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Commit 08457ffe authored by Stephen D Kachman's avatar Stephen D Kachman
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Initial load of files from the 2011 workshop

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Oxygen consumption of frogs
Frog *
Species * !I
Temp * !A
Rest # Resting oxygen consumption
Exercise # Exercise oxygen consumption
frogs.txt !SKIP 1 !ASUV # !MAXIT 100 !EXTRA 5
Rest Exercise ~ Trait Species.Temp.Trait !r Frog.Species.Temp
0 0 1
Frog.Species.Temp 1
0 0 I 1
#Species.Temp 0 I
Germination Example
type !A
extract !A
r
n
y
plate !I
germ.dat !MAXIT=100
r !BINOMIAL !TOTAL n ~mu type*extract !r plate
0 0 1
plate 1
0 0 I 1
predict type extract !TDIFF !PLOT
predict type !TDIFF
\ No newline at end of file
Linear Threshold Example
Origin 2 !I
Sire 6 !I
Season 2 !I
Pelvic_Opening
Sex 2 !A
Birth_Weight
Diff 2 !A
Score
linthresh.dat !ASUV !MAXIT 100
Score Pelvic_Opening !BINOMIAL !LOGIT ~ Trait Trait.Origin,
Trait.Season Trait.Sex !r Trait.Sire
1 2 1
0 0 I
2 0 US 1 -1 1100 !GP
Trait.Sire 2
2 0 US .4 -.1 100 !GP
6 0 I
predict Trait 1
predict Sire Trait 1 !PLOT
Source Model terms Gamma Component Comp/SE % C
Residual UnStructured 1 1 0.907762 0.907762 4.35 0 P
Residual UnStructured 2 1 -3.96806 -3.96806 -1.33 0 P
Residual UnStructured 2 2 1104.53 1104.53 4.41 0 P
Trait.Sire UnStructured 1 1 0.392602 0.392602 0.44 0 P
Trait.Sire UnStructured 2 1 -0.610064 -0.610064 -0.08 0 P
Trait.Sire UnStructured 2 2 114.874 114.874 0.70 0 P
F Add 4*4
F Pheno 4+8*3.3
H H2 7 8
Linear Threshold Covariate Example
Origin 2 !I
Sire 6 !I
Season 2 !I
Pelvic_Opening
Sex 2 !A
Birth_Weight
Diff 2 !A
Score
linthresh.dat !ASUV !MAXIT 100
Score Pelvic_Opening !BINOMIAL !LOGIT ~ Trait Trait.Origin,
Trait.Season Trait.Sex at(Trait,1).Pelvic_Opening !r Trait.Sire
1 2 1
0 0 I
2 0 US 1 0 1100 !GPZP
Trait.Sire 2
2 0 US .4 -.1 100 !GP
6 0 I
\ No newline at end of file
Single Trait Analysis
Anim 300 !P
Sire 300 !P
Dam 300 !P
Day
Generation * !I
Gender * !A
BW2
BW3
BW4_5
BW6 !/10
BW8 !/10
BW12 !/10
ADG !=V11 !-V10 !/14
day !=V4 !/365
M42.dat !SKIP 1 # Pedigree file
M42.dat !SKIP 1 !MAXIT 100 #!EXTRA 5 #Data file
