Trout Manual - Acoustics Unpacked
Contents
1. Data Fields The following provides a more detailed description of the input data fields Input data for the model can be manipulated in either the Access database environment or directly through the program itself by inputting them into the grid in the upper right hand corner If you wish to add trout populations to the data file such as wild or stocked components these must be added in the Access environment Keep in mind that changes made to the data during the execution of the program will also be saved to the database The input data fields discussed correspond with the data tables in the Access database which controls the model output These appear in the upper right hand corner of the window and are controlled by the drop down menu just above the data grid By selecting different headings the program will display the corresponding input data grid with the information for that heading allowing for changes to be made Stocking Data This field provides information on the timing and level of stocking events These data include the date s that fish were stocked the number of fish stocked per acre and a mean and coefficient of variation for lengths of stocked fish If the coefficient of variation is unknown the parameter is typically set to a value of 0 09 Wild Data Contains information regarding the numbers of wild trout collected within electroshocking surveys These data are similar to stocking data in that date numbers and leng2. account for the expected release survival rate Sr 7 F itandling Ril SpR As in all biological systems the natural mortality component M is a key but often immeasurable addition to the total mortality rate In the model the natural mortality rate is divided into fishing season and winter rates Within Trout exe seasonal values can be made to vary monthly but values are usually kept constant throughout the season After all of these mortality rates have been determined they are summed to produce a daily instantaneous total mortality rate Z that determines the number of fish that survive to the next time period This Z is equivalent to the F M term from equation 1 8 Z F F M Creel Handling Length and Weight The weight length relationship used in the Trout exe model is adapted from standard weight length relationships commonly used in fisheries science wherein the weight is stated as a constant times the length taken to a power Anderson amp Neumann 1996 9 W aL gms mm Historically this relationship was specified as the logio transform for the purposes of deriving linear regression estimates 10 logio Wons log a a Blog Lim r In this context the power is usually set to 3 representing weight as volume and the constant a is a variable dependent on the species of fish being evaluated For brook brown and rainbow trout living in streams the a value is usually very close to
3. of the fishing occurs after July 1 Pattern 2 Fishing effort is more concentrated during the early part of the season pg 7 Engstrom Heg 1990 Pattern 2 is the most commonly observed distribution of fishing effort in New York streams See the Data Defaults section below for values of monthly effort distributions of these patterns These two patterns can be specified by choosing the corresponding button below the data grid Harvest Rate or PKL Proportion of legal catch kept Represents the amount of catch and release occurring within the fishery This can also be thought of as the creel rate the likelihood that an angler will remove a legal trout that caught These values are broken into monthly values of the proportion of fish creeled by anglers Illegal Harvest Rate or PKS Proportion of sub legal catch kept Represents the amount of poaching that occurs within a stream applicable only in streams where a minimum size limit is imposed Monthly values corresponding to the proportion of sub legal sized fish creeled by anglers are entered into this table Zn Natural Mortality Natural mortality is a highly variable rate that can change over time and for this reason this parameter is both component and age specific There is also a column for differentiating between in season and winter mortality rates of the components Values in this table must be provided as daily rates Stream type specific values can set by using the option buttons be
4. that cab be used to make predictions under a variety of management and ecosystem scenarios Figure 1 Schematic diagram of how the population dynamics model Trout exe can be used in the context of the overall CROTS program Catch Rate Oriented Ton ana Ecosystem Electrofishing Survey Surveys Carrying Wild Trout Environmental Fishery Inputs Inputs Nat Mort Effort j Numbers Capacity Growth Creel amp Stream Release Type Rates Predicted Stocking Abundances Rates T Trout exe gt Catch Rates amp Biomass If unfavorable re evaluate stocking If favorable compare to survey and creel data adjust as appropriate Pa i Creel Electrofishing Surveys Survey Theoretical Model Structure Population Dynamics Model The population dynamics employed in the Trout exe model follows traditional fisheries science theory e g Van Den Avyle and Hayward 1999 The number of individual fish in the population at any time t 1 can be expressed relative to the number that were present at the previous time after accounting for sources of mortality such as those due to fishing F and other natural causes Me 1 Ni N exp F M Survivorship and mortality are cumulative processes that accrue over time These cumulative effects are often represented as an exponential decline in the size of a cohort over time Changes in population abundance thus reflect the process of survivorship S exp
5. 0 a E NA E cee 15 A O 17 DIAS o A AA AOS 17 DIMAS dt e e do e e O 18 Modifying th Dala ir 20 EXECUTING THE PROGRAM ccscsssssssssssssssssssosesesesececececessessssssesesessssssssceccsscsssesesesecececesesssess 22 ASES AA 22 ADVANCED TOPICS ssvscecisscscsccscacieetecssenscscsasastsasooosotnctceessesssstesesecescaes enssosed gedaasasassdesececdsedaceessesddecvecacaes 25 SENSITIVITY ANALYSIS orones rifa eiii Eo O EE Ea dead cia 26 CCA SA din 27 PROGRAM DETAI A E ssoi sees 29 FORM liesen A R E RE EE a TE 32 WROUD EA A N EEIN EEN EEES A EEEE MET EES R O AE AE TENE S AES EEE EEE E EEES 34 FREQUENTLY ASKED QUESTIONS 00 A E RS 36 ACKNOWLEDGEMENTS isavsscscscacssecssvsesscaceasssasasssescanescscasesoostsnseeasacsevtnsusicntesessasdoestotescoensesscssssessescesesencs 37 CONTACT INFORMATION cccscsssssssssssesesessssssssssssssssesesesssssssssessssssssesesesesececesssessssssssesesesesseeees 37 A A NOS 38 APPENDIX STREAM CLASSI FI CATI ON KEY cscssssssessssssssssssssssssssssesesesesesesesssssssseseseseee 39 Introduction Sound fisheries management requires reliable assessments of population abundance and reasonable predictions of harvest This must be done while accounting for varying levels of fishing effort under different habitat conditions To provide a framework for conducting these analyses population dynamics models are often employed to quantify the changes in abundance while accounting for variations
