Department of Animal Breeding
Department of Computer Sciences
Selection Index Program (SIP)
User manual
Danny Wagenaar
Johan van Arendonk
Mark Kramer
April 1995
Wageningen Agricultural University
Wageningen Agricultural University
Preface
Selection index theory plays an important role in teaching animal breeding. It can be used to
determine the expected response to selection. The department of Animal Breeding and the
department of Informatics have worked on the development of a user friendly program to
calculate selection indexes. The majority of the work was carried out by Danny Wagenaar as a
major thesis for both departments. The work would not have been possible without the help of
people at both departments and in particular Mark Kramer of the department of Informatics.
The program is currently used in several courses given by the department of Animal Breeding.
The program is distributed to other potential users. In case you find errors in the program
please contact me. We hope that you enjoy using the program.
Johan van Arendonk
Department of Animal Breeding
PO Box 338
6700 AH Wageningen
The Netherlands
E-mail: Johan.vanArendonk@Alg.VF.WAU.NL
S.I.P. USER MANUAL
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CONTENTS
1. Introduction ........................................................................................................................................... 1
2. Pulldown menu (overview) ................................................................................................................ 2
3. The program SIP.................................................................................................................................... 3
3.1. Starting the program ......................................................................................................................... 3
3.2. The menubar ......................................................................................................................... 3
3.3. An overview of the important input boxes ..................................................................... 3
3.3.1. Set traits dialog box ............................................................................................. 3
3.3.2. Set rg dialog box & rp dialog box ....................................................................... 4
3.3.3. Set groups dialog box .......................................................................................... 6
3.3.4. Set genetic relations dialog box ......................................................................... 7
3.3.5. Set common environment dialog box .............................................................. 8
3.3.6. Set index sources .................................................................................................. 9
3.3.7. Set breeding goal................................................................................................. 10
3.3.8. Calculation box ................................................................................................... 11
Appendix A: Used formula's ................................................................................................................. 13
S.I.P. USER MANUAL
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1. Introduction
The program SIP can calculate many selection indexes. These selection indexes may be based on
economic values (type 1), on desired gains (type 2) or on a combination of both (type 3). The
program SIP has on-line help so this manual will be a very brief one. In this manual we will only
show how to start the program and we give a screenshot of the most important input boxes.
The program is written in Turbo Vision. When you extract the files from the archive, the following
files will be on your disk. Before archiving the files have been tested for virusses with F-Prot,
Thunderbyte and McAfee.
sipmain.exe
tvsip.hlp
sipman.ps
sip.bat
sipnet.bat
beef.dat
sheep.dat
pig.dat
ex5_6a.dat
ex5_6b.dat
ex6_b.dat
Main program
Helpfile
This manual in Postscript format
The batch file for running SIP
A sample batch file for running SIP in a network environment
A sample data file
A sample data file
A sample data file
A sample data file
A sample data file
A sample data file
The manual is also available in Word Perfect 5.1/5.2 and Word for Windows 6.0 format.
The program creates a number of temporary files which can be deleted after leaving the program.
For technical reasons this step was not included in SIP itself but needs to be handled separately.
This is already done for you when using the enclosed batch file.
To get started: Change your current path to the directory and start the program by typing SIP.
Parameters can be saved using Save which you will find in the pull down menu "File". Results can
be saved using the pull down menu "Window".
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2. Pulldown menu (overview)
┌───┬───────┬──────────┬──────────────┬────────┬─────────┬──────┐
│  │ Files │ Settings │ Calculations │ Window │ Options │ Help │
└─┬─┴───┬───┴─────┬────┴───────┬──────┴────┬───┴────┬────┴──────┘
│
│
│
│
│
│
│
│
│
│
│
└───────────────────────────────────────────────────────────────────┐
│
│
│
│
└──────────────────────────────────────────────────┐
│
│
│
│
└───────────────────────────────┐
│
│
│
│
└──────────────────────┐
│
│
│
│
└─────────────┐
│
│
│
│
┌─┴──────────────┐ ┌─┴─────────────┐ ┌─┴────────────────┐ ┌─┴─────────────────────────┐ ┌─┴────────────────────┐ ┌─┴──────────────────┐
│ About...
