for archival purposes as long as all proprietary notices are reproduced on each copy You may not 1 Modify translate reverse engineer decompile disassemble or create derivative works based upon this program 2 Rent transfer or grant any rights in this program or accompanying documentation in any form to anyone else without the prior written consent of SSI MEC 3 Remove any proprietary notices labels or marks on the program and accompanying documentation 4 Use this program or p
107. throat trout to be more variable post dam than pre dam with more stability and higher habitat availability in the pre dam conditions Figures 36 and 37 Bull trout sub adults in reach 2 show the habitat in pre dam conditions for nighttime was more abundant and more stable during baseflows than the post dam period which has more daily variability in habitat This is shown both in the annual times series in Figures 38 and 39 and also in the ten year time series in Figures 41 through 43 Reach 3 habitat conditions show that the post dam conditions for west slope cutthroat trout have better habitat than were shown in the pre dam conditions Figures 44 and 45 Bull trout habitat for reach 3 shows that there is slightly more quanitity of habitat in the post dam hydrology than pre dam hydrology for sub adults and adults but there is more variability during baseflow conditions of that habitat Figures 46 through 53 Flathead Instream Flow Investigation Project Page 31 Miller Ecological Consultants Inc September 29 2003 Annual habitat time series Reach 1 West slope cutthroat summer 1 400 000 1 200 000 1 000 000 800 000 Pre Dam Post Dam 600 000 Habitat area m2 400 000 200 000 M aO OD aS o9 a GV aS ak 2 GV A ON AD GM d dl ae SNR AD gi Date Figure 26 Annual habitat time series Reach 1 West slope cutthroat su
108. time series Reach 2 Bull trout subadult night 10 8 10 22 11 5 11 19 12 3 12 17 12 31 Pre Dam Post Dam Flathead Instream Flow Investigation Project Miller Ecological Consultants Inc Page 46 September 29 2003 Annual habitat time series Reach 2 Bull trout subadult day 4 000 000 3 500 000 3 000 000 2 500 000 2 000 000 Habitat Area m2 1 500 000 1 000 000 500 000 0 x ODN e st OO GN Fl O st ON e e lt e e OG e e CN e E LT OO LOO C a5 CQ dq IF mo LOO E OO SZ EN DN QN bg te oO 0 Date Figure 41 Annual habitat time series Reach 2 Bull trout subadult day 10 8 10 22 11 5 11 19 12 3 12 17 12 31 Pre Dam Post Dam Flathead Instream Flow Investigation Project Miller Ecological Consultants Inc Page 47 September 29 2003 Annual habitat time series Reach 2 trout adult 3 500 000 3 000 000 2 500 000 2 000 000 1 500 000 Habitat area m2 1 000 000 500 000 0 o O QO N CN e oe re E GO gt S o Ge e e NN te c Date Figure 42 Annual habitat time series Reach 2 Bull trout adult 8 27 9 10 9 24 10 8 10 22 11 5 11 19 12 3 12 17 12 31
109. tion of the study area The following chart shows the daily flows for the dates of data acquisition Table 4 Daily Flow Levels for Flathead River at Columbia Falls Data Source Acquisition Date Flow CFS USGS DRGs 1978 27 000 00005 7 1 90 27 000 IRS 1C 9 6 98 3 570 Resource Photography 7 28 97 8 020 7 16 98 12 600 Field Work 8 2 99 8 810 8 3 99 9 990 Note The USGS DRGs cannot be linked to a specific date therefore no daily flow measurement was available It is estimated that the flow level is less than that of the highest flow of 27 000 cfs 6 0 Methodology 6 1 Rectification Rectification of the satellite imagery is required so that it will geographically register with a specified map coordinate system and other GIS data layers The output land cover data will have the same geometric characteristics as the rectified satellite imagery so rectification of the imagery is an important step The process involves collecting ground control points from a data source with a known map coordinate system and selecting corresponding points on the satellite imagery Over twenty points are usually collected to rectify an entire satellite scene The geometric relationship among the points is used to calculate the root mean square RMS error which is a measure of the accuracy of the rectification A RMS error of about one half of a pixel 0 5 is considered excellent and an error of less than 1 0 is usually acceptable DOQQs were us