6. 10 with a corresponding value for log a of 5 e g Schneider 2000 Because weight length analyses are typically carried out in millimeters and grams in the scientific literature two conversions are applied to convert the information to inches and pounds as required for communication to the public To adjust for this the following transformations have been applied Lmm 25 4 Lin Wps 0 0022 W to obtain W a 0 0022 25 4L Y By inputting an a of 10 we developed the following relationship W 107 0 0022 25 4L y In Trout 4x4 the spreadsheet version of the model a fraction with a large denominator is used to represent the translation from grams to pounds and to include the coefficient a The resulting fraction 1 _ 10 0 0022 45454545 oa is sometimes better in defining the relationship to the appropriate number of significant digits For this reason one might find the following equation _ 25 4L Y 11 W ay bs 45454545 in the Trout 4x4 model Given that hatchery fish are often heavier than wild fish of the same length this equation also incorporates a condition factor k 1 1 that accounts for this difference This condition factor is only used in the initial weight calculation on the stocking day making the first day weight calculation 7 3 12 w 1 1 25 4 L 45454545 This initial weight information is then used to determine the daily weights and len
7. The Cohorts Totals Selection reports results for each of the individual stocking components and the corresponding totals ma Catch Rate Oriented Trout Stocking Model File Help r Calculate Browse Save End Database Documents and Settings tjt Desktop CROTS TedsDefault mdb Perform Calcualtions By Population Size X Age Classes o Cohorts Totals ie Age Classes Cohorts Totals 13 If graphical outputs are not logical in the situation that you request such as weights by age classes the program will instruct you to select a new option usually Cohorts Totals Actual numbers and rates for individual cohorts and totals are available by clicking on the Report button located just below the option buttons By clicking this button again you can switch back to the graphical output an option available at anytime Running the Program To see model results click the Calculate button in the upper left hand corner of the window The default setting of the program shows the graphical representation of the population projections similar to that shown below he Catch Rate Oriented Trout Stocking Model File Help r Calculate Browse Sove End Stocking Data y Maximum Biomass 37 229 Date 1 May one A r month day acre length Database Documents and Settings tjt9 Desktop CROTS CROTS 1 6 17 0 0 0 09 Example mdb 3 1 5 22 25 85 0 09 1 5 1 45 9 0 09 1 4 19 160 8 0 09
8. but only for the early part of the season By plotting the catch per hour and overlaying a line across the plot at catch equal to 0 5 we can see how well the number and timing of stocking events will accommodate this goal Figure 4 Plot of Catch per hour with goal of 0 5 fish hour line overlain Catch Hour Total Number of fish Hour 2 Moy 1 2 Juni 3 Juli 3 Aug i 3 Sep i 4 Octi o o ol a Day In addition to catch rate it is also interesting to look at the daily number of fish being caught on the stream By selecting the Total Catch from the output headings we can view a plot of what the pattern of angler success may look like given the inputted stream parameters In the graph below we can see the influence of a Pattern 2 type effort distribution with quickly decreasing catches punctuated by drastic increases representing stocking events over the first few months of the season Soon after the initial surge of fishing pressure subsides usually around J une the catch falls back to reduced levels 28 Figure 5 Total catch plot representing changes in monthly catch rates Total Catch 4 3 2 1 Tal Day Number per Acre 1 Apri 2 May 1 2 Juni 3 Juli 3 Aug 1 3 Sep i 4 Oct i Program Details The following is a section that may be of most help to those who are familiar with programming code namely Visual Basic 6 0 but may also be of interest to those that are not The flow chart chronologically
9. follows the execution of the program The following few pages are a flow chart representing the execution of the program followed by a list of program procedures in the order that they appear in the actual code Flow Chart for Start the program Trout exe Form Load User locates data file mdb Fill the data grid Perform calculations and fill arrays Calculate Back calculate Calculations for for wild fish stocked fish Select heading from drop down of output data Access database Season data Stock amp wild fish Growth mortality Calculations for wild fish Display data for Age Classes or Cohorts Totals Year Classes Show plot or report format of data with info for yearlings and older fish Show plot or report format of data with info for totals and individual components Select New oR Change Heading Data Inputs 30 Save Save the graphical form of data Yes No Give user choice of file Save as ASCII text file type and save txt emf wmf bmp or jpg At this point the user may choose to select a new data heading load a new file or end the program End 31 Form1 Private Sub about Click determines what happens when the About button is clicked in the Help drop down menu contains contact information concerning the VB model Private Sub Combo1_ Click dictates what happens when the drop down menu corresponding to Stocking an
10. text outputs into manageable Excel workbooks From this location you can also download or view this document that details installation and use of the model and a Sensitivity Analysis of the model parameters Web sites for free ware compression and Zip software http www powerarchiver com http www winzip com http www thefreesite com Free_Software Unzipping_compression_freeware From your own computer open the folder containing Trout exe on your hard drive and then double click the Setup exe file By following the installation instructions that appear you will be able to change program attributes such as the installation directory By default the program will install itself under the Program files of the Start menu although you can direct it to another location during the installation How to use the program Once the Trout exe program and associated files have been installed you may select the Trout heading from under Program files and then click on the Trout exe accompanied by the icon het and the following window will open asking for a data file to use for modeling 10 Please Select a Data File Look in Region 9 Joe Evans e 10 e En e 5 Beaver Meadow Creek Sbs Forks Creek Sbs Buffalo Creek Sbs Goose Creek Sbs My Recent California Hollow asp2 Haskell Creek 6bp Documents 5 Cass Run Sbs Hunt Creek bs Cattaraugus Creek 8asp2 Ischua Creek 6bp O Cazenovia Creek 6bp Little Buffalo Creek 6bp Des
