Initial load of files from the 2011 workshop

ASREML_Programs/frogs.as

+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

ASREML_Programs/germ.as

+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

ASREML_Programs/linthresh.as

+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

ASREML_Programs/linthresh.pin

+ 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

ASREML_Programs/linthresh_cov.as

+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

ASREML_Programs/mouse_42_dm.as

+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

ASREML_Programs/mouse_42_poly.as

+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

ASREML_Programs/mouse_42_spline.as

+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
+

ASREML_Programs/mouse_42_st.as

+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
+

ASREML_Programs/mouse_42_st.pin

+
+F Add. 2
+F Env. 1
+F Phen. 1 + 2 *1
+H h2 2 5

ASREML_Programs/mouse_42_st_cycle.as

+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

ASREML_Programs/mouse_42_st_cycle.pin

+
+F Add. 2
+F Env. 1
+F Phen. 1 + 2 *1
+H h2 2 5

ASREML_Programs/mouse_42_st_pin.as

+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

ASREML_Programs/mouse_42_tt.as

+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   
+
+ 

ASREML_Programs/mouse_42_tt.pin

+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
+

ASREML_Programs/mouse_42_tt_pe.as

+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 
+
+
+ 

ASREML_Programs/mouse_42_tt_sub.as

+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   
+
+ 

Data/frogs.txt

+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

Data/germ.dat

+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

Data/linthresh.dat

+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