diff --git a/ASREML_Programs/frogs.as b/ASREML_Programs/frogs.as
new file mode 100644
index 0000000000000000000000000000000000000000..b830bf151b197f122b14d54fb9f0bc344052788e
--- /dev/null
+++ b/ASREML_Programs/frogs.as
@@ -0,0 +1,12 @@
+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
diff --git a/ASREML_Programs/germ.as b/ASREML_Programs/germ.as
new file mode 100644
index 0000000000000000000000000000000000000000..614d519599981bc43e30f5034817433aa0b8cd34
--- /dev/null
+++ b/ASREML_Programs/germ.as
@@ -0,0 +1,14 @@
+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
diff --git a/ASREML_Programs/linthresh.as b/ASREML_Programs/linthresh.as
new file mode 100644
index 0000000000000000000000000000000000000000..8a283926278fd5b98468dd5e00e132fd36cb1811
--- /dev/null
+++ b/ASREML_Programs/linthresh.as
@@ -0,0 +1,20 @@
+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
diff --git a/ASREML_Programs/linthresh.pin b/ASREML_Programs/linthresh.pin
new file mode 100644
index 0000000000000000000000000000000000000000..646359ffd587caa6d5d00262a00e33163e2c00a3
--- /dev/null
+++ b/ASREML_Programs/linthresh.pin
@@ -0,0 +1,10 @@
+ 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
diff --git a/ASREML_Programs/linthresh_cov.as b/ASREML_Programs/linthresh_cov.as
new file mode 100644
index 0000000000000000000000000000000000000000..c5f3ac8b8b4419015c7a006d96c954765576f1a8
--- /dev/null
+++ b/ASREML_Programs/linthresh_cov.as
@@ -0,0 +1,18 @@
+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
diff --git a/ASREML_Programs/mouse_42_dm.as b/ASREML_Programs/mouse_42_dm.as
new file mode 100644
index 0000000000000000000000000000000000000000..29446fcccbb983e389038f5b5cca7fe1f109c062
--- /dev/null
+++ b/ASREML_Programs/mouse_42_dm.as
@@ -0,0 +1,25 @@
+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
diff --git a/ASREML_Programs/mouse_42_poly.as b/ASREML_Programs/mouse_42_poly.as
new file mode 100644
index 0000000000000000000000000000000000000000..6e0ca98682354ebfc803f10d6cbae7c435e47c71
--- /dev/null
+++ b/ASREML_Programs/mouse_42_poly.as
@@ -0,0 +1,31 @@
+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
diff --git a/ASREML_Programs/mouse_42_spline.as b/ASREML_Programs/mouse_42_spline.as
new file mode 100644
index 0000000000000000000000000000000000000000..6a6928812bce0e2da70b39565d54867f39f0e547
--- /dev/null
+++ b/ASREML_Programs/mouse_42_spline.as
@@ -0,0 +1,34 @@
+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
+
diff --git a/ASREML_Programs/mouse_42_st.as b/ASREML_Programs/mouse_42_st.as
new file mode 100644
index 0000000000000000000000000000000000000000..0d24e2fa0e7c846a24207133604c8ee68ad92bcd
--- /dev/null
+++ b/ASREML_Programs/mouse_42_st.as
@@ -0,0 +1,22 @@
+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
+
diff --git a/ASREML_Programs/mouse_42_st.pin b/ASREML_Programs/mouse_42_st.pin
new file mode 100644
index 0000000000000000000000000000000000000000..cf5bb5c7d7f8243ff2be0346c34cec88b025d640
--- /dev/null
+++ b/ASREML_Programs/mouse_42_st.pin
@@ -0,0 +1,5 @@
+
+F Add. 2
+F Env. 1
+F Phen. 1 + 2 *1
+H h2 2 5
diff --git a/ASREML_Programs/mouse_42_st_cycle.as b/ASREML_Programs/mouse_42_st_cycle.as
new file mode 100644
index 0000000000000000000000000000000000000000..262a12623626b0248a6f7c65d4792bcc73e0f5e0
--- /dev/null
+++ b/ASREML_Programs/mouse_42_st_cycle.as
@@ -0,0 +1,19 @@
+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
diff --git a/ASREML_Programs/mouse_42_st_cycle.pin b/ASREML_Programs/mouse_42_st_cycle.pin
new file mode 100644
index 0000000000000000000000000000000000000000..cf5bb5c7d7f8243ff2be0346c34cec88b025d640
--- /dev/null
+++ b/ASREML_Programs/mouse_42_st_cycle.pin
@@ -0,0 +1,5 @@
+
+F Add. 2
+F Env. 1
+F Phen. 1 + 2 *1
+H h2 2 5
diff --git a/ASREML_Programs/mouse_42_st_pin.as b/ASREML_Programs/mouse_42_st_pin.as
new file mode 100644
index 0000000000000000000000000000000000000000..e3640ff1f579adf66ba800822d21403948026bff
--- /dev/null
+++ b/ASREML_Programs/mouse_42_st_pin.as
@@ -0,0 +1,30 @@
+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
diff --git a/ASREML_Programs/mouse_42_tt.as b/ASREML_Programs/mouse_42_tt.as
new file mode 100644
index 0000000000000000000000000000000000000000..bc77b02aab58d7a62c9c33a8808d74a0373beb32
--- /dev/null
+++ b/ASREML_Programs/mouse_42_tt.as
@@ -0,0 +1,31 @@
+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
+
+
diff --git a/ASREML_Programs/mouse_42_tt.pin b/ASREML_Programs/mouse_42_tt.pin
new file mode 100644
index 0000000000000000000000000000000000000000..f23c561c2383437643ddb902c16475c2a43922e8
--- /dev/null
+++ b/ASREML_Programs/mouse_42_tt.pin
@@ -0,0 +1,13 @@
+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
+
diff --git a/ASREML_Programs/mouse_42_tt_pe.as b/ASREML_Programs/mouse_42_tt_pe.as
new file mode 100644
index 0000000000000000000000000000000000000000..fdd3f4bdc035ce33a8cb6193893f4d3010aeae93
--- /dev/null
+++ b/ASREML_Programs/mouse_42_tt_pe.as
@@ -0,0 +1,29 @@
+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
+
+
+
diff --git a/ASREML_Programs/mouse_42_tt_sub.as b/ASREML_Programs/mouse_42_tt_sub.as
new file mode 100644
index 0000000000000000000000000000000000000000..4c4e6c9cbbb4edb611658fd9d15c6bacec0d8c67
--- /dev/null
+++ b/ASREML_Programs/mouse_42_tt_sub.as
@@ -0,0 +1,31 @@
+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
+
+
diff --git a/Data/frogs.txt b/Data/frogs.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d850fc4224391f89fcb0d522fa3a06d798a15606
--- /dev/null
+++ b/Data/frogs.txt
@@ -0,0 +1,17 @@
+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
diff --git a/Data/germ.dat b/Data/germ.dat
new file mode 100644
index 0000000000000000000000000000000000000000..f5e9678217088cc546c38dc00c8d0f7c8d09f691
--- /dev/null
+++ b/Data/germ.dat
@@ -0,0 +1,17 @@
+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
diff --git a/Data/linthresh.dat b/Data/linthresh.dat
new file mode 100644
index 0000000000000000000000000000000000000000..756fbe22e3619342cf4b456fcc362dd80c53774f
--- /dev/null
+++ b/Data/linthresh.dat
@@ -0,0 +1,47 @@
+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
diff --git a/Data/m42.dat b/Data/m42.dat
new file mode 100644
index 0000000000000000000000000000000000000000..5c620e30d5826c3839d60b945682939140cb732a
--- /dev/null
+++ b/Data/m42.dat
@@ -0,0 +1,387 @@
+Anim Sire Dam Day Gen Gender 2Wk 3Wk 4.5Wk 6Wk 8Wk 12Wk
+6515 5002 4636 31 0 F 104 150 226 . . .