11. then pasting the corresponding report format of the population levels into a graphing spreadsheet application e g Microsoft Excel By plotting these population levels at varying release rates and then superimposing the survey result at the appropriate location we can see how different parameter inputs might affect the dynamics of the system and the predictions of the model This representation assumes that all other parameter values are correct Figure 3 Population trends for Hunt Creek over the season of 2000 with varying harvest rates Point at lower right indicates fall electrofishing survey estimate Harvest Rate 1 0 Harvest Rate 0 8 Harvest Rate 0 6 Harvest Rate 0 4 Harvest Rate 0 2 Number of trout per acre Apr 17 Apr 24 May 1 May 8 May 15 May22 May 29 Jun 5 Jun 12 Jun 19 Jun 26 Jul 3 Jul 10 2000 Catch Analysis Another important rate of concern to fisheries managers is the catch rate and number of fish caught by anglers on a particular stream The Trout exe model can create figures on both these important statistics reporting them in catch per hour and number of fish 27 caught by day Catch per hour is of special interest in that it is an indicator measuring one of the important objectives of the CROTS program specifically quantifying whether we are achieving an sustained catch rate of 0 5 fish per hour on streams type A quality streams for the length of the season and the same rate for a type B
12. CROTS datasheet with example data and the symbols representing the data described above 23 CROTS EVALUATION DATASHEET Date _10 15 _03 Filled out by T Treska STREAM INFORMATION Stream Name_ Fall Creek Watershed ID Mouth to Ithaca Falls Line ID from stocking Book 1254 CROTS Management Type As A J Fishing Pattern 1 or 2 2 C J Fishing Intensity hr acre 175 B J Confidence in Intensity Estimate Circle one High Med Low STOCKING INFORMATION POPULATION ESTIMATES Survey Date 8__ 26 2000 SWDB Survey __ 700916 Estimation Method circle Delury Peterson Zippin Projection Leslie Efficiency Other Were stocking rates similar the three years prior to this survey Add comments if needed Standard Error If Known Comments Confidence in Estimate High Med Low High High 24 Advanced Topics Methods for checking assumptions Two means of testing a model should be employed when evaluating it for use One way is to examine how it performs with known inputs and outputs from a similarly coded simulation model If the model doesn t work well for a known albeit simulated population then it is unlikely to work well in practice Once it is shown to work well in the lab it is then just as important to test it in the field Given known initial population sizes available from the stocking data one should be able to use fall electroshocking surveys to det
13. Command5_ Click this is the toggle button that allows the user to switch back and forth between the report and the graphical representation of the selected data Private Sub DBGrid1_ KeyPress allows the user to move the cursor around the data grid in the upper right hand corner by using the Enter key 32 Private Sub Form_ Load this loads the program itself sets up combo buttons drop down menus Private Sub Help2_ Click dictates what happens when the Help selection is made from the Help menu Private Sub Option1_ Click Private Sub Option2_ Click makes sure that only one of the selections from Year Classes or Totals can be selected Private Sub Command4_ Click dictates the actions that follow the click of the End button Ends the program Private Sub end Click actions for the End selection from under the File menu Ends the program Private Sub open_Click actions for the Open selection from under the File menu allows the user to open a data file for use Calls Command2_Click Private Sub save_ Click actions for the Save selection from under the File menu allows the user to save data from the model Calls Command3_Click 33 Trout Function Func_ FileExists takes in a file name string and performs a series of checks to determine whether or not it is a viable data file Public Function jday takes in year month and day and determines the julian day number of
14. F M Actual observations on the population come in part from surveys which are a direct measure of abundance and in part from catch and harvest which are indirect measures that in effect monitor this process The Baranov catch equation Ricker 1975 F 2 C z TM 1 exp F M N t represents the catch component This equation reflects that of those fish that do not survive 1 S a certain fraction Fy F M fail to survive due to fishing thus resulting in the observed catch In sport fisheries the mortality can be further partitioned into that which is due to harvest creel mortality and that which is due to the stress associated with catch and release handling mortality This combined total mortality rate can be expressed now without showing the time specific subscript as 3 F Fora t EF Handling Both of these components reflect baseline rates corresponding to fishing pressure creel and poaching rates and survival of released fish the mechanics of which will be explored below The total instantaneous fishing rate Frishing can be derived on a per day basis by using monthly measures of effort divided by the number of days per month D The monthly measures of effort are calculated as proportions of the total annual fishing effort Both the total and the proportions per month are specified by the user in the input database Annual effort is measured in hours acre based on the yearly angler press
15. Fishing Pattern Stream Type C Pattern 1 Type A As Asp etc Report Pattern 2 Type B Bs Bp C Other Input Required C Other Input Required Population Size Number per Acre Modification of the settings in the program to change the content and format of the outputs is straightforward The Graph and Report settings can be switched through the use of the toggle button below the Age Classes and Cohorts Totals options When you modify any of the input parameters you must always press the Calculate button to recalculate the outputs more on this later When changing the options Age Classes and Cohorts Totals the program will automatically recalculate the results Use the drop down menu in the upper left side of the window showing Population Size in the above 14 figure to select among alternate output headings This drop down menu may also be operated with a scrollbar A list of possible outputs available on the drop down menu can be found in Table 2 below Table 2 List of outputs available under drop down menu in upper left corner Population Size Biomass Total Catch Catch Hour Catch Biomass Creeled Catch Creeled Catch Hour Released Catch Released Catch Hour Average Creeled Length Average Creeled Weight Length Weight Ft Zt Fc Release Rate Fh Zn Surv Prop of fish dying Fmort Probability of Catch e Remember to click the Calculate button to re compute populatio
16. User Manual for the Trout exe Population Modeling Software developed by Theodore J Treska amp Patrick J Sullivan Coldwater Fisheries Research Program Department of Natural Resources Cornell University Ithaca NY 14850 3001 in collaboration with New York State Department of Environmental Conservation May 2005 Table of Contents INTRODUCTION cscscssecscoctssccscsssesssoatenssssesvaonsossssccecsbesscesssccscensbevobonsonsssasasaotsesdssdedeesbesdcessssesedicbend onseseesiess 3 A BRIEF HISTORY OF THE CROTS PROGRAM oococccocconcconcnnnnnnnnnnncnnnconeconecnncon nono nono nonn conan rin nnnn nano nn cn necinecnneos 3 THEORETI CAL MODEL STRUCTURE ccssscssssssesecssscsssscsesecsssessssssesecsssessssesesecsssesscesseseesesesseeese 5 Population Dynamics MOCEL ccccccccesssesessssseseesesecessssssssescscsesesesenenenenessssssssesesesesenssseseseesecsesesenenenes 5 Length and WEIR E A di tada 7 BOM aan 8 GETTING STARTED Wiwsncsssssssissccsecsescscissnssesensasaescusesnssnsceseavacionsesecsescesesinsosnosentasucuss obonbeckseaavdosensessesentecas 10 Downloading and installing the progra ecececccecscessssssssssesesesescsesesesesesesesensasceeesesesesesestseseensees 10 HOW TOUSE THE PROGRAM 0000 id AR AA AAA eee a ele Aa Eidos 10 CHECKING th DIS A A A da 12 Running the MOL oe cecccccscscsescsssesesesesesesesesesenessucssessseseseneseseuesessseseeeesesesesesessnenenenaeseseaeseaeaeeeeeeenees 14 la II A A 15 SAVING ROS UES