│ │ Open...
F2 │ │ Traits...
│ │ Calculate index...
│ │ Output...
│ │ Colors...
│
│ Information... │ │ Save...
F3 │ │ Groups...
│ │ Calculate correlations... │ │ Summary
│ │ Mouse...
│
└────────┬───────┘ │ New
F4 │ │ Index...
│ │ Use script
│ ├──────────────────────┤ │ 25 Line display
│
│
├───────────────┤ │ Breeding goal... │ └───────┬───────────────────┘ │ Resize/move Ctrl-F5 │ │ 43/50 Line display │
┌───────┘
│ Change dir... │ └──────────────┬───┘
│
│ Zoom
F5 │ └────┬───────────────┘
│
│ Dos shell
│
│
│
│ Close
Alt-F3 │
│
│
├───────────────┤
│
│
└───────────┬──────────┘
│
│
│ Quit
Alt-X │
│
│
│
│
│
└───────┬───────┘
│
│
│
│
│
│
│
│
┌────────┘
│
│
│
│
│
│
│
│
│
│
│
│
│
│
│
│
│
│
┌────────┴────────┐
│
┌────────────────┬┴──────────────┐
│
│
│
│
│
│
│
│
│
│
│
╔═══════╧═════╗
╔══════╧══════╗
╔══════╧══════╗
│ ╔═════╧══════╗
╔═════╧══════╗
╔════╧═══════╗ │
│
║
OUTPUT
║
║
COLORS
║
║
MOUSE
║
│ ║
OPEN
║
║
SAVE
║
║ CHANGE DIR ║ │
│
╚═════════════╝
╚═════════════╝
╚═════════════╝
│ ╚════════════╝
╚════════════╝
╚════════════╝ │
│
│
│
│
└──────────────┐
│
│
│
│
│
┌────────┴────────┐
│
│
│
│
│
│
╔══════╧══════╗
╔══════╧══════╗
│
│
║
ABOUT
║
║ INFORMATION ║
│
│
╚═════════════╝
╚═════════════╝
│
│
│
│
╔═══════════════╗
│
└──────────────────────────────────┐
┌──────╢ CORRELATIONS ║
┌──────────────────────────┬───────┴──────────────────┬──────────────────────────┐
└───────┤
╚═══════════════╝
│
│
│
│
│
│
│
│
│
└───────┐
╔═══════╧═══════╗
PgUp
╔═══════╧═══════╗
PgUp
╔═══════╧═══════╗
PgUp
╔═══════╧═══════╗
╔╧══════════════╗
║
TRAITS
║-----<----║
GROUPS
║-----<----║
INDEX
║-----<----║ BREEDING GOAL ║----->----║
CALCULATE
║
║
║----->----║
║----->----║
║----->----║
║
PgDn
╚═══════════════╝
╚════════╤══════╝
PgDn
╚═══════╤═══════╝
PgDn
╚═══════════════╝
PgDn
╚═══════════════╝
│
│
┌────────┴─────────┐
┌──┴───────────────────┐
│
│
│
│
╔════╧═══╗ Alt-P ╔════╧═══╗ ╔═════╧══════╗ Alt-G ╔═════╧══════╗
║
RG
║---->----║
RP
║ ║ ENVIROMENT ║---->----║ GENETIC
║
║
║----<----║
║ ║ RELATIONS ║----<----║ RELATIONS ║
╚════════╝ Alt-G ╚════════╝ ╚════════════╝ Alt-E ╚════════════╝
Reference:
Note:
╔═════════════╗
║
TEXT
║ = TEXT Dialog Box
╚═════════════╝
Esc
Alt-key = open dialog box
= close dialog box (cmCancel)
Standard statusline:
┌───────────────────┬────────────────────────────────────────────────┐
│ F1 Help F10 Menu │ Use the F10 key for popup menus
│
└───────────────────┴────────────────────────────────────────────────┘
note:
visible when no dialog box is opened.
