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User`s Manual for the Program Package ECOWEIGHT (C Programs

1. 1 3 13 and all remaining elements of the vector are zero The first acsA elements and the last element of A m are zero Furthermore the elements acsA 1 to acsA acdA LLA are zero if acdA gt LLA The remaining elements are h_mfacsA acdA LLA i 4E Ai for i 1 LLA 3414 3 3 Calculation of economic weights The economic weights for direct effects ew d i and for maternal effects ew m i of trait 7 are calculated as follows ew 1 x Ds h d i x m if tt i 0 or tt i 2 ew mi 1 x 3 h m i x m_sum i if tt i 1 or tti 22 3 15 In most cases the same symbols for variables are used in the manual and in the program written in C For differentiating between a vector or a matrix generally an array and its elements we use an index i j k etc for an element of the array and use the symbol instead of an index to refer to the array as such Chapter 4 Production system 2 System with terminal crossing and one production level only In this production system specialized sire and dam breeds are assumed Sire and dam breed flocks are assumed to be self replacing producing both males and females for own replacement selling and purchasing of breeding animals between farms within each breed is not taken into account in the profit function for the calculation of economic values Sire breed flocks produce also sires for terminal crossing in the dam breed flocks
2. RRA expressed as proportion of rams entering any breeding cycle xus 1 I4RB i Rams of breed B entering breeding cycle i i 1 RRB expressed as proportion of rams entering any breeding cycle yin IARD i 1 LLA Number of reproductive cycles for ewes of breed A LLB Number of reproductive cycles for ewes of breed B m gf i Vector m of dimension acm used in the calculation of gene flow see Chapter 2 i 1 acm is the sex and age class m X Vector m of dimension acm used in the calculation of gene flow at the end of the investment period see Chapter 2 i is the sex and age class APPENDIX LIST OF VARIABLES AND CONSTANTS 43 m sumji n2 n3 n sac NT pdA pdB pgdsA pgdsB pgssA pgssB prods l inv Vector 5 ml 1 u of dimension acm used in the calculation of t 1 gene flow see Chapter 2 The vector contains the number of discounted expressions for the group of animals given by the variable n_ sac for the individual sex and age classes Number of the input file Code for the use of capital letters in the name of the input file 0 no letter 1 A 2 B etc Number of the sex and age class for which the gene flow is calculated Number of traits 1 Gene transmission matrix P of dimension acm x acm for gene flow see Chapter 2 Fraction of ewes of breed B crossed with rams of breed A in reproductive cycle i i L LL 1 pcros
3. echo echo gt 2 echo am copying ERROR TXT to the working directory echo gt 2 PROG ERROR TXT echo echo 2 echo I am starting program EWSH2 breed echo 2 PROG ewsh2 exe echo echo 2 echo I am starting program EWSH2 breed A echo 2 PROG ewsh2 exe echo echo 2 echo I am starting program EWSH2 breed A echo 2 PROG ewsh2 exe echo echo 2 echo I am starting program EWSH2 breed echo 2 PROG ewsh2 exe echo echo echo I am starting program GFSH echo PROG gfsh exe echo ec
4. 2 acsA RRA 0 5 x I4RA i for L RRA 4 17 and the elements of matrix P2 are Placm 2 lacsA acdA LLA i 0 5 x IAEA i for 1 LLA 418 That means the elements of Pg are the same as the elements in the first row of P21 and the elements of Pez are the same as the elements in the first row of P22 4 1 7 Submatrices P74 and P7s is the sires B to slaughter animals B matrix and P7s is the dams B to slaughter animals B matrix Both matrices are of type Ss The elements of matrix P74 are 1 acsA acdA acsAB acsB RRB i 0 5 x IARB for i 1 RRB 4 19 and the elements of matrix are 1 pcrossE i 1 LLB 5 1 perossE l 1 l 1 P j k 0 5 x I4EB i x LLB 4 20 where j acm 1 and k acsA acdA acsAB acsB acdB LLB i The elements of P74 are the same as the elements in the first row of P54 CHAPTER 4 TERMINAL CROSSING 18 4 1 8 Submatrix Pas Pas is the sires A to cross bred slaughter animals matrix It is of type Sg Its elements are Placm acsA acdA acsAB RRB i 0 5 x IARB i for i 1 RRB 4 21 4 1 9 Submatrix Ps5 Pas is the dams B to cross bred slaughter animals matrix It is of type Sg Its elements are pcrossE i 1 LLB 5 pcrossE l 1 1 1 P j k 0 5 x x for i 1 LLB 4 29 where j acm and k acsA acdA acsAB acsB acdB LLIB i 4
5. 23 31 TEXTGFS OUT TXT 22 29 TEXTS2 OUT TXT 22 traits 38 transmission matrix 8 11 15 31 uncompressing 24 variables 40 46
6. Cygwin 24 cygwinl dll 22 dam breed 14 23 direct trait 8 discount rate 30 discounted expressions 43 ECOWEIGHT03_5_0_1 tgz 24 ECOWEIGHT03A pdf 24 ECOWEIGHTO3B pdf 24 ERROR TXT 22 EWBC 6 EWDC 6 EWSHI 6 EWSH2 6 ewsh2 exe 22 gcc compiler 24 genetic standard deviation 30 33 41 gfsh c 24 gfsh exe 22 indicator variable 43 input files 23 29 NPUTGFS TXT 25 26 29 35 NPUTGFSO1A TXT 30 NPUTGFSOI1B TXT 30 NPUTGFSO02 TXT 11 31 NPUTGFSO03 TXT 16 31 NPUTGFS04 TXT 33 NPUTGFSO05 TXT 33 NPUTS A TXT 23 25 26 NPUTS B TXT 23 26 investment period 31 32 language 29 license 3 24 marginal economic value 30 maternal trait 8 9 mathematical functions 24 monetary unit 29 MU 29 POI TXT 35 PO1 00 TXT 22 P02 00 TXT 22 PARAGFS TXT 23 25 26 35 parameter file 23 PARASA TXT 23 25 26 PARASB TXT 23 26 production system 29 production system 1 23 25 31 production system 2 23 26 31 pslA bat 23 25 ps1A sh 23 25 ps2AB bat 23 26 ps2A B sh 23 26 quotation marks in input files 29 realization vector 8 reproductive cycle 30 01 26 resA02 27 45 INDEX 03 27 01 27 resB04 27 resgfps01 26 resgfps02 28 results file 29 33 35 sex and age class 8 15 shell script 25 26 sire breed 14 23 slaughter animals 12 15 18 source code 24 terminal crossing 14
7. Re a 62 1 Under LINUX 2 522 933 oe 6 2 2 Under Microsoft 6 3 Running the program sss 4n qoo eee ba 6 3 1 Running the program for production system 1 6 3 2 Running the program for production system 2 6 4 General remarks 242245255544 aS SAS GE Y X X OX xe 7 Input files EL Parameter DES 2 050 uewewe Pace B Bohn ee Re TLL File POLTAT 2 2 82 5883 204 0488 7 1 2 File PARAGFS TXT 2 2 25562424 nee i Data mpat loce we bos ww pep or fem SELLS 7 21 Input file INPUTGFSOIA TXT 72 2 Input fle INPUTGRSOIB TXT 2 242 244 oes 73d dIuputBleINPUTGESUATXT cee eee BA wd 4 7 2 4 Input file INPUTGFS03 TXT 1 2 5 Input file INPUTGFSO4 TRYT i c c 6555686544 246 Input file INPUTGESOUD EXT 2 4 66 42 fe m x om Ra To TEXTGRS OUT DXT ecse oR 9o x xn QU IRBORZEXI gt p sh hue st eee SEE DS 8 Program output pol c sau ee ee SRE PERE SARE EE oo 8 amp 2 JHeGAIHBECRGES 2 54408 42240229554 ROR Aw we eed Bibliography A Numbering of traits in the program B List of variables and constants 24 24 24 25 25 26 28 29 29 29 30 30 30 30 31 31 33 33 33 33 35 35 36 37 38 40 Chapter 1 Introduction The program package ECOWEIGHT is intended for the calculation of economic values of economically importa
8. describing always the same trait in different ways As both positive and negative values occur it is useful to calculate the sum from the absolute values of the economic weights It may be useful to calculate this sum for the economic weights of the direct components of the traits d for the economic weights of the maternal components of the traits ewsum m and for both components together ewsum NT 1 ewsum d 5 delta_d i x abs ewst_ d i i 1 NT 1 ewsum m 3 delta_ mili x abs ewst_m i 5 2 i 1 and ewsum ewsum_d ewsum_m 5 3 The variables delta d i and delta_mJi take only values 1 0 depending on con sidering or not considering the corresponding trait The following proportions of standardized economic weights which are called relative economic weights may be calculated 20 CHAPTER 5 RELATIVE ECONOMIC WEIGHTS 21 e Standardized economic weight for the direct component of trait i expressed as percentage of the sum of all standardized economic weights for the direct components abs ewst d i ewsum d ewr dd i 100 x 5 4 e Standardized economic weight for the direct component of trait i expressed as percentage of the sum of all standardized economic weights for both the direct and the maternal components abs ewst d i ewr da i 100 x ewsum 5 5 e Standardized economic weight for the maternal component of trait i expressed as percentage of the sum of all standardized econ
9. it was used in the source code of the program and a list of all variables used in the source code of the program Chapter 2 General principles of gene flow Gene flow methods which were developed by Elsen and Moquot 2 and Hill 3 allow studying the flow of genes through a population which in turn can be used to define the times at which genes are expressed and by knowing the value of that expression and the number of animals involved the economic value of that expression can be calculated i At any given time animals in a population can be divided into a number of different sex and age classes gene flow diagram can then be constructed to follow the movement of genes through the population over time Time is given in reproductive cycles i e years in the case of one lambing per year vector m is defined the elements of which define the proportion of genes in each sex and age class The dimension of the vector is acm the total number of sex and age classes Assume that the sex and age class n sac is selected for Then at time t 0 all elements of m with the exception of the n sac element will be zero and the n_ sac element of m will be one Let us write mtl for m at time t and P for the transmission matrix which is of dimension acm x acm and the elements pj of which are the probability that genes from the sex and age class j are transmitted to the sex and age class i during one time unit Knowing m9 i e vector m at t