17. aphical capabilities to explore the effects that changes to the fishery might have on the population or rates Changes in the stocking number or schedule can be examined to determine how best to sustain the desired fishery or changes in length regulations can be implemented to see how they will affect size distributions and numbers Below is a look at how by varying the release rate of trout by anglers we can see how this affects the population numbers of the trout in the system By plotting the actual survey number seen in the fall a comparison can be made between the release rate predicted by the model and the estimate of release rate used by biologists Of course other parameters and their estimates must be taken into account when looking at these types of data but exploratory analyses made in this way can introduce ideas that may go on to explain some of the uncertainty and trends that are being seen in a system In this 26 particular stream the model and the corresponding survey data indicate that the release rate my be as high as 50 which is not unthinkable if the stream is one that receives mainly catch and release pressure If this is not the case though you may want to take a look at some of the other parameters and see if other estimates may provide explanation as to why this rate is so high The figure displayed below was generated by running the program with varying release rates each time saving the population report data and
18. ate and for this reason these April 00537 00495 values of are not often changed from May 01030 00759 stream to stream In the default une 00838 00529 data these values differ for yearlings July 00538 00529 versus older fish and vary by month August 00618 00529 September 00618 00529 Oct until Oct 15 6 One of the hardest things to determine about a fishery is the rate at which anglers release fish being that creel surveys are very time and resource intensive This being said it is often the biologists best reasonable estimate that is used for values in the Harvest Rate or PKL proportion of legal sized catch kept and Illegal Harvest Rate or PKS proportion of sublegal sized catch kept tables Obviously if there is no length size limit the Illegal Harvest Rate parameters are all set to 0 for all fish are of legal size 7 Finally if it is desired to model the effects of wild fish on the system and there is data concerning numbers seen in electrofishing surveys this data can be entered in much the same way as the stocked data All that is needed is the number of fish encountered their average sizes and the day the survey was completed The model will then back calculate to the beginning of the modeling period and introduce the expected amount of wild fish that would have been present to produce the numbers seen in the survey after the dynamics of the season have taken their toll The following page is a copy of the
19. cant unused carrying capacity and a light to moderate fishery Stocked with put grow take fish usually two increments Stocked streams managed under a 9 inch length limit typically the larger more productive more heavily fished streams characterized by superior growth and survival 12 14 and NK Special length regulation areas based primarily on stocked trout Heavily fished stocked streams of good quality with significant holdover but not managed under a length limit The early season fishery is provided for by a combination of put and take fish and holdover fish from a late spring stocking during the previous spring 39
20. d Season data grid is utilized sets column widths and table headings Located in the upper right corner Private Sub Combo2_ Click drop down menu concerning what data is of interest to the user population number catch rate etc Calls Public Sub Fill output_grid generate reports and plots of the selected data Also calls Public Sub get_biomass Located in the upper left corner Private Sub Command1_ Click the majority of the calculations are performed in this procedure all based on the original Trout 4x4 creating all the pertinent data that is used and displayed by the program Calculations are done on a daily basis with accommodations being made to account for changes that occur during the modeling period such as winter rates changing values for different months etc There are separate loops for dealing with wild and stocked components Calls Public Sub getseasoninfo and Public Sub Proc_Read_db_new Private Sub Command2_Click dictates what happens when the Browse button is clicked Brings up file selection window for the user Calls Private Sub Combo2_Click Private Sub Command3_ Click dictates action for click of Save button which saves tabular format report or graphical output of selected data in combo box2 the drop down menu on the left Report is saved in a Notepad file while graphical results are saved as bmp wmf emf or jpg files Does this by calling Public Sub Proc_save_data Private Sub
21. er sets up the header structure for the report format depending on the number of stocked and wild components Used when the Totals option is selected 34 Public Sub Proc_save_ data sub that coordinates the saving of output that is created by the model storing the values in a Notepad file Public Function get_ total procedure for summing the total of a given data array Public Function get header age sets up the header structure for the report format depending on the number of stocked and wild components Used when the Year Classes option is selected Public Sub get biomass determines the daily biomass values by summing all components and finds the season high biomass displaying it in a text box in the upper right hand corner Public Sub Proc_Read_db_ new this sub reads all the data from the imported Access files and saves them in locally accessible arrays usually according to component and month or year depending on what data it is using 35 Frequently Asked Questions Q A How do force the program to make predictions for no kill managed areas Enter 1000 for the size limit The program recognizes this value and will set the probability of legal catch equal to 0 for all days of the season How can I be sure that the data modified on the data window are used in calculations After you have changed the data in the data window make sure you click on a new cell or change the topic heading by using t