110. to find suitable habitat The GIS approach presented here provides both a visual characterization of habitat as well as Arcview project data in the distribution cassette disk that can be used for additional analysis of flow regimes and spatial variability of habitat within the three reaches of the river The habitat time series can be used to compare habitat changes over time Flathead Instream Flow Investigation Project Page ES 1 Miller Ecological Consultants Inc September 29 2003 Table of Contents TOO LLL E M M C MD Ed 1 E 1 Objectives e ee eee e e ER ER E 3 4 General Approach de 4 River Channel Change Analysis and Land Usel and Cover Mapping sse 6 Topographic Mapptng RR e ER ER RR RR RR 7 Hydraulic Data Te EE H Two Dimensional Hydraulic Modeling amp Habitat Suitability Curves ec 10 GIS Model mene t tede ee e n e 11 GIS Based Weighted Usable Area Model 11 Habitat versus Discharge Modeling sss 11 Habitat Tire s oc ed n e te E EEN 12 locii C 16 Model Calibration testate edades cs db cree Dc m 16 Habitat Simulations eta et etude te le e e
111. ty of the river system You may want to experiment with the cell size to see what creates the most acceptable results Click OK Processing of the surface finishes CHAPTER 4 HABITAT AREA MODELING RESULTS 1 After processing of the surface the program creates three files from the analysis a continuous surface a summary habitat suitability histogram chart and a summary habitat suitability table in csv format which is saved in the hat subdirectory The window below indicates that the analysis is complete Surface Model Complete Surface Histogram and Comma delimited csv file completed for example1_s Click OK 2 A legend is automatically created for the surface The legend has ten categories of 0 10 increments of habitat suitability These same categories are reflected in the summary csv See the results view below ArcView GIS 3 2a 151 Eile Edit Gallery Chart window Help m 2 MEW eda Histogram of example1_s as a Surface fro E3 Histogram of examplel s as a Surface from 339cms flow shp 5 Value 1000 900 800 700 600 500 400 300 200 0 GIS Based Weighted Useable Area Modeling Manual Flathead River Prepared for Montana Fish Wildlife and Parks 11 9 15 03 Copyright MEC SSI 2003 Miller Ecological Consultants Spatial Sciences amp Imaging 3 The surface that is created by the software is a temporary file To save it to a permanent file f
112. vey Biological Resources Division Midcontinent Ecological Science Center 4512 McMurray Avenue Fort Collins Colorado 80525 Leonard P M and D J Orth 1988 Use of habitat guilds of fishes to determine instream flow requirements North American Journal of Fisheries Management 8 399 409 Marotz B L C L Althen and D Gustafson 1994 Hungry Horse mitigation aquatic modeling of selective withdrawal system Hungry Horse Dam Montana Montana Dept of Fish Wildlife and Parks Prepared for Bonneville Power Administration Milhous R T 1984 The use of one velocity calibration data set with IFG4 PHABSIM Technical Note 4 U S Fish and Wildlife Service Fort Collins Colorado Milhous R T 1985 Worth of Data Seminar on Hydraulics in PHABSIM Presented at Fort Collins Colorado April 11 and 12 1985 Milhous R T M A Updike and D M Schneider 1989 Physical Habitat Simulation System Reference Manual Version II Instream Flow Information Paper No 26 U S Fish and Wildlife Service Biological Report 89 16 Miller Ecological Consultants Inc and SAIC 2000 A conceptual approach to evaluate habitat flow relationships for the fish community in the Middle Rio Grande New Mexico Final Report Prepared for USACE Albuquerque District Albuquerque New Mexico Contract DACA47 97 D 0009 Miller Ecological Consultants Inc 2001 Technical Report Calculation of bivariate habitat suitability functions in the Statistic

Flathead River Instream Flow Investigation Project

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