10. of the parameter s according to your needs In the recent version of the program the file contains only one parameter e Genetic standard deviations for the direct and maternal components of the traits 1 are not known or are not intended to be used for the calculation of relative economic weights 2 are known and given in INPUTGFS04 TXT 7 2 Data input files 7 2 1 Input file INPUTGFSO1A TXT This file is produced by the program EWSH2 and should not be edited It contains the following input values for breed A only numbers no text e Annual discount rate e Number of breeding cycles for rams of breed A RRA e Proportion of rams of breed A entering each breeding cycle l4RA i e Number of reproductive cycles for ewes of breed A LLA e Proportion of ewes of breed A entering each reproductive cycle A i e Marginal economic values for all traits of breed A in the unit as they are printed evpA i 1 by the program EWSH2 The value 0 000000 is inserted for economic values which were not calculated in the given system e Age of rams of breed A used for pure breeding at the beginning of the first breeding cycle ageR11A e Age of ewes of breed A at first lambing ageE14A 7 2 2 Input file INPUTGFSO1B TXT This file is produced by the program EWSH2 and should not be edited It is not read for production system 1 It contains the following input values for breed B only numbers no text e Number of b
11. see Figure 4 1 The number of age classes for sires of breed A used for pure breeding acs A and the number of age classes for dams of breed A acdA are calculated according to equations 3 1 and 3 2 respectively The age classes for sires of breed B acsB and the number of age classes for dams of breed B acdB are calculated in the same way as the corresponding variables for breed A replace A by B in equations 3 1 and 3 2 The number of age classes for sires of breed A used for cross breeding with ewes of breed B acsAB is ageR12A AB int acs in 365 RRB 4 1 The total number of sex and age classes which is identical with the dimension 1 same age structure and the same number of breeding cycles is assumed for rams of breeds A and B in the flock of breed B slaughter animals A male replacement B E CI 8 Sire breed 28 E BS A Qe 9 9 52 Dam breed 5 B 2f B sires A i slaughter animals AxB slaughter animals B Figure 4 1 System with terminal crossing on one production level 14 CHAPTER 4 TERMINAL CROSSING 15 of the transmission matrix P for gene flow acm is then acdA acsAB 3 4 2 4 1 Calculation of the elements of the transmission matrix P Matrix P has a block structure containing 8x8 blocks and can be therefore writt
12. sh gt a tat under LINUX or ps1A bat gt a tat under Windows and press ENTER The shell script ps1A sh for running production system 1 looks like that bin sh echo gt 2 echo I am copying P01_00 TXT to POO TXT echo gt 2 cp PROG P01_00 TXT POO TXT echo echo gt 2 echo am copying TEXT _OUT TXT to the working directory echo gt 2 cp PROG TEXTS2 OUT TXT cp PROG TEXTGFS_OUT TXT echo echo gt 2 echo I am copying ERROR TXT to the working directory echo gt 2 PROG ERROR TXT echo echo gt echo I am starting program EWSH2 echo gt PROG ewsh2 exe echo echo gt echo I am starting program GFSH echo gt CHAPTER 6 INSTALLING AND RUN
13. text file forwarding error messages between succesive runs of the program EWSH2 and the program GFSH The file in this directory contains the starting value 0 which means no error message cygwinl dll This is a file from Cygwin which is necessary for running the pro grams under Windows It is contained only in the distribution for Windows 22 CHAPTER 6 INSTALLING AND RUNNING THE PROGRAM 23 6 1 2 Directory PS1 This directory contains files necessary for running production system 1 Production system 1 is only for one breed Without loss of generality we will call this breed A PARASA TXT Parameter file which contains the most important parameters for running the program EWSH2 For further details see the manual for the program EWSH2 6 PARAGFS TXT Parameter file which contains the most important parameters for running the program GFSH see Section 7 1 2 INPUTS A TXT with 01 02 14 Data input files for program EWSH2 Not all data input files are needed for all calculations For further details see the manual for the program EWSH2 6 INPUTGFS TXT with 01A 02 04 Data input files for program GFSH see Section 7 2 ps1A sh under LINUX or ps1A bat under Windows This is the shell script LINUX or batch file Windows which starts the calculations for production sys tem 1 6 1 3 Directory PS2 This directory contains files necessary for running production system 2 This is a system with terminal crossing
14. weight for the maternal component of trait i expressed as percentage of the sum of all standardized economic weights for both the direct and the maternal components see equation 5 7 ewr mm i Standardized economic weight for the maternal component of trait i expressed as percentage of the sum of all standardized economic weights for the maternal components see equation 5 6 ewst 41 Standardized economic weight for the direct component of trait i see equation 5 1 ewst m i Standardized economic weight for the maternal component of trait i see equation 5 1 ewsum Sum of the absolute values of the standardized economic weights for both the direct and the maternal trait components ewsum d ewsum m ewsum d Sum ofthe absolute values of the standardized economic weights for the direct trait components see equation 5 2 ewsum m Sum of the absolute values of the standardized economic weights for the maternal trait components see equation 5 2 flag i Chooses always between two trait definitions in the calculation of rela tive economic weights see Table B 1 gstd Indicator variable if the genetic standard deviations for the direct and maternal components of the traits are not known or are not intended to be used for the calculation of relative economic weights gstd 1 or are known and given in INPUTGFS04 TXT gstd 2 gstd Genetic standard deviations for the direct component of trait i i 1 NT 1 APPENDIX LIS
15. 0 5 xlARB i for i 1 RRB 4 11 The remaining non zero elements of P44 are PlacsA acdA acsAB i 1 acsA acdA acsAB i 1 for i 1 acsB 1 4 12 The elements of the first row of P55 are P j k 0 5 4 for i 1 LLB 4 13 where j acsA acdA acsAB acsB 1 and k acs A acdA acs AB acsB acdB LLB i The further non zero elements of P55 are Placm acdB 2 i acem acdB 3 i 1 for i 1 acdB 1 4 14 CHAPTER 4 TERMINAL CROSSING 17 4 1 5 Submatrices P45 and P54 P45 is the dams to sires matrix for breed B and Ps is the sires to dams matrix for breed B Both matrices are of type Sz The elements of the first row of Pas may be read in from input file INPUTGFS03 TXT if the dams for the production of rams are selected from certain age classes Otherwise the non zero elements of matrix P45 are calculated in the program P j k 0 5 x IAEB i for i 1 LLB 4 15 where j acsA acdA acsAB 1 and k acsA acdA acs AB acsB acdB LLB 1 The elements of the first row of are calculated as P j k 20 5 x IARB i for i 1 RRB 4 16 where j acsA acdA acsAB acsB 1 and k acsA acdA acsAB acsB RRB i 4 1 6 Submatrices Peg and Ps Pa is the sires A to slaughter animals A matrix and P2 is the dams A to slaughter animals A matrix Both matrices are of type The elements of matrix are Placm
16. 2 Vectorsm m_gf in the program hg and hm Vectors m_gf and m_sum x are calculated in the same way as in production system 1 see section 3 2 on page 13 They are of dimension acm and can be subdivided into 8 blocks in the same way as matrix P Also vectors h_d and m are of dimension acm and have 8 blocks In vector h d only the elements referring to slaughter animals are different from Zero h 2 pdA h_dlacm 1 h_dlacm 4 23 In the vector for maternal effects h non zero elements are in the blocks dams A and dams h m acsA acdA LLA i 1 x pdA for i 1 LLA h m acm 3 LLB i Ii4EB i xpdB for i 1 LLB 4 24 The elements of the vector hm sum to 1 4 3 Calculation of economic weights By multiplying the vectors h_d and h m with the marginal economic values of each trait the matrices he d x and he m are calculated The first index of the matrices refers to the number of the trait and the second index refers to the sex and age class First all elements of the matrices he_d and he_m x are set zero The non zero elements of he d are calculated as follows for i 21 NT 1 he d i acm 2 h_dlacm 2 x evpA i 1 he d i acm 1 1 x evpB i 1 4 25 he_ h_dlacm x 1 CHAPTER 4 TERMINAL CROSSING 19 Table 4 1 Values of tt i