+6696 4531 5306 32 0 F 112 164 222 . . .
+6773 4612 4486 33 0 M 121 172 313 . . .
+6781 4963 5076 33 0 M 114 154 321 . . .
+6855 4513 4814 33 0 F 119 165 279 . . .
+6885 5534 5004 33 0 F 126 182 253 . . .
+6894 4923 5245 33 0 F 111 160 236 . . .
+6936 5252 4701 33 0 F 127 177 273 . . .
+6991 4521 5176 33 0 M 124 164 307 . . .
+7075 5362 5454 34 0 F 124 183 284 . . .
+7092 5362 4806 34 0 M 113 161 284 . . .
+7104 5141 4906 34 0 F 123 185 259 . . .
+7144 5441 4684 34 0 F 113 178 255 . . .
+7215 4442 4664 35 0 F 104 171 255 . . .
+7415 4782 5276 37 0 F 129 172 250 . . .
+7421 5194 4965 37 0 M 115 166 278 . . .
+7455 5483 5444 39 0 F 126 161 . . . .
+0151 6781 7215 149 1 M 111 172 343 403 432 449
+0152 6781 7215 149 1 M 108 172 320 376 399 435
+0153 6781 7215 149 1 M 115 169 323 386 411 440
+0154 6781 7215 149 1 M 108 195 344 415 473 504
+0155 6781 7215 149 1 F 114 172 262 312 324 282
+0156 6781 7215 149 1 F 110 163 272 332 359 349
+0157 6781 7215 149 1 F 110 164 268 316 342 376
+0158 6781 7215 149 1 F 105 161 263 339 373 372
+0221 7092 6936 150 1 M 102 159 318 348 384 424
+0222 7092 6936 150 1 M 092 164 300 347 374 407
+0223 7092 6936 150 1 M 103 166 320 365 406 446
+0224 7092 6936 150 1 F 101 156 250 277 301 312
+0225 7092 6936 150 1 F 103 172 279 314 324 334
+0226 7092 6936 150 1 F 102 163 263 293 328 357
+0227 7092 6936 150 1 F 094 146 240 298 296 317
+0228 7092 6936 150 1 F 101 152 256 291 307 334
+0331 7092 7415 151 1 M 109 179 313 378 400 430
+0332 7092 7415 151 1 M 101 154 297 348 358 404
+0333 7092 7415 151 1 M 103 167 328 374 397 411
+0334 7092 7415 151 1 F 107 169 271 332 329 323
+0335 7092 7415 151 1 F 106 162 243 308 314 320
+0336 7092 7415 151 1 F 106 154 252 291 302 313
+0337 7092 7415 151 1 F 107 158 274 304 314 311
+0338 7092 7415 151 1 F 109 179 265 300 324 324
+0361 6991 7075 151 1 M 124 181 313 366 397 436
+0362 6991 7075 151 1 M 109 168 304 376 411 424
+0363 6991 7075 151 1 M 116 178 304 359 398 421
+0364 6991 7075 151 1 M 112 162 306 360 388 388
+0365 6991 7075 151 1 F 119 174 312 327 367 367
+0366 6991 7075 151 1 F 114 153 277 314 318 360
+0367 6991 7075 151 1 F 085 129 223 259 263 252
+0368 6991 7075 151 1 F 113 166 282 303 320 317
+0371 6991 6696 151 1 M 111 183 291 322 366 380
+0372 6991 6696 151 1 M 107 170 297 336 356 380
+0373 6991 6696 151 1 F 107 161 242 272 274 296
+0374 6991 6696 151 1 F 113 174 245 295 288 320
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diff --git a/Data/m42_rr.dat b/Data/m42_rr.dat
new file mode 100644
index 0000000000000000000000000000000000000000..a42fbf79f93a5314ec1cde8f5e98f94aec6295be
--- /dev/null
+++ b/Data/m42_rr.dat
@@ -0,0 +1,2317 @@
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diff --git a/HTML/ASReml Workshop 2011.html b/HTML/ASReml Workshop 2011.html
new file mode 100644
index 0000000000000000000000000000000000000000..48b8eb2eaafdca11c971d721afc4433e78dcb102
--- /dev/null
+++ b/HTML/ASReml Workshop 2011.html
@@ -0,0 +1,208 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!-- saved from url=(0052)http://statistics.unl.edu/faculty/steve/asreml/2011/ -->
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"><!-- InstanceBegin template="/Templates/unlstandardtemplate.dwt" codeOutsideHTMLIsLocked="false" --><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+
+<!-- InstanceBeginEditable name="doctitle" -->
+<title>
+ASReml Workshop 2011</title>
+<!-- InstanceEndEditable -->
+<!-- Codebase:UNLFramework 20071011 -->
+<link rel="stylesheet" type="text/css" media="screen" href="./ASReml Workshop 2011_files/main.css">
+<link rel="stylesheet" type="text/css" media="print" href="./ASReml Workshop 2011_files/print.css">
+<script type="text/javascript" src="./ASReml Workshop 2011_files/all_compressed.js"></script>
+
+<style type="text/css"></style></head><body id="fixed">
+<!-- InstanceBeginEditable name="head" --><!-- TemplateBeginEditable name="head" -->
+
+<!-- Place ptional header elements here -->
+
+<!-- TemplateEndEditable --><!-- InstanceEndEditable --><!-- InstanceParam name="leftRandomPromo" type="boolean" value="true" --><!-- InstanceParam name="bodyid" type="text" value="fixed" -->
+
+
+
+
+</center>
+
+
+ <center>