BW6 ~ mu Generation*Gender Generation.day ,
!r ![ Anim Dam !] ide(Dam)
0 0 2
Anim 2
2 0 US 1 .1 1 !GP #v11 v21 v22 Lower Triangle by row
0 0 AINV #ide(Dam)
ide(Dam) 1
0 0 I 1
Two Trait Analysis
Anim 300 !P
Sire 300 !P
Dam 300 !P
Day
Generation * !I
Gender * !A
Week
Weight !/10
day !=V4 !/365
M42.dat !SKIP 1 # Pedigree file
M42_rr.dat !SKIP 1 !MAXIT 100 #Data file
Weight ~ fac(Week).Generation.Gender fac(Week).Generation.day ,
!r leg(Week,3).Anim ide(Anim).leg(Week,2) !f mv
1 2 2
386 0 I
6 0 DIAG 1 2 3 4 5 6 !S2==1 !GP
leg(Week,3).Anim 2
4 Week US !GP !+10
16
9 6
0 0 1
0 0 0 .7
419 0 AINV
ide(Anim).leg(Week,2) 2
419 0 IDEN
3 0 US !GP !+6
1
0 1
0 0 1
0 0 0 1
Two Trait Analysis
Anim 300 !P
Sire 300 !P
Dam 300 !P
Day
Generation * !I
Gender * !A
Week
Weight !/10
day !=V4 !/365
M42.dat !SKIP 1 # Pedigree file
M42_rr.dat !SKIP 1 !MAXIT 100 #Data file
!SPLINE spl(Week,3) 2 8 12
Weight ~ fac(Week).Generation*Gender fac(Week).Generation.day ,
!r ![ Anim Week.Anim !] spl(Week,3).Anim ![ ide(Anim) Week.ide(Anim) !],
spl(Week,3).ide(Anim) !f mv
1 2 4
386 0 IDEN
6 0 DIAG 1 2 3 4 5 6 !S2==1 !GP
Anim 2
2 Week US !GP !+3
16
9 6
419 0 AINV
spl(Week,3).Anim 1
0 0 AINV 1 !GP
ide(Anim) 2
2 Week US !GP !+3
1
0 1
419 0 I
spl(Week,3).ide(Anim) 1
0 0 I 1
Single Trait Analysis
Anim 300 !P
Sire 300 !P
Dam 300 !P
Day
Generation * !I
Gender * !A
BW2
BW3
BW4_5
BW6 !/10
BW8 !/10
BW12 !/10
ADG !=V11 !-V10 !/14
day !=V4 !/365
M42.dat !SKIP 1 # Pedigree file
M42.dat !SKIP 1 !MAXIT 100 # !EXTRA 5 #Data file
BW6 ~ mu Generation*Gender Generation.day !r Anim
0 0 1
Anim 1
0 0 AINV 1
F Add. 2
F Env. 1
F Phen. 1 + 2 *1
H h2 2 5
Single Trait Analysis
Anim 300 !P
Sire 300 !P
Dam 300 !P
Day
Generation * !I
Gender * !A
BW !G 6
!CYCLE 1:6
M42.dat !SKIP 1 # Pedigree file
M42.dat !SKIP 1 !MAXIT 100 # !EXTRA 5 #Data file
BW{$I} ~ mu Generation*Gender Generation.Day !r Anim
!VPREDICT
0 0 1
Anim 1
0 0 AINV 1
F Add. 2
F Env. 1
F Phen. 1 + 2 *1
H h2 2 5
Single Trait Analysis
Anim 300 !P
Sire 300 !P
Dam 300 !P
Day
Generation * !I
Gender * !A
BW2
BW3
BW4_5
BW6 !/10
BW8 !/10
BW12 !/10
ADG !=V11 !-V10 !/14
day !=V4 !/365
M42.dat !SKIP 1 # Pedigree file
M42.dat !SKIP 1 !MAXIT 100 # !EXTRA 5 #Data file