17. INPUTGFS03 TXT 4 1 2 Submatrices P3 and P32 Submatrices P31 and P32 are of the structure S2 P31 represents the gene flow from sires of breed used for pure breeding to sires of breed used for cross breeding and P832 represents the gene flow from dams of breed A to sires of breed used for cross breeding P31 and P32 are of dimension acsAB x acsA and acsAB respectively The non zero elements of P31 are PlacsA acdA for 1 4 8 ie they are the same as the elements in the first row of P11 The non zero elements of P32 are PlacsA acd A 1 acsA P l acsA for i 1 acdA 4 9 ie they are the same as the elements the first row of P12 4 1 3 Submatrix P33 Pas is the sires to sires matrix for sires of breed A used for cross breeding with dams of breed B It is of type S4 Consequently its non zero elements are PlacsA acd A i 1 acsA i 1 for i 1 acsAB 1 4 10 4 1 4 Submatrices P44 and P5 P44 is the sires to sires matrix for breed and Pss is the dams to dams matrix for breed B Both matrices are of type S The elements of the first row of P44 may be read in from input file INPUTGFS03 TXT if the sires of breed B for the production of rams are selected from certain age classes Otherwise the elements of the first row of P44 are calculated as follows PlacsA acd A acsAB 1 acs A acd A acsAB acsB RRB i
18. NING THE PROGRAM 26 PROG gfsh exe echo echo echo I am ready echo The following two results files will printed e resA01 This is the results file from program EWSH2 e resgfps01 This is the results file from program GFSH described in this man ual Furthermore the values of all variables are printed for both programs in the follow ing files e 01 Complete list of the values of all variables of breed A from program EWSH2 at the end of the calculation The description of the variables is given in Appendix B in the manual for EWSH2 6 e CHECKSA01a Complete list of the values of all variables of breed A from program EWSH2 before the program starts the calculation of economic values This file is printed mainly as help for further programming and as a check for correct computing With one exception variable zr number of the loop the values of all variables contained in both files must be equal The file CHECKSAO01a does not contain the economic values which are printed only in CHECKSAOI CHECKGFS Complete list of the values of all variables from program GFSH The description of the variables is given in Appendix B of the present manual 6 3 2 Running the program for production system 2 All files needed for running production system 2 are in the directory PS2 Further more the directory PROG is needed where the program files and further files are locate
19. Number of the trait i Value of tt i 4 to 7 9 to 19 20 25 0 8 22 26 to 35 1 1 to 3 21 23 24 2 Appendix A for numbering traits The non zero elements of he m are for 1 NT 1 he h_m j x evpAli 1 for j acsA 1 acsA acdA h_mlj x eupB i 2 4 26 for j acm acdB 2 acm 3 The economic weights for the direct and the maternal components of trait i ew d i and ew are calculated as follows acm ew 4 2 he x m sum j if tt i 0 or tt i 2 acm ew m i 2 he m i j x m sum iftt i 1 or tt i 2 4 27 where 0 if there is only a direct component of trait i tti 4 1 if there is only a maternal component of trait i 2 ifthere are both a direct and maternal component of trait i The values of tt i are fixed in the program see Table 4 1 These economic weights are valid for the sex and age class of animals which is determined by the variable n sac The economic weight of trait i or component of trait i represents the present value in monetary units of one unit genetic superiority of the selected group of animals in this trait transmitted in the evaluated production breeding system during the defined investment period per ewe in this production system If the economic weights are calculated for breed they can be easily converted to be per ewe of breed by dividing the weights calculated by equation 4 27
20. P 1 1 to P 1 acsA These values are only read if indicator variable 1 is set to 1 e Proportions of genes from individual age classes of dams in male progeny path dams to sires the numbers must sum to 0 5 P 1 acsA 1 to P 1 acsA acdA These values are only read if indicator variable 2 is set to 1 7 2 4 Input file INPUTGFS03 TXT This file contains input parameters for calculating the transmission matrix P for gene flow for production system 2 cross bred system with two breeds on one pro duction level applying partly terminal crossing The file has a similar structure as INPUTGFS02 TXT When filling in the numbers you must know the number of sex and age classes which can be calculated as shown at the beginning of Chapter 4 See also the explanations to input file INPUTGFS02 TXT The following values are read from the input file CHAPTER 7 INPUT FILES 32 Proportion of ewes of breed A in the production system pdA Proportion of ewes of breed B in the production system pdB Number of the sex and age class for which the gene flow will be calculated n_ sac Length of the investment period 1 inv Indicator variable 1 pgssA Insert 1 if the proportion of genes from the individual age classes of sires of breed in male progeny are to be read from this file and insert 2 if the proportion of genes from the individual age classes of sires of breed in male progeny are automatically inserted by the program i e equ
21. R 8 PROGRAM OUTPUT 36 Remark A dense network of conditions was used in the program to ensure print ing out only the items relevant for the given production systems But it cannot fully be guaranteed that no variables not meaningful for the given calculation slipped through the meshes In these cases don t worry as the values of these variables are hopefully ignored in the calculation 8 2 File CHECKGFS The file CHECKGFS is mainly thought as a help in programming The file contains only the names and the values of all variables in alphabetic order without further explaining text The names of all variables are given in Appendix B Bibliography 1 Dekkers J C M Gibson J P Bijma P Van Arendonk J A M 2004 Design and optimization of animal breeding programmes Lecture notes Wageningen 2 Elsen J M Mocquot J C 1974 M thode de pr vision de l evolution du niveau g n tique d une population soumise une op ration de s lection et dont les g nerations se chevauchent INRA Bull tech D pt G n t anim 17 30 54 3 Hill W G 1974 Prediction and evaluation of response to selection with over lapping generations Anim Prod 18 117 139 4 Wolf J Wolfov M Krupa E 2010 User s manual for the program package ECOWEIGHT C programs for calculating economic weights in livestock Ver sion 5 0 2 Part 1 Programs EWBC version 2 1 3 and EWDC version 2 0 5 for ca
22. RTIES PROVIDE THE PROGRAM AS IS WITHOUT WARRANTY OF ANY KIND EITHER EX PRESSED OR IMPLIED INCLUDING BUT NOT LIMITED TO THE IM PLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PAR TICULAR PURPOSE THE ENTIRE RISK AS TO THE QUALITY AND PER FORMANCE OF THE PROGRAM IS WITH YOU SHOULD THE PROGRAM PROVE DEFECTIVE YOU ASSUME THE COST OF ALL NECESSARY SER VICING REPAIR OR CORRECTION 12 IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER OR ANY OTHER PARTY WHO MAY MODIFY AND OR REDISTRIBUTE THE PROGRAM AS PER MITTED ABOVE BE LIABLE TO YOU FOR DAMAGES INCLUDING ANY GENERAL SPECIAL INCIDENTAL OR CONSEQUENTIAL DAMAGES ARIS ING OUT OF THE USE OR INABILITY TO USE THE PROGRAM INCLUD ING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PRO GRAMS EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES Contents Preface 2 License conditions 3 1 Introduction 6 2 General principles of gene flow 8 3 Pure bred system 10 3 1 Calculation of the elements of the transmission matrix P 11 Sd Ps 2229212 oe ee ond xg 11 231 2 Pues od x IER ERES a 12 Jl Sub Basi 12 SLA Submebrx Pag sss rasna ihh eee eke eS 12 Slo Pig e 22 24 ed
23. T OF VARIABLES AND CONSTANTS 42 Table B 1 Possible values of the variable flag i The values of the variable corre spond to the numbers of the trait definitions as given in Appendix A Value of i Possible values of flag i 1 2 8 4 5 26 27 28 29 30 31 32 33 gstd m i Genetic standard deviations for the maternal component of trait i i 1 AU es h d i Realization vector hg of dimension acm for direct effects used in the calculation of gene flow see Chapter 2 h mij Realization vector hy of dimension acm for maternal effects used in the calculation of gene flow see Chapter 2 he d ij Vector ha multiplied with economic weights of trait i j is the sex and age class he m ij Vector hm multiplied with economic weights of trait 7 j is the sex and age class i Index variable j Index variable L Maximal number of reproductive cycles 1 set to 16 used for dimen sioning arrays in the program 1 inv length of the investment period in years in time units in years for production systems with one calving per year I4EA i Ewes of breed A entering reproductive cycle i i 1 LL A ex pressed as proportion of ewes entering any reproductive cycle ene l4E Ali 1 14EB il Ewes of breed B entering reproductive cycle i i 1 LLB ex pressed as proportion of ewes entering any reproductive cycle Tar IAEB i 1 I4RA i Rams of breed A entering breeding cycle i i 1
24. There are two breeds Breed is the sire breed and breed B is the dam breed PARASA TXT PARASB TXT Parameter files for breeds and B respec tively which contain the most important parameters for running the program EWSH2 for the given breed For further details see the manual for the program EWSH 2 6 PARAGFS TXT Parameter file which contains the most important parameters for running the program GFSH see Section 7 1 2 INPUTS A TXT and INPUTS B TXT with 01 02 14 Data input files for breeds and B respectively for program EWSH2 Not all data input files are needed for all calculations For further details see the manual for the program EWSH2 6 INPUTGFS TXT with 01A 01B 03 04 Data input files for program GFSH see Section 7 2 ps2AB sh under LINUX or ps2AB bat under Windows This is the shell script LINUX or batch file Windows which starts the calculations for production system 2 CHAPTER 6 INSTALLING AND RUNNING THE PROGRAM 24 6 1 4 Directory DOC license This file contains the license conditions Read them carefully and do not use the program package ECOWEIGHT if you do not agree with the license conditions ECOWEIGHTO3A pdf Part of the documentation of the program package ECOWEIGHT manual for the program EWSH2 ECOWEIGHTOS3B pdf Part of the documentation of the program package ECOWEIGHT manual for the program GFSH 6 1 5 Directory SRC This directory contains the source fil