22. ermine how well the model is approximating the dynamics of the stocked population With the Trout exe program this can be done by plotting the resulting population curve computed for a particular stocking level and stream type and then identifying the location on the plot of the observed survey abundance for the appropriate date Figure 2 shows the application of this method to the model output of Mansfield Creek in Region 9 for the season of 1997 The point represents the number of stocked yearlings seen in the fall depletion survey estimates 25 Figure 2 Population curve and survey point data for trout numbers in Mansfield Creek Region 9 1997 Population Size 20 Total Number per Acre LH o e 3 m a a ES 5 x gt m x H w N m m m Day Point represents survey results for number of stocked yearlings found on September 4 Model prediction 33 4 Survey estimate 39 As we can see in this example the program has done a reasonably good job at modeling the dynamics of the system with the given parameter inputs but this might not always be the case One might also wish to run the data with varying parameter sets to test if other combinations will give similar or better predictions or to see what effect changes might have on the population s dynamics Sensitivity Analysis Sensitivity analyses can be used with data created by the model most often by using a statistics package with gr
23. gths of the fish as the season progresses Daily weights at time t 1 are calculated by using the weight at time tand a time and age dependent growth value depending on the age year class of the fish and whether the calculation is taking place during the fishing season or over winter 13 W W er t 1 Lengths are then calculated using a derivation of equation 11 and a measure of standard deviation determined from the coefficient of variation which is usually set at the default value of 0 09 W 45454545 14 tas Z a 25 4 Biomass Daily biomass figures 8 are finally determined with a simple calculation involving the number of fish alive at time Ws and their respective average weights W where tis day and c is used here as an indicator of stocking component representing each individual stocking group 14 B Y N W gt c 1 Table 1 List of variable definitions and their notations in both Engstrom Heg Engstrom Heg R 1991 and this report Note some of the report definitions correspond to vectors in the program and therefore do not have a matching definition in Engstrom Heg Used Here Engstrom Heg Definition N Number of fish present F Fishing mortality M zn Natural mortality rate F Fishing zf1 Daily instantaneous total fishing rate q c Catchability figure E Effort monthly percentage of total F creel zf Instantaneous creel mortality rate Pr Proportion of legal sized fish that a
24. he drop down menu thus saving the entered data If you see a pencil icon in the row label on the lefthand side of the form then the data is not been saved Make sure there is a triangle symbol gt signifying your data is saved before you run your predictions Note that when you save the changes made to the data in the data window the changes are also saved in the Access database 36 Acknowledgements The Trout exe program was written and developed as part of Cornell University s Department of Natural Resources Coldwater Fisheries Research Program and is supported by the New York State Department of Environmental Conservation and the U S Federal Aid in Sportfish Restoration Program The Microsoft Visual Basic form of the Trout exe program was written and developed by G Scott Boomer Patrick J Sullivan and Ted Treska NYSDEC scientists Jim Daley Pat Festa Dan Zielinski Phil Hulbert and Joe Evans provided comment while this model was being developed NYSDEC scientists Dan Zielinski Joe Evans Dave Lemon Wayne Elliot Frank Flack and Al Schiavone provided data and information for model evaluation Contact I nformation Dr Patrick J Sullivan Dr Clifford Kraft Coldwater Fisheries Research Program Coldwater Fisheries Research Program Department of Natural Resources Department of Natural Resources Fernow Hall Fernow Hall Cornell University Cornell University Ithaca NY 14853 Ithaca NY 14853 pjs31 cornell edu cek7 c
25. in survivorship growth and in the case of self sustaining populations reproduction In New York State an approach known as the Catch Rate Oriented Trout Stocking CROTS program has been used for nearly three decades to establish New York State Department of Environmental Conservation NYSDEC trout stocking policies CROTS provides guidance on the selection of streams suitable for stocking and establishes appropriate stocking levels with the goal of providing high quality trout fisheries Although the software used to run the population dynamics model that provides the basis for CROTS stocking rates has evolved over the years being re written in three different software formats the basic elements of the model have remained unchanged We have written a version of the modeling software in Microsoft Visual Basic VB called Trout exe that uses data stored in a Microsoft Access database This report is designed to serve as a manual for that program and provides the biological and historical background relevant to its use A Brief History of the CROTS Program In order to quantify the likely catch per angler hour under different trout stocking levels and for different stream types NYSDEC biologist Robert Engstrom Heg developed a population model that predicted population abundance over time as a function of growth natural mortality and angling pressure Figure 1 The model made use of a trout population dynamics framework as described by Clark et a
26. ktop Chatauqua Creek 6bp Mansfield Creek as 2 Chenunda Creek Sbs Oatka Creek as Ur clear Creek as Red House Brook bp 5 Cryder Creek Sbs Trib 17 of Red House bs East Koy Creek 9asp2 E Wiscoy Creek as Elton Creek 5bs Fenton Brook 9asp2 My Documents My Computer My Network Files of type Access Database Files mdb X Cancel Places File name iii Open Eer I Open as read only After selecting a file for ease select example file included in zip file the following screen will appear after which you need only press Calculate to show the default model prediction of population levels 11 e Catch Rate Oriented Trout Stocking Model File Help Calculate Browse Save End Stocking Data w Maximum Biomass 37 229 Date j1 May 6 f acre length Database C ts and Settings tjt Desktop CROTS CROTS b Perform Calcualtions By e Population Size Fishing Pattern Stream Type Pattern 1 Type A As Asp ete Report C Pattern 2 C Type B Bs Bp Other Input Required C Other Input Required Population Size Total Number per Acre Checking the Data Enter or modify data by using the drop down menu in the upper right corner of the active window Select the appropriate heading to view the data contained within this file Stocking Data Maximum Biomass Date When the stocking data has been entered the next step
27. l 1980 coupled with a trout stocking formula proposed by Kelly 1965 Model predictions were used to explore predicted population abundances under different stocking levels and in comparison to carrying capacity as defined by habitat or stream type With such a model stocking levels could be adjusted to meet the demands of fishing pressure without exceeding the biological capacity of the ecosystem to sustain the population throughout the sport fishing season In addition to number stocked data from creel censuses were used to assess fishing pressure and angling harvest while in stream surveys were conducted to assess population levels of native trout and other species To assess the carrying capacity of the system three measures of trout ecosystem quality were developed N abundance number of non trout species present H a quantitative assessment of non fish biotic and abiotic habitat attributes e g cover F the overall fertility of the stream which included physical and chemical attributes Engstrom Heg 1990 Engstrom Heg and Engstrom Heg 1984 later developed this population dynamics model into two versions of a FORTRAN program known as STREAM SOURCE1 and 2 Engstrom Heg 1984 This computer program was subsequently translated into a LOTUS worksheet format known as Trout 4x4 which was used for many years by NYSDEC staff to establish trout stocking levels We have re written the program as an interactive Microsoft Visual Basic program