+ <table width="100%" border="5" cellpadding="0" bgcolor="#d0d0d0" background="./ASReml Workshop 2011_files/gray.jpg" bordercolor="#607080" bordercolorlight="#e0e0e0">
+ <tbody><tr><td>
+ <table border="0" background="./ASReml Workshop 2011_files/gray.jpg" cellpadding="5" width="100%">
+ <tbody><tr><td colspan="5"><h1>ASReml Workshop 2011</h1></td></tr>
+ </tbody></table>
+ </td></tr>
+ </tbody></table>
+ </center>
+
+
+
+
+
+
+
+
+
+
+<p>
+
+</p><center>
+<h2> Monday October 17, 2011 9:00am-4:00pm and Tuesday October 18,
+2011 9:00am-Noon</h2>
+<p>
+</p><h2> A230 Animal Science Building on the East Campus of the University of Nebraska-Lincoln</h2>
+</center>
+<p>
+
+</p>
+
+
+<!--You can register at <a
+href=http://statistics.unl.edu/asreml/online_reg.shtml>http://statistics.unl.edu/asreml/online_reg.shtml</a>
+or <a href=http://go.unl.edu/rhw>http://go.unl.edu/rhw</a>
+
+<p>
+
+The deadline for registration is <b>Monday October 10th</b>. -->
+
+
+
+<h2>Slides</h2>
+
+<ul>
+
+ <li> <a href="../Slides/ASREML.pdf">Slides</a>
+ <br> <!-- #flastmod file="ASREML2up.pdf"-->
+ </li><li> <a href="../Slides/ASREML2up.pdf">Slides 2/page</a>
+ <br> <!-- #flastmod file="ASREML2up.pdf"-->
+</li></ul>
+
+<h2> Data files</h2>
+ <ul>
+ <li> <a href="../Data/frogs.txt">Frog data</a>
+ <br> <!-- #flastmod file="frogs.txt"-->
+ <br> Original data was obtained
+ from <a href="http://www.statsci.org/data/general/frogs.html">
+ http://www.statsci.org/data/general/frogs.html</a>
+ </li><li> <a href="../Data/M42.dat">Mouse data</a>
+ <br> <!-- #flastmod file="M42.dat"-->
+ </li><li> <a href="../Data/M42_rr.dat">Mouse data for Random Regression</a>
+ <br> <!-- #flastmod file="M42_rr.dat"-->
+
+ </li><li>
+ <a href="../Data/germ.dat">Germination rate data</a><br><!-- #flastmod
+ file="germ.dat"-->
+ </li><li> <a href="../Data/linthresh.dat">Linear-Threshold data</a>
+<br> Source: Foulley, Gianola, and Thompson (1983)
+ <i>Prediction of genetic merit from data on binary and
+ quantitative variates with an application to calving
+ difficulty, birth weight and pelvic opening.</i>
+ Genet. Sel. Evol. <b>15</b>, 407-424
+ <br> <!-- #flastmod file="linthresh.dat"-->
+
+
+
+ </li></ul>
+<h2> ASReml Programs</h2>
+ <ul>
+ <li> <a href="../ASREML_Programs/frogs.as">Frog program</a>
+ <br> <!-- #flastmod file="frogs.as"-->
+ </li><li> <a href="../ASREML_Programs/mouse_42_st.as">Single Trait analysis</a>
+ <br> <!-- #flastmod file="mouse_42_st.as"-->
+ </li><li> <a href="../ASREML_Programs/mouse_42_st.pin">Single Trait .pin file</a>
+ <br> <!-- #flastmod file="mouse_42_st.pin"-->
+ </li><li> <a href="../ASREML_Programs/mouse_42_st_cycle.as">Single Trait analysis using !CYCLE</a>
+ <br> <!-- #flastmod file="mouse_42_st_cycle.as"-->
+ </li><li> <a href="../ASREML_Programs/mouse_42_st_cycle.pin">Single Trait using !CYCLE .pin file</a>
+ <br> <!-- #flastmod file="mouse_42_st_cycle.pin"-->
+ </li><li> <a href="../ASREML_Programs/mouse_42_st_pin.as">Single Trait using !PIN</a>
+ <br> <!-- #flastmod file="mouse_42_st_pin.as"-->
+ </li><li> <a href="../ASREML_Programs/mouse_42_dm.as">Correlated Random Effects analysis</a>
+ <br> <!-- #flastmod file="mouse_42_dm.as"-->
+ </li><li> <a href="../ASREML_Programs/mouse_42_tt.as">Two Trait analysis</a>
+ <br> <!-- #flastmod file="mouse_42_tt.as"-->
+ </li><li> <a href="../ASREML_Programs/mouse_42_tt_sub.as">Two Trait analysis with $1 $2</a>
+ <br> <!-- #flastmod file="mouse_42_tt_sub.as"-->
+ </li><li> <a href="../ASREML_Programs/mouse_42_tt.pin">Two Trait .pin file</a>
+ <br> <!-- #flastmod file="mouse_42_tt.pin"-->
+ </li><li> <a href="../ASREML_Programs/mouse_42_tt_pe.as">Trait Specific analysis</a>
+ <br> <!-- #flastmod file="mouse_42_tt_pe.as"-->
+ </li><li> <a href="../ASREML_Programs/mouse_42_poly.as">Random Regression (Polynomial)</a>
+ <br> <!-- #flastmod file="mouse_42_poly.as"-->
+ </li><li> <a href="../ASREML_Programs/mouse_42_spline.as">Random Regression (Splines)</a>
+ <br> <!-- #flastmod file="mouse_42_spline.as"-->
+ </li><li><a href="../ASREML_Programs/germ.as">Germination Rate ASReml Program</a>
+ <br><!-- #flastmod file="germ.as"--> </li>
+ <li><a href="../ASREML_Programs/linthresh_cov.as">Linear Threshold Covariate ASReml Program</a>
+ <br><!-- #flastmod file="linthresh_cov.as"--> </li>