25. User s Manual for the Program Package ECOWEIGHT C Programs for Calculating Economic Weights in Livestock Version 5 0 2 Part Program GFSH for Gene Flow in Sheep Version 1 0 2 by J Wolf M Wolfova May 14 2010 Authors addresses Jochen Wolf and Marie Wolfov Institute of Animal Science P O Box 1 CZ 10401 Praha Uh n ves Czech Republic E mail addresses wolf jochen vuzv cz wol fova marieQ vuzv cz Preface The program GFSH together with the program EWSH2 6 form the third part of the program package ECOWEIGHT The program GFSH was written within the framework of the research project MZE0002701404 of the Ministry of Agricul ture of the Czech Republic starting in the year 2009 Travelling was funded by the Ministries of Education of the Czech Republic and Slovak Republic Program KON TAKT project number MEB 080802 or SK CZ 0007 07 The technical assistance of Renata Proskov Prague Uhiin ves Praha Ur n ves is acknowledged License conditions This program is distributed under the conditions of the GNU GENERAL PUBLIC LICENSE You will find the details of the license in the enclosed file license Please read this file carefully Especially notice the following part of the license NO WARRANTY 11 BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE THERE IS NO WARRANTY FOR THE PROGRAM TO THE EXTENT PERMITTED BY APPLICABLE LAW EXCEPT WHEN OTHERWISE STATED IN WRIT ING THE COPYRIGHT HOLDERS AND OR OTHER PA
26. al proportions as in the ram flock are assumed Indicator variable 2 pgdsA Insert 1 if the proportion of genes from the individual age classes of dams of breed in male progeny are to be read from this file and insert 2 if the proportion of genes from the individual age classes of dams of breed in male progeny are automatically inserted by the program i e equal proportions as in the ewe flock are assumed Indicator variable 3 pgssB Insert 1 if the proportion of genes from the individual age classes of sires of breed B in male progeny are to be read from this file and insert 2 if the proportion of genes from the individual age classes of sires of breed B in male progeny are automatically inserted by the program i e equal proportions as in the ram flock are assumed Indicator variable 4 pgdsB Insert 1 if the proportion of genes from the individual age classes of dams of breed B in male progeny are to be read from this file and insert 2 if the proportion of genes from the individual age classes of dams of breed B in male progeny are automatically inserted by the program i e equal proportions as in the ewe flock are assumed Proportions of genes from individual age classes of sires of breed in male progeny A path sires to sires A the numbers must sum to 0 5 P 1 1 to Pl1 acsA These values are only read if indicator variable 1 is set to 1 Proportions of genes from individual age classes of dams of breed i
27. artificial rearing The economic weight is calculated only if there is a pricing system where dressing percentage is paid for Dressing percentage of fattened lambs The economic weight is calculated only if there is fattening and if there is a pricing system where dressing percentage is paid for Dressing percentage of adult sheep The economic weight is calculated only if there is a pricing system where dressing percentage is paid for Average quality class for lambs at weaning or at the end of artificial rearing when paid for live weight The economic weight is calculated only if animals are paid for live weight Average quality class for fattened lambs when paid for live weight The eco nomic weight is calculated only if animals are paid for live weight Average quality class for adult sheep when paid for live weight The economic weight is calculated only if animals are paid for live weight 38 APPENDIX NUMBERING OF TRAITS IN THE PROGRAM 39 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 Average class for fleshiness for adult sheep The economic weight is calculated only if animals are paid for carcass quality Average class for fat covering for adult sheep The economic weight is calcu lated only if animals are paid for carcass quality Average class for fleshiness for fattened lambs and or for heavy lambs carcass weight gt 13 kg slaughtered aft
28. bers see Section 7 2 The information read from the input files is selected according to the parameters given in the parameter file Therefore the results file does not contain a simple copy of the input files but only data from input files which will be needed for the given calculation The third part of the results file contains the results in the following order e Number of the production system e Number of the sex and age class the cumulative number of discounted expres sions and the economic weights are calculated for e Cumulative number of discounted expressions in all sex and age classes at the end of the investment period vector m sum e Length of the investment period e Economic weights for direct and maternal components of the individual traits expressed in monetary units per unit of trait and per ewe in the whole breeding system e Economic weights per genetic standard deviation for direct and maternal com ponents of the individual traits and per ewe in the whole breeding system e Relative economic weights Standardized economic weights for direct or maternal trait components as percentage of the sum of absolute values of standardized economic values for direct or maternal trait components respectively Standardized economic weights for direct or maternal trait components as percentage of the sum of absolute values of standardized economic values for both direct or maternal trait components 35 CHAPTE
29. by the proportion of ewes of breed A in the production system pdA Similarly the economic weights per ewe of breed B may be calculated by dividing the weights from equation 4 27 by the proportion of ewes of breed B in the production system pdB Chapter 5 Relative economic weights The economic weights of the individual traits as they are calculated in sections 3 3 and 4 3 cannot be compared among each other as they have different units One way to make the economic weights comparable is to refer them to the genetic standard deviation of the trait These so called standardized economic weights for the direct and the maternal trait components ewst_d i and ewst_mli are calculated as ewst_dli dli gstd dli ewst m i x 951 m i 5 1 where gstd_d i and gstd_mli are the genetic standard deviations for the direct and maternal components of trait i i 1 NT 1 The standardized economic weights are given in monetary units per standard deviation of the trait component and per ewe in the whole production system As the standardized economic weights have the same units for all traits they can be expressed as percentage of the sum of all standardized economic weights When calculating the sum care must be taken of not including the same trait twice Therefore in input file INPUTGFS05 TXT see Subsection 7 2 6 you must choose always one trait definition from two alternatives for six paires of definitions
30. d which should not be edited The directories PS1 DOC and SRC are not needed for the calculation Edit the parameter files PARASA TXT PARASB TXT and PARAGFS TXT and the input files INPUTS A TXT with 01 02 14 INPUTS B TXT with 01 02 14 and INPUTGFSZ TXT with 01 01B 03 04 in directory PS2 Under LINUX type ps2AB sh and press ENTER to start the shell script which runs several times the program EWSH2 and then the program GFSH Under Windows type ps2A B bat and press ENTER to start the batch file which runs the programs EWSH2 and GFSH For redirecting the text written to the screen to a text file say a txt type ps2A B sh gt a tat under LINUX or ps2AB bat gt a tat under Windows and press ENTER The shell script ps2AB sh for running production system 2 has the following structure bin sh echo echo I am copying PO2 00 TXT to POO TXT echo cp PROG P02_00 TXT POO TXT echo CHAPTER 6 INSTALLING AND RUNNING THE PROGRAM echo 2 echo am copying TEXT OUT TXT to the working directory echo 2 cp PROG TEXTS2_OUT TXT cp PROG TEXTGFS OUT TXT
31. dimension 1 x acsA The elements of its only row are the same as the elements in the first row of submatrix P21 Placm acsA RRA i 0 5 x IARA i where i 1 RRA 3 11 3 1 6 Submatrix P32 The submatrix P32 is the dams to slaughter animals part of the transmission matrix and is of dimension 1 x acdA The elements of its only row are the same as the elements in the first row of submatrix P31 Placm acsA acdA LLA i 0 5 x IAE A i where i 1 LLA 3 12 CHAPTER 3 PURE BRED SYSTEM 13 3 1 7 Submatrices P13 P23 and P33 The matrices P23 and P33 are the slaughter animals to sires slaughter animals to dams and slaughter animals to slaughter animals parts respectively of the transmission matrix The dimension of these matrices is 1 x acsA 1 x acdA and 1x 1 As no genes are transmitted from slaughter animals all elements of these submatrices are zero 3 2 Calculation of vectors m m gf in the pro gram hg and hy Given is n sac the number of the sex and age class the selection is carried out for get m9 from equation 2 1 all elements of the vector m gf x are set to zero and m gf n sac 1 Then equation 2 1 is applied to calculate mtl The 1 inv expression 5 mil 1 u is calculated as vector m_sum x in the program t 1 The notations h_d and h_m x are used in the program for hg and hm The last element of the vector h_ d is one _