28. low the data grid Growth Like natural mortality growth is separated by year and component along with season and winter columns The winter growth rate is set for the whole winter season usually to a rate of 1 04 meaning that the fish will be 4 larger on April 1 than they were on Oct 15 when the season ended Wild growth rates can also be entered allowing for differences between wild and stocked components Catchability q As a fish ages it often becomes more difficult to catch thus reducing its catchability The catchability data field takes into account the age of the fish accounting for this fact by allowing differing rates for yearling and older fish based on a monthly value Data Defaults The data contained in the table below is a generalized form of the default values derived by Engstrom Heg for the three main stream types For more detailed stream types and their corresponding parameters including those with length regulations see Appendix at the end of this manual explaining each stream type Predictions for the month of October are now possible under the current model formulation but default values for this month have not yet been established As a result empty data cells exist for October Changes are yet to be made as to how to distribute weights such as catchability and effort to accommodate the season which now runs until October 15 Table 3 Default values for mortality and growth of stream types along with patte
29. n Arbor http www michigandnr com PUBLI CATIONS PDFS ifr manual SMI1 20Chapter17 pdf Van Den Avyle M J amp R S Hayward 1999 Dynamics of exploited fish populations Pages 127 166 in C C Kohler amp W A Hubert editors Inland fisheries management in North America 2 edition American Fisheries Society Bethesda Maryland 38 Appendix Stream Classification Key Source Engstrom Heg R 1990 page 5 Bw Bs Bp Aw Aw9 Aw10 Awp As As9 As10 Asp Infertile or habitat deficient wild trout streams lacking significant unused carrying capacity Not stocked Infertile or habitat deficient streams often small with significant unused carrying capacity and a light to moderate fishery Stocking provides for an early season fishery and some holdover Put and take streams characterized by a moderate to heavy fishery and relatively little potential for wild and holdover contribution Productive wild trout streams with light to moderate fisheries Not Stocked No size limit Wild trout stream managed under a 9 inch limit Special regulation areas based on wild populations with a 10 inch 3 fish artificials only regulation Heavily fished wild trout streams lacking significant unused carrying capacity and inappropriate for a size limit Wild population is supplemented by stocking of put and take fish to provide for the early season fishery Stocked streams with no length limit having signifi
30. n predictions after changing table inputs Accessing Other Data The Browse button in the upper left hand corner can be selected to determine which stream database file is to be used The window that appears is identical to the one that appeared when you began the program so all you need to do is browse to find the appropriate Microsoft Access database file mdb then double click the file corresponding to your particular stream of interest If a database has not yet been created for the stream you are interested in see the Data section below for information on developing one Saving Results When you click on the Save button at the top of the form the program will ask whether you would like to save the graphical output or report format Depending on the chosen alternative the program will allow you to save the data in either a Notepad file report format or a Bitmap bmp Metafile mtf or Jpeg jpg file graphical output format Another option is to use the screen capture feature that will copy the screen that is displayed then paste it as an image onto the clipboard This is done by pressing the PrintScrn key located near F12 usually above Home and Insert keys on your keyboard This will copy the screen image to the clipboard and then you can paste it into a document e g MS Word After this you can use the Crop function on the Picture toolbar to trim the full screen image to the desired size Keep in mind that only graphs of the c
31. nge the database this only means you are not allowed to change the data structure The individual data components can in fact be changed and saved You may be asked to convert to the newer version of Microsoft Access but this it not necessary The program can import Access 1997 and newer data files without a problem 21 Executing the Program Worked example What follows is an example of how to use Trout exe to make predictions from data that may be contained in a standard CROTS datasheet as shown down below E Using the Stream type indicator as identified by the description near the AJ on the sample CROTS datasheet below we can find the appropriate default parameters corresponding to that stream type as found in the data defaults in the Data section of this manual For the following example using stream type As these values are Stream Type Natural Growth Rate Growth Rate Winter Mortality 1 Year 2 4 Year Growth Zn Rate As 002 004 0025 1 04 These data are used in the Natural Mortality and Growth data fields although natural mortality can be set using the radio buttons corresponding to Stream Type in the upper right corner 2 The fishing pressure intensity that the stream receives is found on the form near the B and is inputted into the Season Data grid This is also the grid that allows you to specify the time period over which you want the population modeled an
32. ntinue this process until all the data has been appropriately modified and then make sure that the symbol in the first row of the selected data grid looks like this gt rather than a symbol of a pencil writing The arrow symbol indicates that the data has been saved If the pencil icon is still visible when the Calculate button is selected that cell of new data will not be used so make sure to save it You can also select another heading from the list to ensure that all changes have been saved Stocking bata Meoctrum Biomoss 129 172 Date 23 Aug Data notsaved Data is saved and will be used Modifying Data in Microsoft Access The easiest way to create a new stream database file is to copy and rename an existing file and make the necessary changes to this new file You can usually alleviate some work by copying a file associated with a stream type similar to that which you are creating since much of the data will remain the same Upon opening a file you may be presented with this message from Access 20 Microsoft Access You can t make changes to the database objects in the database Datka Creek ID 1537 as 01 This database was created in an earlier version of Microsoft Access To convert this database to the current version of Microsoft Access close the database point to Database Utilities on the Tools menu and then click Convert Database OK Do not worry While it says you cannot cha