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3. The program SIP
3.1. Starting the program
To start the program all you have to do is type SIP at the DOS-prompt and the program will start.
It is possible to give a commandline option namely /c which will give you a clock in the upper
right corner of the screen.
3.2. The menubar
After you have started the program F10-key will make the pulldown menus vissible. The complete
menubar with submenus is printed here below. You can select an option by using the cursor-keys
and select an option with the enter-key, or you can use <Alt-fat>. It is also possible to use a mouse
to select an option.
┌───┬───────┬──────────┬──────────────┬────────┬─────────┬──────┐
│ ║ │ Files │ Settings │ Calculations │ Window │ Options │ Help │
└─┬─┴───┬───┴─────┬────┴───────┬──────┴────┬───┴────┬────┴──────┘
│
│
│
│
│
│
│
│
│
│
│
└──────────────────────────────────────────────────────────────┐
│
│
│
│
└──────────────────────────────────────────────┐
│
│
│
│
└────────────────────────────┐
│
│
│
│
└────────────────────┐
│
│
│
│
└────────────┐
│
│
│
│
┌─┴──────────────┐ ┌─┴─────────────┐ ┌─┴────────────────┐ ┌─┴─────────────────────────┐ ┌─┴────────────────────┐ ┌─┴──────────────────┐
│ About...
│ │ Open...
F2 │ │ Traits...
│ │ Calculate index...
│ │ Output...
│ │ Colors...
│
│ Information... │ │ Save...
F3 │ │ Groups...
│ │ Calculate correlations... │ │ Summary
│ │ Mouse...
│
└────────────────┘ │ New
F4 │ │ Index...
│ │ Use script
│ ├──────────────────────┤ │ 25 Line display
│
├───────────────┤ │ Breeding goal... │ └───────────────────────────┘ │ Resize/move Ctrl-F5 │ │ 43/50 Line display │
│ Change dir... │ └──────────────────┘
│ Zoom
F5 │ └────────────────────┘
│ Dos shell
│
│ Close
Alt-F3 │
├───────────────┤
└──────────────────────┘
│ Quit
Alt-X │
└───────────────┘
3.3. An overview of the important input boxes
In this chapter we will show you the most important screens you will see when the program is
running. In all the dialogs you can use mouse and/or keyboard. When you use the keyboard it is
important to know that the Tab-key and the Enter-key will step inside a dialog to other options.
3.3.1. Set traits dialog box
In this dialog box you must set all the different trait parameters of the traits you will use with your
selection indexes. You must give a trait description, a phenotypic standard deviation, common
environment component for full and half sibs and a repeatability. These trait descriptions are used
in other dialogs but you only can edit them here.