32. en as Pir Pi2 joe Pig P21 P22 P28 o La 4 3 Pai Ps2 05 Pss This structure is the consequence of the following 8 groups of sex and age classes in parentheses the number of classes is given e Age classes for sires of breed A used for pure breeding acs e Age classes for dams of breed A acdA e Age classes for sires of breed A used for crossing with ewes of breed B acsAB e Age classes for sires of breed B acsB e Age classes for dams of breed B acdB e Age class for slaughter animals of breed A 1 e Age class for slaughter animals of breed B 1 e Age class for slaughter animal AxB 1 All submatrices of P with non zero elements have one of the following structures S to S4 the symbol x characterizes elements which may be different from zero X X X x X 100 0 0 0 1 0 0 0 51 0 0 1 0 0 4 4 000 0 0 000 1 0 ECE d 000 0 0 000 0 0 92 0 0 0 0 4 5 000 0 0 000 0 0 5 x x x x 4 6 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 S4 0 0 1 0 0 4 7 0 0 0 0 0 0 0 0 1 0 CHAPTER 4 TERMINAL CROSSING 16 4 1 1 Submatrices P11 Piz P21 and P22 The elements of submatrices P11 P12 P21 and P22 are calculated in the same way as in production system 1 subsections 3 1 1 to 3 1 4 equations 3 5 to 3 10 so that submatrices P11 and P22 are of the structure S and submatrices P12 and P2 are of the structure Sg The elements of the first rows of submatrices P11 and may be read in from input file
33. er weaning or after artificial rearing The economic weight is calculated only if animals are paid for carcass quality Lambs slaughtered after weaning are included only for non dairy breeds Average class for fat covering for fattened lambs and or for heavy lambs car cass weight gt 13 kg slaughtered after weaning or after artificial rearing The economic weight is calculated only if animals are paid for carcass quality Lambs slaughtered after weaning are included only for non dairy breeds Average class for carcass quality for lambs slaughtered after weaning or arti ficial rearing The economic weight is calculated only if animals are paid for carcass quality Conception rate of female lambs Average conception rate of ewes Average litter size for lambing ewes Average survival rate of lambs at lambing Average survival rate of lambs till weaning The economic weight is calculated only if there is customary weaning Average survival rate of lambs till the end of artificial rearing The economic weight is calculated only if there is artificial rearing Average productive lifetime of ewes in numbers of reproductive cycles Average productive lifetime of ewes in years Total milk yield in the standardized milking period Average daily milk yield for the whole milking period Fat content in milk Milk fat yield in the standardized milking period Protein content in milk Milk protein yield in the standardized milking period Somatic cel
34. es in C language ewsh2 c Source code of the program EWSH2 gfsh c Source code of the program GFSH 6 2 Installation 6 2 1 Under LINUX The program GFSH together with the program EWSH2 come to you as a com pressed tar file with the name ECOWEIGHTOS3 of version tgz for example ECOWEIGHTO3 5 0 2 tgz contains the programs from version 5 0 2 of the pro gram package Copy this file to a directory of your choice and enter the command tar xvf ECOWEIGHTOS3 of version tgz for uncompressing and unarchiving the file You will get the file structure as de scribed in Section 6 1 Only for experts in programming If you want to do changes in the program source code by yourself then you must use the option lm for compiling the source code when using the compiler gcc because otherwise the mathematical functions would not work e g gcc lm o gfsh exe gfsh c will compile the source file gfsh c to the executable file gfsh exe 6 2 2 Under Microsoft Windows The Windows version of the program is distributed as zip file with the name ECOWEIGHTO3 of version zip It contains the compiled programs ewsh2 exe and gfsh eze The programs were compiled under Cygwin http www cygwin com and run only in the presence of the file cygwin1 dll which is part of the Windows distribution Only for experts in programming If you intend to change the source code and to compile the program you are recommended to install Cygwin which is freely a
35. f the traits are read for traits 1 to 3 21 23 and 24 see Appendix A genetic standard deviations are read only for the direct component in traits 4 to 7 9 to 20 and 25 and for traits 8 22 and 26 to 35 the genetic standard deviation is read only for the maternal component of the trait 7 2 6 Input file INPUTGFS05 TXT This file is important for the calculation of relative economic weigts It is read only if the genetic standard deviations of the traits are known In this file you are asked to choose between two alternative definitions of the same trait The two definitions are presented with the number of the traits as given in Appendix A in parantheses Type the number of the definition you prefer The appropriate input is skipped if the trait is not considered in the calculation The following selections are to be made the variable to which the numbers are read is given in parentheses e Select 2 weaning weight or 3 average daily gain from birth till weaning flag 1 Select 4 weight at the end of artificial rearing or 5 average daily gain in artificial rearing flag 2 Select 26 productive lifetime of ewes in reproductive cycles or 27 productive lifetime of ewes in years flag 3 Select 28 total milk yied in the standardized milking period or 29 average daily milk yield flag 4 Select 30 fat content in milk or 31 fat yield in the standardized milking period flag 5 Select 32 protein content in mi
36. he texts are read in and printed out to the result file as they are Therefore you can freely change the text in all input files as long as you do not modify the quotation marks For example you can translate all texts in the input files to another language what will cause the appropriate part of the result file to be printed in the same language as the input files may be there are some exceptions where the English text will be remained The length of the texts can be changed but each text must start and finish with quotation marks A great part of the text for the results file s is read from the file TEXTGFS_OUT TXT which is located in the directory PROG You can translate all the text in this file But be very careful not to change quotation marks 7 1 Parameter files 7 1 1 File PO1 TXT The file POI TXT is generated by the program EWSH2 and contains only one number the code for the production system prods This code is e 1 for a pure bred system of breed A with one production level e 2 for a production system with breeds and B each on one production level partially terminal crossing is applied 29 CHAPTER 7 INPUT FILES 30 7 1 2 File PARAGFS TXT This file contains basic information for running the program GFSH At the be ginning of the file between the first two quation marks you can write any text characterizing your calculation Then the value of a parameter is always followed by its description Modify the values
37. he time 0 mlt is calculated as mlt p2gt72 2 1 According to Wolfova Nitter 7 most traits can be considered to belong to one of two groups in animal breeding The first group of traits occurs only once in an animal s life e g growth and carcass traits The second group is realised mostly by females several times in their life e g lactation and fertility traits but also wool traits For simplicity we will designate the first group as direct traits and the second group as maternal traits having in mind that the second group of traits may be exceptionally also expressed in males wool traits Some traits growth of lambs until weaning or conception rate are composite traits with a direct and a maternal genetic component the direct component realized once by the offspring and the maternal component realized several times during the female s life For the calculation of the number of discounted expressions we need so called realization vectors hg and hy for direct and maternal effects respectively A realization vector describes the extend of the expression of a trait in the individual sex and age classes Therefore both realization vectors are of dimension acm Examples for realization vectors are given in the following chapters Out of the analyzed traits see Appendix A the following ones are considered to be direct traits growth rates in artificial rearing in fattening and in rearing of breedi