+ <li><a href="../ASREML_Programs/linthresh.as">Linear Threshold (Over Dispersion) ASReml Program</a>
+ <br><!-- #flastmod file="linthresh.as"--> </li>
+ <li><a href="../ASREML_Programs/linthresh.pin">Linear Threshold (Over Dispersion) Pin File</a>
+ <br><!-- #flastmod file="linthresh.pin"--> </li>
+ </ul>
+<h2> SAS Programs</h2>
+ <ul>
+ <li> <a href="../SAS_Programs/frog.sas">Frog program</a>
+ <br> <!-- #flastmod file="frog.sas"-->
+ </li><li> <a href="../SAS_Programs/varfunc.sas">Covariance matrices</a>
+ <br> <!-- #flastmod file="varfunc.sas"-->
+ </li><li> <a href="../SAS_Programs/predfun.sas">Genetic Merit</a>
+ <br> <!-- #flastmod file="predfun.sas"-->
+ </li></ul>
+<h2> R Programs</h2>
+ <ul>
+ <li> <a href="../R_Programs/varfunc.R">Covariance matrices</a>
+ <br> <!-- #flastmod file="varfunc.R"--><br>
+ <ul>
+ <li> <a href="../R_Programs/leg2.dat">leg2.dat</a>
+ <br> <!-- #flastmod file="leg2.dat"--><br>
+ </li><li> <a href="../R_Programs/leg3.dat">leg3.dat</a>
+ <br> <!-- #flastmod file="leg3.dat"--><br>
+ </li><li> <a href="../R_Programs/polyVarcomp.dat">polyVarcomp.dat</a>
+ <br> <!-- #flastmod file="polyVarcomp.dat"--><br>
+ </li></ul>
+ </li><li> <a href="../R_Programs/predfun.R">Genetic Merit</a>
+ <br> <!-- #flastmod file="predfun.R"-->
+ <ul>
+ <li> <a href="../R_Programs/spline.dat">spline.dat</a>
+ <br> <!-- #flastmod file="spline.dat"--><br>
+ </li></ul>
+ </li></ul>
+
+
+<h2>Other Resources</h2>
+<ul>
+<li> <a href="http://uncronopio.org/ASReml/">ASReml Cookbook</a>
+</li><li> <a href="http://www.contexteditor.org/">Context Editor</a></li>
+<li> <a href="../asreml2.chl">Context Editor Modified ASReml Highlighter File</a>
+ <br> <!-- #flastmod file="asreml2.chl"--></li>
+</ul>
+
+
+
+
+
+
+ <!-- TemplateEndEditable -->
+ <!--THIS IS THE END OF THE MAIN CONTENT AREA.-->
+ <!-- InstanceEndEditable --> </div>
+ </div>
+ <!-- close main right -->
+ </div>
+</div>
+<!-- close container -->
+
+
+
+ </div>
+</div>
+
+<!-- close footer -->
+<!-- sifr -->
+
+
+<!-- InstanceEnd -->
+
+
+
+
+</body></html>
\ No newline at end of file
diff --git a/HTML/ASReml Workshop 2011_files/all_compressed.js b/HTML/ASReml Workshop 2011_files/all_compressed.js
new file mode 100644
index 0000000000000000000000000000000000000000..a089c4dc968278e4772c0a4ef626cbdc7bed78a2
--- /dev/null
+++ b/HTML/ASReml Workshop 2011_files/all_compressed.js
@@ -0,0 +1,9 @@
+<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
+<html><head>
+<title>404 Not Found</title>
+</head><body>
+<h1>Not Found</h1>
+<p>The requested URL /ucomm/templatedependents/templatesharedcode/scripts/all_compressed.js was not found on this server.</p>
+<hr>
+<address>Apache Server at statistics.unl.edu Port 80</address>
+</body></html>
diff --git a/HTML/ASReml Workshop 2011_files/gray.jpg b/HTML/ASReml Workshop 2011_files/gray.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..a8bef7f0b26619c9f92758bcb9fa963367ca4693
Binary files /dev/null and b/HTML/ASReml Workshop 2011_files/gray.jpg differ
diff --git a/HTML/ASReml Workshop 2011_files/main.css b/HTML/ASReml Workshop 2011_files/main.css
new file mode 100644
index 0000000000000000000000000000000000000000..a01fa9d5d8e59d8ba53d8370a0a48b8effcc0cf0
--- /dev/null
+++ b/HTML/ASReml Workshop 2011_files/main.css
@@ -0,0 +1,9 @@
+<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
+<html><head>
+<title>404 Not Found</title>
+</head><body>
+<h1>Not Found</h1>
+<p>The requested URL /ucomm/templatedependents/templatecss/layouts/main.css was not found on this server.</p>
+<hr>
+<address>Apache Server at statistics.unl.edu Port 80</address>
+</body></html>
diff --git a/HTML/ASReml Workshop 2011_files/print.css b/HTML/ASReml Workshop 2011_files/print.css
new file mode 100644
index 0000000000000000000000000000000000000000..c52cedda4a6f0e5a43a18afddaa768a79b83fa99
--- /dev/null
+++ b/HTML/ASReml Workshop 2011_files/print.css
@@ -0,0 +1,9 @@
+<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
+<html><head>
+<title>404 Not Found</title>
+</head><body>
+<h1>Not Found</h1>
+<p>The requested URL /ucomm/templatedependents/templatecss/layouts/print.css was not found on this server.</p>
+<hr>
+<address>Apache Server at statistics.unl.edu Port 80</address>