╔═[n]═══════════════════════ Set Traits ═══════════════════════════╗
║
║
║ Trait description
sp
h▓
c▓fs
c▓hs
r
║
║ ███████████████████████ ███████ ███████ ███████ ███████ ███████ ║
║ ███████████████████████ ███████ ███████ ███████ ███████ ███████ ║
║ ███████████████████████ ███████ ███████ ███████ ███████ ███████ ║
║ ███████████████████████ ███████ ███████ ███████ ███████ ███████ ║
║ ███████████████████████ ███████ ███████ ███████ ███████ ███████ ║
║ ███████████████████████ ███████ ███████ ███████ ███████ ███████ ║
║ ███████████████████████ ███████ ███████ ███████ ███████ ███████ ║
║ ███████████████████████ ███████ ███████ ███████ ███████ ███████ ║
║ ███████████████████████ ███████ ███████ ███████ ███████ ███████ ║
║ ███████████████████████ ███████ ███████ ███████ ███████ ███████ ║
║
║
║
[
OK
] [ Cancel ] [ Cor rp ] [ Cor rg ] [ Help ] ║
╚══════════════════════════════════════════════════════════════════╝
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Explanation:
* text:
Trait description = just a description of the trait
p
= phenotypic standard deviation
h²
= heritability
c²fs
= c² full sibs
c²hs
= c² half sibs
r
= repeatability
* symbols:
[ text ] = button
█████
= input box
* buttons:
OK
= close dialog box (keep changes)
Cancel = close dialog box (don't keep changes)
Cor rp = open phenotypic correlations dialog box
Cor rg = open genetic correlations dialog box
Help = about this dialog box
[]
= close dialog box with mouse (don't keep changes)
* keys to press button:
<Alt-K> = [ OK ]
<Alt-C> = [ Cancel ]
<Alt-P> = [ Cor rp ]
<Alt-G> = [ Cor rg ]
<Alt-H>= [ Help ]
* other keys:
Esc
= close dialog box (don't keep changes)
PgDn
= close dialog box (keep changes) and open Groups dialog box
Tab
= goto next dialog box item
<Shift-Tab> = goto previous dialog box item
<Ctrl-F4> = reset dialog
3.3.2. Set rg dialog box & rp dialog box
The rp and rg dialog box are allmost identical. The only difference is the type of correlations you
have to set in this dialog box. There is one box for genetic correlations and one box for phenotypic
correlations.
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╔═[]══════════════════════ Set Correlations rg ══════════════════════════╗
║
║
║ Trait
2
3
4
5
6
7
8
9
10
║
║ 1 Trait desc.
█████ █████ █████ █████ █████ █████ █████ █████ █████ ║
║ 2 Trait desc.
█████ █████ █████ █████ █████ █████ █████ █████ ║
║ 3 Trait desc.
█████ █████ █████ █████ █████ █████ █████ ║
║ 4 Trait desc.
█████ █████ █████ █████ █████ █████ ║
║ 5 Trait desc.
█████ █████ █████ █████ █████ ║
║ 6 Trait desc.
█████ █████ █████ █████ ║
║ 7 Trait desc.
█████ █████ █████ ║
║ 8 Trait desc.
█████ █████ ║
║ 9 Trait desc.
█████ ║
║ 10 Trait desc.
║
║
║
║
[
OK
] [ Cancel ] [ Cor rp ] [ Help ] ║
╚═════════════════════════════════════════════════════════════════════════╝
╔═[]══════════════════════ Set Correlations rp ══════════════════════════╗
║
║
║ Trait
2
3
4
5
6
7
8
9
10
║
║ 1 Trait desc.
█████ █████ █████ █████ █████ █████ █████ █████ █████ ║
║ 2 Trait desc.
█████ █████ █████ █████ █████ █████ █████ █████ ║
║ 3 Trait desc.
█████ █████ █████ █████ █████ █████ █████ ║
║ 4 Trait desc.
█████ █████ █████ █████ █████ █████ ║
║ 5 Trait desc.
█████ █████ █████ █████ █████ ║
║ 6 Trait desc.
█████ █████ █████ █████ ║
║ 7 Trait desc.
█████ █████ █████ ║
║ 8 Trait desc.
█████ █████ ║
║ 9 Trait desc.
█████ ║
║ 10 Trait desc.