38. ho echo I am ready echo The following results files will printed 27 e resB01 This is the results file from the first run of program EWSH2 which is for breed B e resA02 This is the results file from the second run of program EWSH2 which is for breed A e resA03 This is the results file from the third run of program EWSH2 which is for breed A e resB04 This is the results file from the forth run of program EWSH2 which 1This file contains the final results for breed A from the program EWSH as the third run of EWSH is the last run for breed A This file contains the final results for breed B from the program EWSH2 as the forth run of EWSH 2 is the last run for breed B CHAPTER 6 INSTALLING AND RUNNING THE PROGRAM 28 is for breed resgfps02 This is the results file from program GFSH described in this man ual Furthermore the values of all variables are printed for both programs in the follow ing files 6 4 CHECKSBO01 Complete list of the values of all variables of breed B from the first run of program EWSH2 at the end of the calculation The description of the variables is given in Appendix B in the manual for EWSH2 6 CHECKSB01a Complete list of the values of all variables of breed B from the first run of program EWSH2 before the program starts the calculation of economic values This file is printed mainly as help for further programming a
39. ion matrix P for gene flow acm is then acm acsA acdA 1 3 3 3 1 Calculation of the elements of the transmission matrix P Matrix P has a block structure containing 3x3 blocks see Algorithm 3 1 There fore we can write matrix P in the form Pj P412 P21 P23 3 4 Pai Pa2 P33 The elements P i j of P are the proportions of genes in the sex and age class i at time t which come from the sex and age class j at time t 1 The sum of all elements 5 within each row is 1 The sum of all elements 3 within each row belonging to the same sex is 0 5 if there are non zero elements for both sexes in this row This is the case when vertically new blocks start see Algorithm 3 1 For calculating the elements P i j i j 1 acm of P first all elements are set to zero Then the non zero elements are inserted as given below 3 1 1 Submatrix P11 Submatrix P11 is the sires to sires part of the transmission matrix and is of di mension acsA x acsA The elements of the first row may be read in from input file INPUTGFSO02 TXT if the sires for the production of rams are selected from certain age classes If there is no selection among sires of rams the elements in the first row are calculated as follows Pli acsA RRA i 0 5 x IARA i where i 1 RRA 3 5 CHAPTER 3 PURE BRED SYSTEM 12 The further elements different from zero are Pili 1 1 for i 1 acsA 1 3 6 The diag
40. l score Fleece weight Appendix List of variables and constants This list contains all variables used in the program Some additional variables which are used only in the manual as they are useful for a clear arrangement and which are explained there are not part of the list a2 a3 acdA acdB ACM acm acsA acsAB acsB ageE1A ageE1B ageR11A ageR11B ageR12A CB delta d i delta mil Temporary variable Temporary variable Number of age classes for dams in breed A Number of age classes for dams in breed B Maximal dimension of the transmission matrix for gene flow Dimension of the transmission matrix for gene flow Number of age classes for sires of breed used for pure breeding Number of age classes for sires of breed used for cross breeding with ewes of breed B Number of age classes for sires of breed B used for pure breeding Age of ewes of breed A at the first lambing Age of ewes of breed B at the first lambing Age of rams of breed used for pure breeding at the beginning of the first breeding cycle Age of rams of breed B at the beginning of the first breeding cycle Age of rams of breed used for crossing with ewes of breed B at the beginning of the first breeding cycle Differentiates between cross breeding and pure breeding set to 3 used for dimensioning arrays in the program Variable which indicates if the relative economic weight for the direct component of trait i is calcula
41. lk or 33 protein yield in the standardized milking period flag 6 7 3 TEXTGFS OUT TXT This file contains texts which are used for printing the results It contains headings of sections of the results files comments and names of variables the values of which are printed in the results files For editing the file read carefully the remarks at the beginning of Chapter 7 on page 29 7 4 ERROR TXT This file contains only the value of the variable errmess At the start of each calculation of the program EWSH2 this file is read with the value 0 for errmess If there occurs an error during the calculation of the program EWSH2 the value of errmess is changed to 1 and written to the file ERROR TXT In the next run of CHAPTER 7 INPUT FILES 34 EWSH or in the run of the program GFSH the file ERROR TXT is read again If errmess 1 all subsequent programs including GFSH will stop and write an error message Chapter 8 Program output 8 1 The results file The name of the file the results are written to is fixed to resgfpszz where 01 for production system 1 and 02 for production system 2 The first part of the file contains information on the version of the program copyright and con tact to the authors and the values of the system variables read from P01 TXT and PARAGFS TXT see Section 7 1 2 The second part of the file copies more or less the data input files INPUTGFS TXT where is to be replaced by the cor responding num
42. n male progeny A path dams A to sires A the numbers must sum to 0 5 P 1 acsA 1 to P 1 acsA acdA These values are only read if indicator variable 2 is set to 1 Proportions of genes from individual age classes of sires of breed B in male progeny B path sires B to sires the numbers must sum to 0 5 PlacsA acdA acs 1 A acd A acsAB 1 to P acsA acd A acsAB 1 acdA acsAB acsB These values are only read if indicator variable 3 is set to 1 Proportions of genes from individual age classes of dams of breed B in male progeny B path dams B to sires the numbers must sum to 0 5 P acsA acdA acsAB 1 acd A acsB 1 to P acsA acd A acsAB acd A acsAB acsB acdB These values are only read if indicator variable 4 is set to 1 CHAPTER 7 INPUT FILES 33 7 2 5 Input file INPUTGFS04 TXT This input file contains the genetic standard deviations for calculating the relative economic weights for direct and maternal components of all traits Keep attention that the units of the genetic standard deviations are the same as the units of the economic weights the units given in this file The genetic standard deviations must be for the breed the economic weights are calculated for The appropriate input is skipped if the trait is not considered in the calculation Genetic standard deviations for both direct and maternal components o
43. nd as a check for correct computing With one exception variable zr number of the loop the values of all variables contained in both files must be equal The file CHECKSBO01a does not contain the economic values which are printed only in CHECKSBOI CHECKSA02 Complete list of the values of all variables of breed A from the second run of program EWSH2 at the end of the calculation CHECKSA02a Complete list of the values of all variables of breed from the second run of program EWSH 2 before the program starts the calculation of economic values CHECKSA03 Complete list of the values of all variables of breed A from the third run of program EWSH2 at the end of the calculation CHECKSA03a Complete list of the values of all variables of breed from the third run of program EWSH2 before the program starts the calculation of economic values CHECKSB04 Complete list of the values of all variables of breed B from the forth run of program EWSH2 at the end of the calculation CHECKSB04a Complete list of the values of all variables of breed B from the forth run of program EWSH2 before the program starts the calculation of economic values CHECKGFS Complete list of the values of all variables from program GFSH The description of the variables is given in Appendix B of the present manual General remarks Several checks of input parameters are included in the programs For example certain input parameters have to sum to one war
44. ng animals survival rates in artificial rearing and all carcass traits traits CHAPTER 2 GENERAL PRINCIPLES OF GENE FLOW 9 4 to 7 9 to 19 and 25 On the other hand mature weight milk yield fat and protein content or yield somatic cell count average litter size wool production and productive life of ewes are considered to be maternal traits traits 8 22 and 26 to 35 Mature weight is considered as maternal trait because there are maintenance costs in each reproductive cycle Wool is repeatedly sheared Productive lifetime may be understood as a result of successive surviving in the individual reproductive cycles Several traits have direct and maternal components birth weight weaning weight growth rate from birth till weaning survival rate of lambs at birth and until weaning and conception rate traits 1 to 3 20 21 23 and 24 The direct component of growth traits till weaning expresses the genetic potential of lambs for growth the maternal component expresses the genetic potential of the dam for milk available to lambs The direct effect of the lamb survival rate expresses the health status of the lambs the maternal effect is determined by the mothering ability of a ewel 1 Maternal components of growth traits and survival rates till weaning will therefore be expressed both on pure bred and on cross bred progeny Chapter 3 Production system 1 Pure bred system with one production level In this system the p