BW6 ~ mu Generation*Gender Generation.day !r Anim
!PIN !define
F Add. 2
F Env. 1
F Phen. 1 + 2 *1
H h2 2 5
0 0 1
Anim 1
0 0 AINV 1
Two Trait Analysis
Anim 300 !P
Sire 300 !P
Dam 300 !P
Day
Generation * !I
Gender * !A
BW2 !/10
BW3 !/10
BW4_5 !/10
BW6 !/10
BW8 !/10
BW12 !/10
ADG !=V11 !-V10 !/14
day !=V4 !/365
M42.dat !SKIP 1 # Pedigree file
M42.dat !SKIP 1 !MAXIT 100 #Data file
BW6 BW8 ~ Trait*Generation*Gender Trait.Generation.day mv ,
!r !{ Trait.Anim Trait.Dam !}
1 2 1
0 0 I
2 0 US 3.885 3.271 6.963 !GP
Trait.Anim 2
4 0 US !GP !+10
3.724
4.356 6.372
.1 .1 1.927
.1 .1 1.414 1.329
0 0 AINV
F M1 9 #14:16
F M12 12
F M2 13
F AM1 7 #17:19
F AM12 8 *.5 10*.5
F AM22 11
F Phen. 1:3 + 4:6 + 14:16 +17:19 #20:22
H h2D1 4 20
H h2D2 6 22
R Dr 4 5 6
R Mr 14 15 16
R Pr 20 21 22
Two Trait Analysis
Anim 300 !P
Sire 300 !P
Dam 300 !P
Day
Generation * !I
Gender * !A
BW2 !/10
BW3 !/10
BW4_5 !/10
BW6 !/10
BW8 !/10
BW12 !/10
ADG !=V11 !-V10 !/14
day !=V4 !/365
M42.dat ! SKIP 1 # Pedigree file
M42.dat !SKIP 1 !MAXIT 100 #Data file
BW6 ADG ~ Trait*Generation*Gender Trait.Generation.day ,
!r ![ Trait.Anim at(Trait,1).Dam !] !f mv
predict Generation
1 2 1
0 0 I
2 0 US 3.885 3.271 6.963 !GP
Trait.Anim 2
3 0 US 1 .01 2 .1 .1 3 !GP
0 0 AINV
Two Trait Analysis $1 $2
Anim 300 !P
Sire 300 !P
Dam 300 !P
Day
Generation * !I
Gender * !A
BW2 !/10
BW3 !/10
BW4_5 !/10
BW6 !/10
BW8 !/10
BW12 !/10
ADG !=V11 !-V10 !/14
day !=V4 !/365
M42.dat !SKIP 1 # Pedigree file
M42.dat !SKIP 1 !MAXIT 100 #Data file
$1 $2 ~ Trait*Generation*Gender Trait.Generation.day mv ,
!r !{ Trait.Anim Trait.Dam !}
1 2 1
0 0 I
2 0 US 3.885 3.271 6.963 !GP
Trait.Anim 2
4 0 US !GP !+10
3.724
4.356 6.372
.1 .1 1.927
.1 .1 1.414 1.329
0 0 AINV
Subject Species Temperature Rest Exercise
1 1 Low 0.107 0.152
2 1 Low 0.114 0.163
3 1 High 0.133 0.194
4 1 High 0.14 0.198
5 2 Low 0.098 0.144
6 2 Low 0.093 0.136
7 2 High 0.118 0.171
8 2 High 0.11 0.165
9 3 Low 0.126 0.182
10 3 Low 0.138 0.196
11 3 High 0.159 0.196
12 3 High 0.166 0.204
13 4 Low 0.154 0.207
14 4 Low 0.141 0.191
15 4 High 0.184 0.244
16 4 High 0.192 0.232
O_aeg_75 Bean 10 39 0.25641 1
O_aeg_75 Cucumber 5 6 0.833333 2
O_aeg_73 Bean 8 16 0.5 3