║
║
║
║
[
OK
] [ Cancel ] [ Cor rg ] [ Help ] ║
╚═════════════════════════════════════════════════════════════════════════╝
Explanation:
* text:
Trait desc. = just a description of the trait with a corresponding number; this description comes
from the traits dialog box
* symbols:
[ text ] = button
█████
= input box
* buttons:
OK
Cancel
Cor rg
Cor rp
Help
[]
= close dialog box (keep changes)
= close dialog box (don't keep changes)
= open genetic correlations dialog box and close this dialog box (keep changes)
= open phenotypic correlations dialog box and close this dialog box (keep changes)
= about this dialog box
= close dialog box with mouse (don't keep changes)
* keys to press button:
<Alt-K>
= [ OK ]
<Alt-C>
= [ Cancel ]
<Alt-P>
= [ Cor rp ]
<Alt-G>
= [ Cor rg ]
<Alt-H>
= [ Help
]
* other keys:
Esc
= close dialog box (don't keep changes)
Tab
= goto next dialog box item
<Shift-Tab> = goto previous dialog box item
<Ctrl-F4> = reset dialog
Note: when one of these boxes is closed the trait dialog box will reappear.
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3.3.3. Set groups dialog box
In this dialog box you have to name all the groups of animals you will use as an information source
to calculate the index. You have to give a group description, the additive genetic relationship within
the group, the number of observations and you can pick an option for environmental correlation
within the group you want to use. These group descriptions are used in other dialogs but you only
can edit them here.
╔═[]════════════════════ Set Groups ════════════════════════╗
║
use
║
║ Group description
a
n
c²fs c²hs r none ║
║ ████████████████████ ███████ ███████
( ) ( ) ( ) (•) ║
║ ████████████████████ ███████ ███████
( ) ( ) ( ) (•) ║
║ ████████████████████ ███████ ███████
( ) ( ) ( ) (•) ║
║ ████████████████████ ███████ ███████
( ) ( ) ( ) (•) ║
║ ████████████████████ ███████ ███████
( ) ( ) ( ) (•) ║
║ ████████████████████ ███████ ███████
( ) ( ) ( ) (•) ║
║ ████████████████████ ███████ ███████
( ) ( ) ( ) (•) ║
║ ████████████████████ ███████ ███████
( ) ( ) ( ) (•) ║
║ ████████████████████ ███████ ███████
( ) ( ) ( ) (•) ║
║ ████████████████████ ███████ ███████
( ) ( ) ( ) (•) ║
║
║
║
relationship
║
║ [ OK ] [ Cancel ] [Environment] [Genetic] [ Help ] ║
╚════════════════════════════════════════════════════════════╝
Explanation:
* text:
Group description = just a description of the group
a
= additive genetic relationship in the group
n
= number of observations in the group
use:
c²fs
= c² full sibs
c²hs = c² half sibs
r
= repeatability
none = none of the others
* symbols:
[ text ]
█████
()
(•)
= button
= input box
= not selected item |--> only one selectable at the same time
= selected item
|/
* buttons:
OK
Cancel
Environment
Genetic
Help
[]
S.I.P. USER MANUAL
= close dialog box (keep changes)
= close dialog box (don't keep changes)
= open environmental relations dialog box
= open genetic relations dialog box
= about this dialog box
= close dialog box with mouse (don't keep changes)
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* keys to press button:
<Alt-K> = [ OK ]
<Alt-C> = [ Cancel ]
<Alt-E> = [ Environment ]
<Alt-R> = [ Genetic ]
<Alt-H> = [ Help ]
* other keys:
Esc
PgUp
PgDn
Tab
<Shift-Tab>
<Ctrl-F4>
= close dialog box (don't keep changes)
= close dialog box (keep changes) and open Traits dialog box
= close dialog box (keep changes) and open Index dialog box
= goto next dialog box item
= goto previous dialog box item
= reset dialog
3.3.4. Set genetic relations dialog box
In this box you must set the additive genetic correlation between groups and the additive genetic