+</body></html>
diff --git a/HTML/ASReml Workshop 2011_files/sifr_replacements.js b/HTML/ASReml Workshop 2011_files/sifr_replacements.js
new file mode 100644
index 0000000000000000000000000000000000000000..7ff69392db49d25567921c440e3abf1802585a92
--- /dev/null
+++ b/HTML/ASReml Workshop 2011_files/sifr_replacements.js
@@ -0,0 +1,9 @@
+<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
+<html><head>
+<title>404 Not Found</title>
+</head><body>
+<h1>Not Found</h1>
+<p>The requested URL /ucomm/templatedependents/templatesharedcode/scripts/sifr_replacements.js was not found on this server.</p>
+<hr>
+<address>Apache Server at statistics.unl.edu Port 80</address>
+</body></html>
diff --git a/HTML/ASReml Workshop 2011_files/wordmark.png b/HTML/ASReml Workshop 2011_files/wordmark.png
new file mode 100644
index 0000000000000000000000000000000000000000..8928d63924bed353fae7bf30823eb547da5c682d
--- /dev/null
+++ b/HTML/ASReml Workshop 2011_files/wordmark.png
@@ -0,0 +1,9 @@
+<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
+<html><head>
+<title>404 Not Found</title>
+</head><body>
+<h1>Not Found</h1>
+<p>The requested URL /ucomm/templatedependents/templatecss/images/wordmark.png was not found on this server.</p>
+<hr>
+<address>Apache Server at statistics.unl.edu Port 80</address>
+</body></html>
diff --git a/R_Programs/leg2.dat b/R_Programs/leg2.dat
new file mode 100644
index 0000000000000000000000000000000000000000..87172d164330e1f8eda485bdd01f2bfbf9d09906
--- /dev/null
+++ b/R_Programs/leg2.dat
@@ -0,0 +1,22 @@
+x p0 p1 p2
+ 2.00000 0.70711 -1.22474 1.58114
+ 2.50000 0.70711 -1.10227 1.13051
+ 3.00000 0.70711 -0.97980 0.72732
+ 3.50000 0.70711 -0.85732 0.37157
+ 4.00000 0.70711 -0.73485 0.06325
+ 4.50000 0.70711 -0.61237 -0.19764
+ 5.00000 0.70711 -0.48990 -0.41110
+ 5.50000 0.70711 -0.36742 -0.57712
+ 6.00000 0.70711 -0.24495 -0.69570
+ 6.50000 0.70711 -0.12247 -0.76685
+ 7.00000 0.70711 0.00000 -0.79057
+ 7.50000 0.70711 0.12247 -0.76685
+ 8.00000 0.70711 0.24495 -0.69570
+ 8.50000 0.70711 0.36742 -0.57712
+ 9.00000 0.70711 0.48990 -0.41110
+ 9.50000 0.70711 0.61237 -0.19764
+ 10.00000 0.70711 0.73485 0.06325
+ 10.50000 0.70711 0.85732 0.37157
+ 11.00000 0.70711 0.97980 0.72732
+ 11.50000 0.70711 1.10227 1.13051
+ 12.00000 0.70711 1.22474 1.58114
\ No newline at end of file
diff --git a/R_Programs/leg3.dat b/R_Programs/leg3.dat
new file mode 100644
index 0000000000000000000000000000000000000000..4c07f55ff16b7a6e4d9132ee9060bbdb12559074
--- /dev/null
+++ b/R_Programs/leg3.dat
@@ -0,0 +1,22 @@
+x po p1 p2 p3
+ 2.00000 0.70711 -1.22474 1.58114 -1.87083
+ 2.50000 0.70711 -1.10227 1.13051 -0.88397
+ 3.00000 0.70711 -0.97980 0.72732 -0.14967
+ 3.50000 0.70711 -0.85732 0.37157 0.36013
+ 4.00000 0.70711 -0.73485 0.06325 0.67350
+ 4.50000 0.70711 -0.61237 -0.19764 0.81849
+ 5.00000 0.70711 -0.48990 -0.41110 0.82316
+ 5.50000 0.70711 -0.36742 -0.57712 0.71559
+ 6.00000 0.70711 -0.24495 -0.69570 0.52383
+ 6.50000 0.70711 -0.12247 -0.76685 0.27595
+ 7.00000 0.70711 0.00000 -0.79057 0.00000
+ 7.50000 0.70711 0.12247 -0.76685 -0.27595
+ 8.00000 0.70711 0.24495 -0.69570 -0.52383
+ 8.50000 0.70711 0.36742 -0.57712 -0.71559
+ 9.00000 0.70711 0.48990 -0.41110 -0.82316
+ 9.50000 0.70711 0.61237 -0.19764 -0.81849
+ 10.00000 0.70711 0.73485 0.06325 -0.67350
+ 10.50000 0.70711 0.85732 0.37157 -0.36013
+ 11.00000 0.70711 0.97980 0.72732 0.14967
+ 11.50000 0.70711 1.10227 1.13051 0.88397
+ 12.00000 0.70711 1.22474 1.58114 1.87083
\ No newline at end of file
diff --git a/R_Programs/polyVarcomp.dat b/R_Programs/polyVarcomp.dat
new file mode 100644
index 0000000000000000000000000000000000000000..bbebeade215d569d7b0184e7b02efd7ddd5f0ec6
--- /dev/null
+++ b/R_Programs/polyVarcomp.dat
@@ -0,0 +1,23 @@
+ Source Model terms Gamma Component Comp/SE % C
+ Residual DIAGonal 1 0.580048E-07 0.580048E-07 0.00 4 B
+ Residual DIAGonal 2 0.569417 0.569417 8.23 0 P
+ Residual DIAGonal 3 1.14199 1.14199 5.00 0 P
+ Residual DIAGonal 4 2.35376 2.35376 9.38 0 P
+ Residual DIAGonal 5 2.14731 2.14731 4.68 0 P
+ Residual DIAGonal 6 0.908636 0.908636 0.25 0 P
+ leg(Week,3).Anim UnStructured 1 1 8.53724 8.53724 3.48 0 P
+ leg(Week,3).Anim UnStructured 2 1 3.62088 3.62088 2.74 0 P