33. orkbook you must enable the macro Now execute the macro by either using the keyboard shortcut Control t or by using the Macro selection under Tools and then select Macros When a list of macros appears containing only one option select CROTSTextConverter and then click Run Either way the macro will then open a dialog box asking you to select the desired input text file that you created in Trout exe After you select the file the macro will manipulate the data and create a workbook with worksheets corresponding to different output headings from Trout exe In order to create this workbook the macro creates a page with all the original data from the text file called Base which contains all data and used this to create the subsequent pages Pages with titles containing rel correspond to release for space conservation i e rel per hr released per hour The top three lines of each worksheet contain data pertaining to the file time and data of text file creation database name mdb and heading titles 16 Data The following data are required to compute predictions of population abundance and catch 1 the timing and level of stocking including date number acre and average length of stocked fish 2 the timing and level of fishing effort 3 release rate and 4 population dynamics parameters natural mortality and growth associated with a given stream type Default settings are provided based upon the stream type selected
34. ornell edu 607 255 8213 607 255 2775 37 References Anderson R O R M Neumann 1996 Length weight ad associated structural indices Pages 447 482 in B R Murphy amp D W Willis editors Fisheries Techniques 2 edition American Fisheries Society Bethesda Maryland Clark R D G R Alexander amp H Gowing 1980 Mathematical description of trout stream fisheries Transactions of the American Fisheries Society 109 587 602 Engstrom Heg R 1990 Guidelines for stocking trout streams in New York state New York State Department of Environmental Conservation Engstrom Heg R 1991 Program Documentation for Trout 4x4 Bureau of Fisheries New York State Department of Environmental Conservation Engstrom Heg V R Engstrom Heg 1984 A FORTRAN program for predicting yields of stocked trout from stream fisheries under various management alternatives North American Journal of Fisheries Management 4 440 454 Kelly W H 1965 A stocking formula for heavily fished trout streams New York Game and Fish Journal 12 170 179 Ricker W E 1975 Computation and interpretation of biological statistics of fish populations Fisheries Research Boards of Canada Bulletin 191 Schneider J C P W Laarman H Gowing 2000 Length weight relationships Chapter 17 n Schneider J C ed 2000 Manual of fisheries survey methods II with periodic updates Michigan Department of Natural Resources Fisheries Special Report 25 An
35. re kept creel rate Pks Proportion of sublegal sized fish that are kept poaching rate PL PG Proportion of population that is legal sized length gt size limit R Zr Rate at which fish are released F Handling Zh Instantaneous mortality due to handling Sr Expected release survival rate hooking survival Z zt Total mortality rate Fcreei FHandiing M W Weight of average fish in pounds B Total daily biomass Getting Started Downloading and installing the program To facilitate access to and use of this program a website has been developed from which interested parties can download the program access the documentation and query software support To access this material go to the Coldwater Fisheries Research Program website http www dnr cornell edu pjs31 Coldwater ColdwaterFisheries htm Click on the Trout Setup Zip File located at the site to download Trout exe and the associated support files An unzipping program or software PowerArchiver WinZip etc will be necessary to extract these files to a usable form on the computer Using this program extract these files to a location on your computer where you wish to save this data The zip file contains the Trout exe set up executable file along with necessary support files an example Access database CROTS Example mdb a folder containing general stream type databases and an Excel file CROTS_ConvertToExcel xls containing a macro to convert saved Trout exe
36. rns of fishing effort and catchability and coefficient of variation for length measurements Stream Type Natural Growth Rate Growth Rate Winter Mortality 1 Year 2 Year Growth Zn Rate Bp 004 002 001 1 04 Bs 004 004 0025 1 04 As and As9 002 004 0025 1 04 As length limit 002 005 003 1 04 gt 10 Awp 004 002 001 1 04 Fishing patterns of monthly effort Month Pattern 1 Pattern 2 April 0 350 0 493 May 0 219 0 273 June 0 158 0 094 July 0 107 0 055 August 0 095 0 045 September 0 069 0 041 Oct until Oct 15 0 0 0 0 Catchability Month Year 1 Year 2 April 0 00537 0 00495 May 0 01030 0 00759 June 0 00838 0 00529 July 0 00538 0 00529 August 0 00618 0 00529 September 0 00618 0 00529 Oct until Oct 15 0 0 0 0 Coefficient of variation for length 0 09 Modifying the Data There are two simple ways to modify the data that is used to run the Trout exe program one way is to change the data in the data grid of the program and the other is by opening the database itself in Microsoft Access Modifying Data Within the Program To change data while the program is open is very simple First select the heading of the data that you wish to change from the drop down menu to display the appropriate data set Next click in the cell that contains the data that you would like to modify and make your changes Co
37. that day for use in tracking daily figures throughout the program Public Sub Fill output grid takes in a data array number of stocked components and wild components season start day and start year Formats and fills flexgrid report with data in the array and then calls the appropriate plotting procedure depending on the type of data that is being analyzed Utilizes get_header and calls either lwgraph or linegraph Public Sub Fill output_grid_age very similar to the above procedure taking in the same things but outputting numbers in terms of year classes for example yearlings and 2 year olds Also contains its own plotting code Public Sub getseasoninfo takes in information concerning the working database along with component numbers and start day Extracts and sets to local variables the information contained in the Season Data field Public Function get_ date takes in julian day number alone with the start year to return date information in the form of 15 Apr instead of sometimes confusing julian day numbers Public Sub linegraph called from the Public Sub Fill output_grid to produce line plots representing totals Takes in data array and array of totals and the start year Public Sub lwgraph called from the Public Sub Fill output grid to produce plots representing individual component data in the form of lines receiving a data array and number of stocked and wild components Public Function get_ head