relation between the group and animal (in column bg) for whom we are calculating the selection
index
╔═[]═════════════════════════ Set Genetic Relations ═════════════════════════╗
║
║
║
bg
Group
2
3
4
5
6
7
8
9
10
║
║ █████ 1 animal(s) █████ █████ █████ █████ █████ █████ █████ █████ █████ ║
║ █████ 2 animal(s)
█████ █████ █████ █████ █████ █████ █████ █████ ║
║ █████ 3 animal(s)
█████ █████ █████ █████ █████ █████ █████ ║
║ █████ 4 animal(s)
█████ █████ █████ █████ █████ █████ ║
║ █████ 5 animal(s)
█████ █████ █████ █████ █████ ║
║ █████ 6 animal(s)
█████ █████ █████ █████ ║
║ █████ 7 animal(s)
█████ █████ █████ ║
║ █████ 8 animal(s)
█████ █████ ║
║ █████ 9 animal(s)
█████ ║
║ █████ 10 animal(s)
║
║
║
║
[
OK
] [ Cancel ] [Environment] [ Help ] ║
╚═════════════════════════════════════════════════════════════════════════════╝
Explanation:
* text:
Group = just a group of animal(s) with a corresponding number; this description comes from
the groups dialog box
bg
= additive genetic relation of the group with the animal in the breeding goal
* symbols:
[ text ]
█████
= button
= input box
* buttons:
OK
Cancel
Environment
Help
[]
S.I.P. USER MANUAL
= close dialog box (keep changes)
= close dialog box (don't keep changes)
= open environmental relations dialog box
= about this dialog box
= close dialog box with mouse (don't keep changes)
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* keys to press button:
<Alt-K> = [ OK ]
<Alt-C> = [ Cancel ]
<Alt-E> = [ Environment ]
<Alt-H> = [ Help ]
* other keys:
Esc
Tab
<Shift-Tab>
<Ctrl-F4>
= close dialog box (don't keep changes)
= goto next dialog box item
= goto previous dialog box item
= reset dialog
Note: when this box is closed the group dialog box will appear
3.3.5. Set common environment dialog box
In this box you must decide which type of common environment component you want to use when
it is the same trait but a different group.
╔═[]═════ Set Common Environment Between Groups ═══════════════╗
║
║
║ Group
2
3
4
5
6
7
8
9
10
║
║ 1 animal(s)
<fs> <hs> <no> <no> <no> <no> <no> <no> <no> ║
║ 2 animal(s)
<no> <no> <no> <no> <no> <no> <no> <no> ║
║ 3 animal(s)
<no> <no> <no> <no> <no> <no> <no> ║
║ 4 animal(s)
<no> <no> <no> <no> <no> <no> ║
║ 5 animal(s)
<no> <no> <no> <no> <no> ║
║ 6 animal(s)
<no> <no> <no> <no> ║
║ 7 animal(s)
<no> <no> <no> ║
║ 8 animal(s)
<no> <no> ║
║ 9 animal(s)
<no> ║
║ 10 animal(s)
║
║
║
║
[
OK
] [ Cancel ] [Genetic] [ Help ] ║
╚═══════════════════════════════════════════════════════════════╝
Explanation:
* text:
Group = just a group of animal(s) with a corresponding number; this description comes from
the groups dialog box
* symbols:
[ text ] = button
<text> = environment button:
options: no - use c²=0
fs - use c²fs (from the traits dialog box)
hs - use c²hs (from the traits dialog box)
changes are made by pressing the enter-key
* buttons:
OK
Cancel
Genetic
Help
[]
= close dialog box (keep changes)
= close dialog box (don't keep changes)
= open genetic relations dialog box
= about this dialog box
= close dialog box with mouse (don't keep changes)
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* keys to press button:
<Alt-K> = [ OK
<Alt-C> = [ Cancel
<Alt-R> = [ Genetic
<Alt-H> = [ Help
* other keys:
Esc
Tab
<Shift-Tab>
<Ctrl-F4>
]
]
]
]
= close dialog box (don't keep changes)
= goto next dialog box item
= goto previous dialog box item
= reset dialog
Note: when this box is closed the group dialog box will reappear
3.3.6. Set index sources
In this dialog you can pick to a maximum of twenty index sources you want to use in your selection
index.