+ leg(Week,3).Anim UnStructured 2 2 2.02703 2.02703 2.48 0 P
+ leg(Week,3).Anim UnStructured 3 1 -1.14875 -1.14875 -2.64 0 P
+ leg(Week,3).Anim UnStructured 3 2 -0.703737 -0.703737 -3.48 0 P
+ leg(Week,3).Anim UnStructured 3 3 0.371288 0.371288 2.18 0 P
+ leg(Week,3).Anim UnStructured 4 1 -0.735158 -0.735158 -2.56 0 P
+ leg(Week,3).Anim UnStructured 4 2 -0.627428 -0.627428 -3.28 0 P
+ leg(Week,3).Anim UnStructured 4 3 0.342983 0.342983 2.80 0 P
+ leg(Week,3).Anim UnStructured 4 4 0.415515 0.415515 4.29 0 P
+ ide(Anim).leg(WeekUnStructured 1 1 6.28396 6.28396 4.20 0 P
+ ide(Anim).leg(WeekUnStructured 2 1 2.84486 2.84486 3.03 0 P
+ ide(Anim).leg(WeekUnStructured 2 2 1.81997 1.81997 2.42 0 P
+ ide(Anim).leg(WeekUnStructured 3 1 -0.112084 -0.112084 -0.36 0 P
+ ide(Anim).leg(WeekUnStructured 3 2 0.147997 0.147997 0.55 0 P
+ ide(Anim).leg(WeekUnStructured 3 3 0.172062 0.172062 1.41 0 P
diff --git a/R_Programs/predfun.R b/R_Programs/predfun.R
new file mode 100644
index 0000000000000000000000000000000000000000..2a22fb19e5ae3a019fbd99436b46a044c948b3fc
--- /dev/null
+++ b/R_Programs/predfun.R
@@ -0,0 +1,26 @@
+spldat=read.table("spline.dat",header=TRUE)
+spldat
+slndat=read.table("mouse_42_spline.sln",header=FALSE,col.names=c("factor","level","sol","se"))
+levels(slndat$factor)
+Z=as.matrix(spldat)
+Z=cbind(rep(1,nrow(spldat)),Z)
+int=slndat$sol[slndat$factor=="Anim"]
+slope=slndat$sol[slndat$factor=="Week.Anim"]
+spline=slndat$sol[slndat$factor=="spl(Week,3).Anim"]
+GM=as.matrix(cbind(int,slope,spline))
+EBV=GM%*%t(Z)
+colnames(EBV)=paste("W",spldat$Week,sep="")
+rownames(EBV)=slndat$level[slndat$factor=="Anim"]
+library(MASS)
+EBVdata=data.frame(EBV=c(t(EBV)),
+ Anim=rep(rownames(EBV),each=nrow(spldat)),
+ Week=rep(spldat$Week,dim(EBV)[1])
+ )
+library(lattice)
+xyplot(EBV~Week,type="l",groups=Anim,
+ data=EBVdata[EBVdata$Anim %in% rownames(EBV)[1:25],])
+
+#And Violin boxplots
+library(UsingR)
+simple.violinplot(EBV~Week,data=EBVdata[EBVdata$Week %in% c(2,3,4.5,6,8,12),],
+ col="lightblue")
diff --git a/R_Programs/spline.dat b/R_Programs/spline.dat
new file mode 100644
index 0000000000000000000000000000000000000000..3779632adb88788d94b57c6940b0a2529d074a2c
--- /dev/null
+++ b/R_Programs/spline.dat
@@ -0,0 +1,22 @@
+Week sp1
+ 2.00000 0.98453
+ 2.50000 0.46518
+ 3.00000 -0.04444
+ 3.50000 -0.53457
+ 4.00000 -0.99547
+ 4.50000 -1.41740
+ 5.00000 -1.79062
+ 5.50000 -2.10538
+ 6.00000 -2.35194
+ 6.50000 -2.52056
+ 7.00000 -2.60149
+ 7.50000 -2.58500
+ 8.00000 -2.46134
+ 8.50000 -2.22482
+ 9.00000 -1.88600
+ 9.50000 -1.45949
+ 10.00000 -0.95992
+ 10.50000 -0.40189
+ 11.00000 0.19998
+ 11.50000 0.83109
+ 12.00000 1.47680
diff --git a/R_Programs/varfunc.R b/R_Programs/varfunc.R
new file mode 100644
index 0000000000000000000000000000000000000000..973c948ade062c9c3301a67e947e81abfa94a18c
--- /dev/null
+++ b/R_Programs/varfunc.R
@@ -0,0 +1,75 @@
+leg3=read.table("leg3.dat",header=TRUE)
+leg2=read.table("leg2.dat",header=TRUE)
+
+P3=as.matrix(leg3[,-1])
+P2=as.matrix(leg2[,-1])
+
+weeks=leg3[,1]
+
+vardata=read.fwf("polyVarcomp.dat",skip=1,
+ widths=c(-1,18,13,4,13,14,7,-1,3,-1,1))
+vardata$V1=gsub(" ","",vardata$V1)
+R=diag(vardata[vardata$V1=="Residual",4])
+
+varmat=function(data,s){
+ C=data[data$V1==s,4]
+ idx=data[data$V1==s,3]
+ idx=t(sapply(strsplit(as.character(idx)," "),as.numeric))
+ n=max(idx)
+ x=matrix(nrow=n,ncol=n)
+ for(i in 1:nrow(idx)){
+ x[idx[i,1],idx[i,2]]=C[i]
+ x[idx[i,2],idx[i,1]]=C[i]
+ }
+ return(x)
+}
+
+GP=varmat(vardata,"leg(Week,3).Anim")
+RP=varmat(vardata,"ide(Anim).leg(Week")
+
+Obsweeks=c(2,3,4.5,6,8,12)
+xidx=weeks %in% Obsweeks
+Nobs=length(Obsweeks)
+
+GCov=P3[xidx,]%*%GP%*%t(P3[xidx,])
+RCov=P2[xidx,]%*%RP%*%t(P2[xidx,])+R
+GPCorr=sqrt(diag(1/diag(GPCov)))%*%GPCov%*%sqrt(diag(1/diag(GPCov)))
+GCorr=sqrt(diag(1/diag(GCov)))%*%GCov%*%sqrt(diag(1/diag(GCov)))
+
+RCorr=sqrt(diag(1/diag(RCov)))%*%RCov%*%sqrt(diag(1/diag(RCov)))
+
+GPCov=P3%*%GP%*%t(P3)
+RPCov=P2%*%RP%*%t(P2)
+X11()
+plot(Obsweeks,diag(GCov),ylab="Genetic Variance",xlab="Weeks")
+plot(Obsweeks,diag(RCov),ylab="Environmental Variance",xlab="Weeks")
+plot(Obsweeks,diag(GCov)/(diag(GCov)+diag(RCov)),ylab="Heritability",