45. ning will appear if these input parameters are invalid and the program will stop You will be told which input parameters to correct before restarting the program In general it is your respon sibility to use input parameters which are realistic and fit together because it is impossible to predict any possible erroneous combinations of input parameters Do not forget to have always a critical look on your results before using them for further purposes 3See footnote 1 on the previous page See footnote 2 on the preceding page Chapter 7 Input files Important remark When editing the input files keep attention not to change quotation marks All files are read as sequential files and the program rec ognizes the beginning and the end of texts on the basis of quotation marks Adding or deleting a quotation mark will cause the program to break down or to calculate wrong results Monetary unit In all input files the abbreviation MU is used for monetary unit All values in the distributed version of the program refer to Euros You can globally replace the abbreviation MU by the abbreviation of your monetary unit in all data input files INPUTGFS TXT with 01A 01B 02 03 04 and in the input file TEXTGFS_OUT TXT which is located in the directory PROG using any text editor the results file s will then contain the monetary unit specified by you Language of the program The program will need just the numbers for calcu lations T
46. nt traits in livestock At the given stage in its fifth version two programs for cattle and three programs for sheep are available see Table 1 1 The two programs for cattle EWBC and EWDC are described in the first part of the manual 4 The second part of the program package is a stand alone program EWSH1 for sheep with one lambing per year 5 Table 1 1 Survey on the program package ECOWEIGHT version 5 0 2 Part Installation Package Program s Species remarks 01 ECOWEIGHTO1 5 0 2 tgz EWBC beef cattle EWDC dairy cattle 02 ECOWEIGHTO2 5 0 2 tgz EWSHI sheep one lambing per year stand alone program 03A ECOWEIGHTO3 5 0 2 tgz EWSH2 sheep one lambing per for both parts 03A and 03B year used in combination with GFSH 03B GFSH sheep program for gene flow used in combination with EWSH2 There is one manual for each part its name is ECOWEIGHTJ part pdf where part is to be replaced by the two or three digits given in this column PReplace tgz by zip for Windows The third part of the program package which is distributed as one installation package consists of the programs for sheep EWSH2 and GFSH which are docu mented in two separate manuals In the present manual the program GFSH is described which models gene flow in sheep and allows to calculate economic weights for direct and maternal trait components This program is used in connection with the program EWSH2 6 In dependence of the production sy
47. omic weights for the maternal components ewr_mm t 100 x qu 5 6 ewsum m e Standardized economic weight for the maternal component of trait i expressed as percentage of the sum of all standardized economic weights for both the direct and the maternal components abs ewst m i ewr mali 100 x 5 7 Chapter 6 Installing and running the program 6 1 List of files in the installation package The program GFSH is distributed together with the program EWSH2 6 There fore files for both programs are in the installation package The files are in five directories 6 1 1 Directory PROG This directory contains executable program files and text files which are not to be edited ewsh2 exe Executable file for program EWSH2 6 gfsh exe Executable file for program GFSH TEXTS2 OUT TXT This file contains text for writing the results for the pro gram EWSH2 For further details see the manual for the program EWSH2 6 TEXTGFS OUT TXT This file contains text for writing the results for the program GFSH See also Section 7 3 P01 00 TXT This file contains the initial parameters for the production system prods 1 the breed breed 1 and the number of the run of EWSH2 calc 1 for production system 1 P02 00 TXT This file contains the initial parameters for the production system prods 2 the breed breed 2 and the number of the run of EWSH2 calc 1 for production system 2 ERROR TXT A
48. onal of elements 1 describes aging of animals of the given group 3 1 2 Submatrix P12 The submatrix P12 is the dams to sires part of the transmission matrix and is of dimension acsA x acdA The elements of the first row may be read in from input file INPUTGFS02 TXT if the dams for the production of rams are selected from certain age classes If there is no selection among dams of rams the elements in the first row are calculated as follows Pli acsA 4 acdA LLA i 0 5 x IAE Ai where i 1 LLA 3 7 These are the only elements different from zero in this submatrix 3 1 3 Submatrix P5 The submatrix P21 is the sires to dams part of the transmission matrix and is of dimension acdA x acsA The elements of its first row are PlacsA 1 acsA RRA i 0 5 x IARA i where i 1 RRA 3 8 These are the only elements different from zero in this submatrix 3 1 4 Submatrix The submatrix P22 is dams to dams part of the transmission matrix and is of dimension acdA x acdA The elements of its first row are PlacsA 1 acs A acdA LLA i 0 5 x IKE Ali where i 1 LLA 3 9 The further elements different from zero are PlacsA i 1 acsA i 1 for ti 1 acdA 1 3 10 The diagonal of elements 1 again describes aging of animals of the given group 3 1 5 Submatrix P31 The submatrix P3 is the sires to slaughter animals part of the transmission ma trix and is of
49. opulation of sheep is not distinguished in nucleus and commer cial herds The system is similar as in cattle where the dams of sires are selected from the whole population see Fig 3 1 Only one breed is considered in this production system and the capital letter A is used to designate this breed this letter is used at the end of several variables to make clear that these variables refer to breed A The number of age classes for sires acsA is calculated as ageR11A A int int 365 RRA 3 1 and the number of age classes for dams acdA is 1 365 acdA int LLA 3 2 variables are explained in Appendix Pure bred population male replacement female replacement Slaughter animals Figure 3 1 Pure bred system with one production level 10 CHAPTER 3 PURE BRED SYSTEM 11 Algorithm 3 1 Structure of matrix P The symbol x characterizes elements which can be different from zero The values of x are in the range from 0 to 0 5 Slaughter Sires Dams animals X X X X X X X X X X 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 Sires 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 x x X X X X X x x 0 0 0 0 0 0 100 0 0 0 Dams 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 Slaughter X X X x X X X x 0 animals The dimension of the transmiss
50. reeding cycles for rams of breed B RRB e Proportion of rams of breed B entering each breeding cycle IARB i e Number of reproductive cycles for ewes of breed B LLB e Proportion of ewes entering each reproductive cycle IAE B i e Marginal economic values for all traits expressed in pure bred animals of breed B 7 1 or in cross bred animals AxB j 2 in the unit as they are printed in the program EWSH2 evpD i The values for all traits of pure bred animals are given first followed by the values for cross bred animals The value 0 000000 is inserted for economic values which were not calculated in the given system CHAPTER 7 INPUT FILES 31 e Age of rams of breed B at the beginning of the first breeding cycle ageR11B e Age of rams of breed A used for crossing with ewes of breed B at the beginning of the first breeding cycle ageR12A e Age of ewes of breed at first lambing ageE1B Fraction of ewes of breed B crossed with rams of breed A for reproductive cycles i 0 LLB 1 pcrossE 0 is the fraction of female lambs crossed 7 2 3 Input file INPUTGFS02 TXT This file contains input parameters for calculating the transmission matrix P for gene flow for production system 1 pure bred system with one production level When filling in the numbers you must know the number of age classes for sires and dams which you can easily calculate from equations 3 1 and 3 2 For example assume that the age of rams a
51. sE 0 is the fraction of female lambs crossed with breed A Proportion of ewes of breed in the production system Proportion of ewes of breed B in the production system Indicator variable for reading data Insert 1 if the proportion of genes from the individual age classes of dams of breed in male progeny are to be read from the file INPUTGFSO2 TXT or INPUTGFS03 TXT and insert 2 if the proportion of genes from the individual age classes of dams of breed in male progeny are automatically inserted by the program i e equal proportions as in the ewe flock are assumed Indicator variable for reading data Insert 1 if the proportion of genes from the individual age classes of dams of breed B in male progeny are to be read from the file INPUTGFS03 TXT and insert 2 if the proportion of genes from the individual age classes of dams of breed B in male progeny are automatically inserted by the program i e equal proportions as in the ewe flock are assumed Indicator variable for reading data Insert 1 if the proportion of genes from the individual age classes of sires of breed in male progeny are to be read from the file INPUTGFS02 TXT or INPUTGFS03 TXT and insert 2 if the proportion of genes from the individual age classes of sires of breed A in male progeny are automatically inserted by the program i e equal proportions as in the ram flock are assumed Indicator variable for reading data Insert 1 if the proportion of genes from