╔═══[]═══════════ Select index sources ═════════════════════╗
║
║
║ Group
Trait--> text..........
║
║
1
2
3
4
5
6
7
8
9 10
║
║ animal(s)
[X] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] ║
║ animal(s)
[ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] ║
║ animal(s)
[ ] [X] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] ║
║ animal(s)
[ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] ║
║ animal(s)
[ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] ║
║ animal(s)
[ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] ║
║ animal(s)
[ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] ║
║ animal(s)
[ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] ║
║ animal(s)
[ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] ║
║ animal(s)
[ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] ║
║
║
║ Nr Selected
[
OK
] [ Cancel ] [ Help ] ║
╚════════════════════════════════════════════════════════════╝
Explanation:
* text:
Group
= name of a group of animal(s); this name comes from the groups dialog box
Trait--> text... = name of the trait in which column the cursor finds itself; this name comes from
the traits dialog box
Nr Selected = how many items are already selected, green when 20 or less, red flashing when
more then 20 items are selected (20 is the maximum)
* symbols:
[ text ] = button
[]
= not selected item
[X]
= selected item
* buttons:
OK
Cancel
Help
[]
= close dialog box (keep changes)
= close dialog box (don't keep changes)
= about this dialog box
= close dialog box with mouse (don't keep changes)
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* keys to press button:
<Alt-K> = [ OK ]
<Alt-C> = [ Cancel ]
<Alt-H> = [ Help ]
* other keys:
Esc
PgUp
PgDn
Tab
<Shift-Tab>
<Ctrl-F4>
= close dialog box (don't keep changes)
= close dialog box (keep changes) and open Groups dialog box
= close dialog box (keep changes) and open Breeding goal dialog box
= goto next dialog box item
= goto previous dialog box item
= reset dialog
Note: a maximum of 20 items is selectable at once. It is not possible to close this dialog and keeping
the changes when there are 20 (or more) items selected.
3.3.7. Set breeding goal
In this dialog box you can set which traits are in the breeding goal what kind of trait (economic or
desired gain) and you can insert a value for each trait.
╔═[]══════════ Set breeding goal ═══════════════╗
║
║
║ Trait
skip
v
d
value
║
║ description
( ) (•) ( ) ███████
║
║ description
( ) (•) ( ) ███████
║
║ description
( ) (•) ( ) ███████
║
║ description
( ) (•) ( ) ███████
║
║ description
( ) (•) ( ) ███████
║
║ description
( ) (•) ( ) ███████
║
║ description
( ) (•) ( ) ███████
║
║ description
( ) (•) ( ) ███████
║
║ description
( ) (•) ( ) ███████
║
║ description
( ) (•) ( ) ███████
║
║
║
║
[
OK
] [ Cancel ] [ Help ] ║
╚════════════════════════════════════════════════╝
Explanation:
* text:
Trait = description of a trait; this description comes from the traits dialog box
skip = don't put this trait in the breeding goal
v
= economic trait
d
= desired gain trait
value = economic value or relative change
* symbols:
[ text ]
()
(•)
█████
S.I.P. USER MANUAL
= button
= not selected item
= selected item
= input box
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* buttons:
OK
Cancel
Help
[]
= close dialog box (keep changes)
= close dialog box (don't keep changes)
= about this dialog box
= close dialog box with mouse (don't keep changes)
* keys to press button:
<Alt-K> = [ OK ]
<Alt-C> = [ Cancel ]
<Alt-H> = [ Help ]
* other keys:
Esc
PgUp
PgDn
Tab
<Shift-Tab>
<Ctrl-F4>
= close dialog box (don't keep changes)
= close dialog box (keep changes) and open Index dialog box
= close dialog box (keep changes) and open Calculate dialog box
= goto next dialog box item
= goto previous dialog box item
= reset dialog
3.3.8. Calculation box
In this box you can start the calculations and when it is an index of type 3 you must give an e-value.