+ xlab="Weeks",ylim=c(0,1))
+X11()
+persp(weeks,weeks,GPCov,col="lightgreen",shade=.75,ticktype="detailed",zlab="Genetic Covariance")
+persp(weeks,weeks,GPCorr,col="lightgreen",shade=.25,ticktype="detailed",zlab="Genetic Correaltion",zlim=c(0,1))
+
+library("scatterplot3d")
+color=matrix(grey(.5),Nobs,Nobs)
+for(i in 1:Nobs) color[i,i]=palette="red"
+Rows=rep(weeks[xidx],each=Nobs)
+Cols=rep(weeks[xidx],Nobs)
+
+#color=grey(abs(Rows-Cols)/15)
+
+scatterplot3d(Rows,Cols,
+ GCov,c(color),
+ type="h",xlim=c(0,13),ylim=c(0,13),lwd=2,
+ xlab="Weeks",ylab="Weeks",zlab="Genetic Covariance")
+scatterplot3d(Rows,Cols,
+ RCov,c(color),
+ type="h",xlim=c(0,13),ylim=c(0,13),lwd=2,
+ xlab="Weeks",ylab="Weeks",zlab="Environmental Covariance")
+scatterplot3d(Rows,Cols,
+ GCorr,c(color),
+ type="h",xlim=c(0,13),ylim=c(0,13),lwd=2,
+ xlab="Weeks",ylab="Weeks",zlab="Genetic Correlation")
+scatterplot3d(Rows,Cols,
+ RCorr,c(color),
+ type="h",xlim=c(0,13),ylim=c(0,13),lwd=2,
+ xlab="Weeks",ylab="Weeks",zlab="Environmental Correlation")
diff --git a/SAS_Programs/frog.sas b/SAS_Programs/frog.sas
new file mode 100644
index 0000000000000000000000000000000000000000..147dae63b90a8bc379a3cc9d43b10c308cb823e7
--- /dev/null
+++ b/SAS_Programs/frog.sas
@@ -0,0 +1,18 @@
+data frogs;
+ length cond $ 8;
+ infile "ASREML/frogs.txt" expandtabs firstobs=2;
+ input frog species temp $ rest exercise;
+ Y=rest;cond="Rest";output;
+ Y=Exercise;cond="Exercise";output;
+proc print;
+proc mixed data=frogs;
+ class frog species temp Cond;
+ model y=species|temp|cond/ddfm=kr;
+ random frog(species temp);
+run;
+proc mixed data=frogs;
+ class frog species temp Cond;
+ model y=species|temp|cond/ddfm=contain;
+ repeated cond/subject=frog(species temp) type=un;
+run;
+
diff --git a/SAS_Programs/predfun.sas b/SAS_Programs/predfun.sas
new file mode 100644
index 0000000000000000000000000000000000000000..9723d29984799e248d6848abfbf9dc039ccca148
--- /dev/null
+++ b/SAS_Programs/predfun.sas
@@ -0,0 +1,65 @@
+data spl3;
+ int=1;
+ input x sp1;
+ cards;
+0.500 2.547
+1.000 2.026
+1.500 1.506
+2.000 0.985
+2.500 0.465
+3.000 -0.044
+3.500 -0.535
+4.000 -0.995
+4.500 -1.417
+5.000 -1.791
+5.500 -2.105
+6.000 -2.352
+6.500 -2.521
+7.000 -2.601
+7.500 -2.585
+8.000 -2.461
+8.500 -2.225
+9.000 -1.886
+9.500 -1.459
+10.000 -0.960
+10.500 -0.402
+11.000 0.200
+11.500 0.831
+12.000 1.477
+data sln int slope spline;
+length level $ 15;
+length factor $20;
+infile "mouse_42_spline.sln" expandtabs;
+input factor $ level $ sol se;
+output sln;
+if factor="Anim" then output int;
+if factor="Week.Anim" then output slope;
+if factor="spl(Week,3).Anim" then output spline;
+run;
+proc iml;
+ use spl3;
+ read all into Z;
+ use sln;
+ read all;
+ use int;
+ read all var {sol} into aint;
+ read all var {level} into Anim;
+ use slope;
+ read all var {sol} into aslope;
+ use spline;
+ read all var {sol} into aspline;
+ GM=aint||aslope||aspline;
+ Zx=Z[{2 3 4.5 6 8 12}*2,];
+ print Zx;
+ GW=GM*Zx`;
+ week={W2 W3 W4_5 W6 W8 W12};
+ print GW[rowname=Anim colname=week];
+ create Gdata from GW[colname=week];
+ append from GW;;
+ create Anim var {Anim};
+ append;
+ quit;
+run;
+data Gdata;
+ merge Anim Gdata;
+run;
diff --git a/SAS_Programs/varfunc.sas b/SAS_Programs/varfunc.sas
new file mode 100644
index 0000000000000000000000000000000000000000..8a308a192f5938fc8f098923ab9b028523189565
--- /dev/null
+++ b/SAS_Programs/varfunc.sas
@@ -0,0 +1,115 @@
+data leg3;
+ input x p0 p1 p2 p3;
+ cards;
+ 0.500 0.707 -1.225 1.581 -1.871
+ 1.000 0.707 -1.118 1.187 -0.998
+ 1.500 0.707 -1.012 0.828 -0.318
+ 2.000 0.707 -0.905 0.505 0.186
+ 2.500 0.707 -0.799 0.218 0.533
+ 3.000 0.707 -0.692 -0.033 0.742
+ 3.500 0.707 -0.586 -0.248 0.830
+ 4.000 0.707 -0.479 -0.427 0.818
+ 4.500 0.707 -0.373 -0.571 0.722
+ 5.000 0.707 -0.266 -0.678 0.562
+ 5.500 0.707 -0.160 -0.750 0.356
+ 6.000 0.707 -0.053 -0.786 0.122
+ 6.500 0.707 0.053 -0.786 -0.122
+ 7.000 0.707 0.160 -0.750 -0.356
+ 7.500 0.707 0.266 -0.678 -0.562
+ 8.000 0.707 0.373 -0.571 -0.722
+ 8.500 0.707 0.479 -0.427 -0.818
+ 9.000 0.707 0.586 -0.248 -0.830
+ 9.500 0.707 0.692 -0.033 -0.742
+ 10.000 0.707 0.799 0.218 -0.533
+ 10.500 0.707 0.905 0.505 -0.186
+ 11.000 0.707 1.012 0.828 0.318