O_aeg_73 Cucumber 3 12 0.25 4
O_aeg_75 Bean 23 62 0.370968 5
O_aeg_75 Cucumber 53 74 0.716216 6
O_aeg_73 Bean 10 30 0.333333 7
O_aeg_73 Cucumber 22 41 0.536585 8
O_aeg_75 Bean 23 81 0.283951 9
O_aeg_75 Cucumber 55 72 0.763889 10
O_aeg_73 Bean 8 28 0.285714 11
O_aeg_73 Cucumber 15 30 0.5 12
O_aeg_75 Bean 17 39 0.435897 13
O_aeg_75 Cucumber 46 79 0.582278 14
O_aeg_73 Bean 0 4 0 15
O_aeg_73 Cucumber 3 7 0.428571 16
O_aeg_75 Cucumber 10 13 0.769231 17
1 1 1 328.0 M 41.0 E 0 328.0 M 41.0
1 1 1 304.5 M 37.5 E 0 304.5 M 37.5
1 1 1 354.8 F 41.5 E 0 354.8 F 41.5
1 1 2 374.0 F 40.0 E 0 374.0 F 40.0
1 1 2 285.0 F 43.0 E 0 285.0 F 43.0
1 1 2 310.0 F 42.0 E 0 310.0 F 42.0
1 1 2 270.0 F 35.0 E 0 270.0 F 35.0
2 1 1 336.0 F 46.0 E 0 336.0 F 46.0
2 1 1 374.0 F 40.5 E 0 374.0 F 40.5
2 1 2 346.5 F 39.0 E 0 346.5 F 39.0
1 2 1 346.5 M 41.4 E 0 346.5 M 41.4
1 2 1 333.3 M 43.0 D 1 333.3 M 43.0
1 2 2 346.5 F 34.0 E 0 346.5 F 34.0
1 2 2 307.5 M 47.0 D 1 307.5 M 47.0
1 2 2 315.0 M 42.0 E 0 315.0 M 42.0
2 2 2 300.0 M 44.5 E 0 300.0 M 44.5
2 2 2 273.0 M 49.0 E 0 273.0 M 49.0
1 3 1 341.0 M 41.6 E 0 341.0 M 41.6
2 3 1 300.0 M 36.0 E 0 300.0 M 36.0
2 3 1 328.0 F 42.7 E 0 328.0 F 42.7
2 3 2 266.0 F 32.5 E 0 266.0 F 32.5
2 3 2 302.3 F 44.4 E 0 302.3 F 44.4
2 3 2 320.0 M 46.0 E 0 320.0 M 46.0
1 4 2 328.0 M 47.0 D 1 328.0 M 47.0
1 4 2 344.0 F 51.0 D 1 344.0 F 51.0
1 4 2 243.0 F 39.0 E 0 243.0 F 39.0
2 4 1 333.3 M 44.5 E 0 333.3 M 44.5
1 5 1 346.5 M 40.5 E 0 346.5 M 40.5
1 5 1 304.5 F 43.5 E 0 304.5 F 43.5
1 5 2 396.0 M 42.5 E 0 396.0 M 42.5
1 5 2 285.0 M 48.8 D 1 285.0 M 48.8
1 5 2 328.0 M 38.5 E 0 328.0 M 38.5
1 5 2 346.5 M 52.0 E 0 346.5 M 52.0
1 5 2 344.0 F 48.0 E 0 344.0 F 48.0
2 5 1 357.0 F 41.0 E 0 357.0 F 41.0
2 5 1 357.0 M 50.5 D 1 357.0 M 50.5
2 5 2 317.8 M 43.7 D 1 317.8 M 43.7
2 5 2 346.5 M 51.0 D 1 346.5 M 51.0
1 6 1 290.0 F 51.6 D 1 290.0 F 51.6
1 6 1 260.0 M 45.3 D 1 260.0 M 45.3
1 6 1 357.0 F 36.5 E 0 357.0 F 36.5
1 6 2 354.8 M 50.5 E 0 354.8 M 50.5
1 6 2 273.0 M 46.0 D 1 273.0 M 46.0
1 6 2 315.0 M 45.0 E 0 315.0 M 45.0
1 6 2 256.5 F 36.0 E 0 256.5 F 36.0
2 6 1 317.8 F 43.5 E 0 317.8 F 43.5
2 6 1 290.0 F 36.5 E 0 290.0 F 36.5
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