52. stem one or more runs of EWSH2 are necessary before GFSH is started At the beginning of the present manual a short description of the general prin ciples of gene transfer is given Chapter 2 The simplest production system which can be modelled is pure bred system with one production level where no distinc tion is made between nucleus and commercial herds The calculation of economic weights for direct and maternal trait components for this system is described in Chapter 3 Next a production system with terminal crossing is described where also only one production level is assumed Chapter 4 In this system two breeds CHAPTER 1 INTRODUCTION 7 are included A pure bred system is modelled for sire breed A In the production system for dam breed B a part of progeny are pure bred animals of breed B and another part of progeny are cross bred animals AxB That means the production systems for both breeds are connected via sires from breed A which are crossed to ewes of breed B Next relative economic weights are calculated which allow to compare economic weights between traits Chapter 5 The next chapters deal with technical details of using the program GFSH First information on installing and running the program is given Chapter 6 The fol lowing chapter gives a list of the input files needed for running the program and finally the program output is commented Chapter 8 The Appendix contains a list of traits with their numbering as
53. t the beginning of the first breeding cycle is 580 days Dividing this age by 365 you get the age in years which is 1 59 Applying the function int integer which truncates the decimal portion of the value of the argument you get the value 1 Assume that the number of breeding cycles is 5 Then you get 6 age classes for sires as result In the first age class there are animals with an age up to 1 year in the second class animal with an age up to 2 years etc The following values are read from the input file e Number of sex and age class for which the gene flow will be calculated n_ sac e Length of the investment period 1 inv e Indicator variable 1 pgssA Insert 1 if the proportion of genes from the individual age classes of sires in male progeny are to be read from this file and insert 2 if the proportion of genes from the individual age classes of sires in male progeny are automatically inserted by the program i e equal proportions as in the ram flock are assumed Indicator variable 2 pgdsA Insert 1 if the proportion of genes from the individual age classes of dams in male progeny are to be read from this file and insert 2 if the proportion of genes from the individual age classes of dams in male progeny are automatically inserted by the program i e equal proportions as in the ewe flock are assumed e Proportions of genes from individual age classes of sires in male progeny path sires to sires the numbers must sum to 0 5
54. ted delta d i 1 or not delta d i 0 Variable which indicates if the relative economic weight for the maternal component of trait 4 is calculated delta 1 or not delta 0 40 APPENDIX LIST OF VARIABLES AND CONSTANTS 41 errmess Variable indicating the presence errmess 1 or the absence errmess 0 of an error during the calculation when running EWSH2 The value of this variable is forwarded to the next run of EWSH2 and to GFSH and causes the following calculations to stop if an error occurred in one of the preceding programs evpA i 1 Marginal economic value of trait expressed in pure bred animals of breed A with units used for printing the results in the program EWSH2 evpB ilj Marginal economic value of trait 4 expressed in pure bred j 1 or cross bred j 2 animals of breed B with units used for printing the results in the program EWSH2 ew_d i Economic weight for the direct effect of trait i ew m i Economic weight for the maternal effect of trait i ewr dali Standardized economic weight for the direct component of trait i ex pressed as percentage of the sum of all standardized economic weights for both the direct and the maternal components see equation 5 5 ewr dd i Standardized economic weight for the direct component of trait i ex pressed as percentage of the sum of all standardized economic weights for the direct components see equation 5 4 ewr mali Standardized economic
55. the individual age classes of sires of breed B in male progeny are to be read from the file INPUTGFS03 TXT and insert 2 if the propor tion of genes from the individual age classes of sires of breed B in male progeny are automatically inserted by the program i e equal propor tions as in the ram flock are assumed Production system input parameter in the file 1 see Section 7 1 1 on page 29 Maximal number of breeding cycles for rams 1 set to 6 used for dimensioning arrays in the program APPENDIX LIST OF VARIABLES AND CONSTANTS 44 RRA Number of breeding cycles for rams of breed A input parameter RRB Number of breeding cycles for rams of breed B input parameter tt i Type of trait 0 for direct traits 1 for maternal traits 2 for traits with direct and maternal components i 1 NT 1 u Discount rate per time unit used in the gene flow method The time unit is one year for production systems with one lambing per year ZZ Variable used for numbering the input files in the results file Index age classes 31 age of ewes 30 31 age of rams 30 31 aging 12 batch file 25 26 breed A 30 breed B 30 breeding cycle 30 CHECKGFS 26 28 36 checks of input parameters 28 CHECKSAOI 26 CHECKSAD01a 26 CHECKSAO02 28 CHECKSA02a 28 CHECKSAO3 28 CHECKSA03a 28 CHECKSBOI 28 01 28 CHECKSB04 28 CHECKSB04a 28 compilation 24 constants 40 crossing 14 currency 29
56. ttle 171 pp 5 Wolf J Wolfov M Krupov Z Krupa E 2010 User s manual for the program package ECOWEIGHT C programs for calculating economic weights in livestock Version 5 0 2 Part 2 Program EWSHI for sheep Version 1 1 6 223 pp 6 Wolf J Wolfova M Krupova Z Krupa E 2010 User s Manual for the Pro gram Package ECOWEIGHT C Programs for Calculating Economic Weights in Livestock Version 5 0 2 Part 3A Program EWSH2 for Sheep Version 1 0 2 229 pp 7 Wolfov M Nitter 2004 Relative economic weights of maternal versus direct traits in breeding schemes Livest Prod Sci 88 117 127 37 Appendix Numbering of traits in the program 10 11 12 13 14 Birth weight Weaning weight The economic weight is calculated only if there is customary weaning Average daily gain from birth until weaning The economic weight is calcu lated only if there is customary weaning Weight at the end of artificial rearing The economic weight is calculated only if there is artificial rearing Average daily gain in artificial rearing The economic weight is calculated only if there is artificial rearing Average daily gain of breeding animals during rearing Average daily gain in fattening The economic weight is calculated only if there is fattening Mature weight Dressing percentage of lambs at weaning or at the end of
57. vailable When compiling the source code the following statement works for the program EWSH 2 gcc Wl1 stack 55000000 o ewsh2 exe ewsh2 c The program GFSH can be simply compiled by the statement CHAPTER 6 INSTALLING AND RUNNING THE PROGRAM 25 gcc o gfsh exe gfsh1 c Alternatively it should be possible to use commercial C compilers we did not test commercial compilers 6 3 Running the program You are recommended to create one directory for each calculation where you will copy and edit all files you will need The program may be also in this directory or may be copied to a directory for executable files e g to the directory usr local bin in LINUX 6 3 1 Running the program for production system 1 All files needed for running production system 1 are in the directory PS1 Further more the directory PROG is needed where the program files and further files are located which should not be edited The directories PS2 DOC and SRC are not needed for the calculation Edit the parameter files PARASA TXT and PARAGFS TXT and the input files INPUTSZ A TXT with 01 02 14 and INPUTGFS TXT with 014A 02 04 in directory PS1 Under LINUX type ps1A sh and press ENTER to start the shell script which runs the programs EWSH2 and GFSH Under Windows type ps1A bat and press ENTER to start the batch file which runs the programs EWSH2 and GFSH For redirecting the text written to the screen to a text file say a txt type ps1A
58. wee ee 0 eR 12 31 6 Submst x Pes a ge tae ve RS 12 3 1 7 Submatrices Pis P23 and P33 C 13 3 2 Calculation of vectors m m gf x in the program ha and hma 13 3 3 Calculation of economic 13 4 Terminal crossing 14 4 1 Calculation of the elements of the transmission matrix P 15 41 1 Submatrices Pio P21 and P22 Sr iy un 16 41 2 Submatrices 16 41 3 lt a accede eee xXx ro 4 16 4 1 4 Submatrices Pag and Pgg 16 4 1 5 Submatrices P45 and P54 17 4 1 6 Submatrices Pg and Paga Ln 17 4 1 7 Submatrices 5 17 ALS Psg Sess ee ead aed a RR 373 Ae 18 41 9 Pee lt o ser 2008 50825 6 629 Re 18 4 2 Vectors m m gf in the program ha and hm 18 4 3 Calculation of economic 18 5 Relative economic weights 20 6 Installing and running the program 22 6 1 List of files in the installation package 22 G LI Directory PROG ss oS eo ee A 22 0 L2 Directory PSl c mss scos fue x6 xs 23 Glo Directory PS2 o uuu eee bbe ORE RRS 23 Ol Directory DOC oso 24 Lo Directory SRO ee sd eines SEE See RU 24 CONTENTS i9 Wri AE cour ute corr peti ents Se RO ID

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