╔═[]════════════ Calculate index ═══════════════╗
║
║
║ index type (1,2 or 3)
e-value ███████ ║
║
║
║ Action: text
║
║ 
║
║
║
║ Matrix:On [ Start ] [ Cancel ] [ Help ] ║
╚════════════════════════════════════════════════╝
Explanation:
* text:
index type (1,2 or 3) that will be used during calculation
* symbols:
[ text ]
= button
█████
= input box
Action: text
= what is going on

= indicator during calculation
Matrix:On/Off = Matrices are written (or not) with the results
* buttons:
Start
Cancel
Help
[]
S.I.P. USER MANUAL
= start index calculation
= close dialog box
= about this dialog box
= close dialog box with mouse
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* keys to press button:
<Alt-S> = [ Start
]
<Alt-C> = [ Cancel ]
<Alt-H> = [ Help ]
* other keys:
Esc
Tab
<Shift-Tab>
<Alt-T>
= close dialog box
= goto next dialog box item
= goto previous dialog box item
= toggle matrix on/off
Remark: e-value only by type 3 visible
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Appendix A: Used formula's
The P-matrix
The used formulas are:
diagonal:
n=1: 
n>1: use r:
((1+(n-1)r))/n
use c2: ((1+(n-1)(ah2+c2))/n
p
r
h2
n
c2
a
= phenotypic standard deviation
= repeatability
= heritability
= number
= common environment component
= additive genetic relation in group
off-diagonal:
same group, different trait:
n=1: rpij Pi Pj
n>1: 1/n( rpij Pi Pj + (n-1) a rgij Ai Aj)
different group, same trait:
(aijh2 + c2) 
different group, different trait:
aij rgij Ai Aj
pi
n
r
c2
a
aij
rpij
rgij
Ai
S.I.P. USER MANUAL
= phenotypic standard deviation trait i
= number
= repeatability
= common environment component
= additive genetic relation in group
= additive genetic relation between group i and j
= phenotypic correlation between trait i and j
= genetic correlation between trait i and j
= genetic standard deviation trait i
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The G-matrix
The used formula is: a rgij Ai Aj
a
rgij
Ai
= additive relation with breeding goal animal
= genetic correlation between trait i and j
= genetic standard deviation trait i
The C-matrix
The used formula is: rgij Ai Aj
rgij
Ai
= genetic correlation between trait i and j
= genetic standard deviation trait i
Selection index formula's
There are three types of indices, namely the indices based on economic values (type 1), on desired
gains (type 2) or on a combination of both (type 3). The calculations of each type are pretty much the
same, so we can use the same code.The formula's will be presented later but when we schematize
the calculations it is like this
Index type 3 ──┐
│
└──>── Index type 2 ──┐
│
└──>── Index type 1
Thus the calculations of index type 1 are made for every selection index, but the calculations of
index type 3 only when it is really an index type 3.
Index type 1
b = P-1Gv
[1]
 = b'Pb
[2]
 = 2I - (bi)2/Wii
[3]
W = P-1
[3a]
rvi = 100% - ( /  ) * 100%
[4]
 = v'Cv
[5]
RIH = I / H
[6]
dj = b'(column j of G) / I (i=1)
[7]
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Index type 2
S = (G'P-1G)-1
[8]
v = S
[9]
b = P-1Gv
[1]
... and so on (just like index type 1)
Index type 3
S = (G1'P-1G1)-1
[10]
max = (1/'S)
[11]
 = E * max
[12]
R = P-1[I - G1SG1'P-1]
[13]
b = (1-E2)½* (v0'G0'RG0v0)-½* RG0v0 + P-1G1S (I=1) [14]
f0 = v0'G0'b
[15]
d = G'b (i=1)
[16]
... followed by an index type 2;
were we use =d to start the calculations
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