38. ths are required The program uses this information to estimate the abundance of wild trout present throughout the season by back calculating from fall numbers to account for the number of fish that are creeled and die due to a natural mortality figure given in the data file To be sure that the wild fish have influences on outputs make sure to check that values pertaining to wild components such as catchability and natural mortality are set at appropriate values Season Data Fishery parameters such as fishing intensity in units of yearly hours per acre of fishing effort the time span over which the user wants to evaluate model predictions regulatory size limits if present and an estimate of release survival Release survival is the proportion of fish released by anglers that survive If you would like to model a situation representing a no kill area enter 1000 into the size limit keeping in mind that the illegal harvest rate PKS and release survival will have substantial impacts on the outputs of the model in this scenario Effort Month The monthly distribution of yearly fishing effort during the sport fishing season Each value is the proportion of the effort that is expended in that month These values are usually chosen from the set of values defined by trends categorized as pattern 1 or 2 with the patterns being defined as follows Pattern 1 April fishing accounts for less than 40 of the total fishing effort and at least 20
39. to select the appropriate stream type and effort distribution which will set the natural mortality value and indicate how to distribute the yearly fishing effort in the heading Season Data found under the drop down with Stocking Data If more specific data than the baselines associated with stream type and fishing patterns is available from previous studies or creel surveys this information can be entered by selecting the Other Input Required option in either of the fields When this option is selected the field heading in the drop down menu will change to show 12 the grid of the particular input that is affected by that decision natural mortality ZN for the Stream Type selection and effort per month for Fishing Pattern zN y Maximum Biomoss 20 637 Date 19 Apr Year Componer Fishing Pattern Pattern 1 le Type A As Asp etc e Pattern 2 Type B Bs Bp C Other Input Required C Other Input Required After reviewing the data indicate whether you want the program to calculate results by age classes or by stocking increments cohorts with their associated totals by selecting one of the two designated option buttons in the upper left This calculation option can be changed at any time during the execution of program The Age Classes option returns results organized as groups by age for instance all stocked fish will be considered yearlings and wild fish will be considered separate populations
40. ure applied over the entire stream reach This daily measure of effort is then multiplied by catchability which may vary by stocking component month and year Ay Fin 2 Fishing D Each stocking event is represented as a separate component that is tracked through time as distinct populations These separate stocking components are combined when the totals are finally calculated In order to determine the rate at which anglers remove fish or the instantaneous creel rate Fcreen the model requires information regarding the proportion of fish that are legal sized P and the proportion that are sublegal sized 1 P the proportion that are kept or creeled from the legal sized component Px creel rate and the proportion that are kept from the sublegal sized component Pxs poaching rate 5 Foree F Fishing P KL JP Lt P KS Ma P a Not all fish that are caught by anglers are removed from the system Sub legal fish are usually released and some anglers release legal fish i e catch and release anglers The rate at which they are released R is the difference between the instantaneous fishing rate and the instantaneous creel rate 6 R F Fishing Foree s A proportion of the fish that are released do not survive the stresses that accompany being hooked and therefore add to total mortality This additional mortality is represented through the term Fyanaling TO account for those fish that die due to this stress we must
41. urrently selected heading will be saved To save the full report output containing tabular data from a variety of rates and figures ranging from population numbers to lengths and weights answer No when asked if you want to save the graphical output thus indicating you wish to save the report format This then saves a compiled list of these headings into a text file txt which you can name Viewing Outputs in Excel To view the data in a comprehensible and manageable setting open either the CROTS ConvertToExcel v2003 xls or CROTS ConvertToExcel_v97 amp 2000 x s file using Microsoft Excel Choose the file version that corresponds to the version of Excel that you are running and when in doubt choose the earlier version newer versions of Excel can work with older formats but not vice versa Depending on the security setting of your system it may tell you that your security setting does not allow you to open macros like the one in this file To change the security setting of Excel select Macro from the Tools drop down and then select Security from the list When given the choice of settings select the Medium security level This will tell your computer to always ask for permission before opening any macros that might be of questionable origin After opening the file which should contain a blank spreadsheet the program will ask if you would like to enable macros To convert the text file you have saved using Trout exe to a usable Excel w
42. y size limit regulation and the expected release survival rate usually set to 0 9 In this example our intensity is 175 hrs acre 3 Most streams in New York receive the bulk of the fishing pressure early in the season soon after the Month Pattern 2 fish are stocked and hence most of the streams are April 493 classified as Pattern 2 fisheries with a skewed May WIE distribution of effort In our example the given une 094 stream is indicated to be Pattern 2 as denoted near u y 055 the C so we enter data corresponding to pattern 2 August 045 from the Data section into the grid with the heading September 041 Effort Month or select the Pattern 2 radio button Oct until Oct 15 4 The Stocking Data table is one of the most important fields in the model storing the number size and release date of stocked fish Individual stocking events are denoted in the first table on the CROTS datasheet as indicated by the D The information is entered in much the same way as it appears on the data sheet with the first increment being the earliest stocking event and the data for each event having its own separate row 22 as seen below It is not essential but it makes it easier to follow in the results if you enter the first stocking in the row labeled Component 1 and so on 5 Catchability is often hard to Month Year 1 Year 2 estim
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