+ 11.500 0.707 1.118 1.187 0.998
+ 12.000 0.707 1.225 1.581 1.871
+data leg2;
+ input x p0 p1 p2;
+ cards;
+ 0.500 0.707 -1.225 1.581
+ 1.000 0.707 -1.118 1.187
+ 1.500 0.707 -1.012 0.828
+ 2.000 0.707 -0.905 0.505
+ 2.500 0.707 -0.799 0.218
+ 3.000 0.707 -0.692 -0.033
+ 3.500 0.707 -0.586 -0.248
+ 4.000 0.707 -0.479 -0.427
+ 4.500 0.707 -0.373 -0.571
+ 5.000 0.707 -0.266 -0.678
+ 5.500 0.707 -0.160 -0.750
+ 6.000 0.707 -0.053 -0.786
+ 6.500 0.707 0.053 -0.786
+ 7.000 0.707 0.160 -0.750
+ 7.500 0.707 0.266 -0.678
+ 8.000 0.707 0.373 -0.571
+ 8.500 0.707 0.479 -0.427
+ 9.000 0.707 0.586 -0.248
+ 9.500 0.707 0.692 -0.033
+ 10.000 0.707 0.799 0.218
+ 10.500 0.707 0.905 0.505
+ 11.000 0.707 1.012 0.828
+ 11.500 0.707 1.118 1.187
+ 12.000 0.707 1.225 1.581
+proc iml;
+
+ start vec2var(vector);
+ nd=ncol(vector);
+ n=(-1+sqrt(1+8*nd))/2;
+ matrix=j(n,n,0);
+ idx=0;
+ do i=1 to n;
+ do j=1 to i;
+ idx=idx+1;
+ matrix[i,j]=vector[idx];
+ matrix[j,i]=vector[idx];
+ end;
+ end;
+ return(matrix);
+ finish vec2var;
+
+ use leg3;
+ read all var {p0 p1 p2 p3} into P3;
+ read all var {x};
+ use leg2;
+ read all var {p0 p1 p2} into P2;
+ print x P3 P2;
+ xidx=2*{2 3 4.5 6 8 12};
+ xp=[xidx,];
+ print tp;
+ RC={0.1000000E-06 0.5688098 1.137154
+ 2.355232 2.147434 1.145474 };
+ GPC={7.152305 3.827207
+ 2.396900 -0.4676474 -0.2903185 0.1660231
+ -1.100170 -0.7353516 -0.5993249E-01 0.9576310};
+ RPC={4.467746 2.694879 2.173887 -0.1536786
+ 0.3924026E-01 0.2849811};
+ RD=diag(RC);
+ GP=vec2var(GPC);
+ RP=vec2var(rpc);
+ GCov=P3[xidx,]*GP*P3[xidx,]`;
+ RCov=P2[xidx,]*Rp*P2[xidx,]`+Rd;
+ print Gcov RCov;
+ G=P3*GP*P3`;
+ create Gdata from G;
+ append from G;
+
+ quit;
+run;
+
+data Gdata2;
+set gdata;
+array col{*} col1-col24;
+weekx=_N_/2;
+do weeky=.5 to 12 by .5;
+cov=col{weeky*2};
+output;
+end;
+proc g3d data=gdata2;
+plot weekx*weeky=cov;
+run;
+symbol i=join;
+proc gplot data=gdata2;where weekx=weeky;
+plot cov*weekx;
+run;
diff --git a/Slides/asreml.pdf b/Slides/asreml.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..b19b7efd0b4d65a92128ab826dd86e6130d38f9a
Binary files /dev/null and b/Slides/asreml.pdf differ
diff --git a/Slides/asreml2up.pdf b/Slides/asreml2up.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..400aa1816a535b7184dc5293e3c2b31a3c22231f
Binary files /dev/null and b/Slides/asreml2up.pdf differ
diff --git a/asreml2.chl b/asreml2.chl
new file mode 100644
index 0000000000000000000000000000000000000000..2114b1d5606e040430628b8ecf88f97726067fcd
--- /dev/null
+++ b/asreml2.chl
@@ -0,0 +1,197 @@
+//////////////////////////////////////////////////////////////////////////////
+//
+// ASReml highlighter written by Luis A. Apiolaza, Luis.Apiolaza@utas.edu.au
+// Version 2 additions by Mick Carrick mick.carrick@dpi.vic.gov.au
+//
+//////////////////////////////////////////////////////////////////////////////
+
+//////////////////////////////////////////////////////////////////////////////
+// language name
+
+Language: ASReml V2
+
+
+//////////////////////////////////////////////////////////////////////////////
+// default file filter
+// note: if more than one extension is associated, eg:
+// C/C++ files (*.c,*.cpp,*.h,*.hpp)|*.c;*.cpp;*.h;*.hpp
+
+Filter: ASReml files (*.as,*.aov,*.asr,*.pin,*.pvs,*.res,*.rsv,*.sln)|*.as;*.aov;*.asr;*.pvs;*.pin;*.res;*.rsv;*.sln
+
+
+//////////////////////////////////////////////////////////////////////////////
+// help file which will be invokend when F1 is pressed
+
+HelpFile:
+
+
+//////////////////////////////////////////////////////////////////////////////
+// language case sensitivity
+// 0 - no
+// 1 - yes
+
+CaseSensitive: 0
+
+
+//////////////////////////////////////////////////////////////////////////////
+// comment type: LineComment - comment to the end of line
+// BlockCommentBeg - block comment begin, it could be
+// multiline
+// BlockCommentEnd - block comment end
+
+LineComment: #
+BlockCommentBeg:
+BlockCommentEnd:
+
+
+//////////////////////////////////////////////////////////////////////////////
+// identifier characters
+// note: characters shouldn't be delimited, except arrays
+// array of chars could be defined as from_char..to_char
+
+IdentifierBegChars: a..z A..Z _!~$
+IdentifierChars: a..z A..Z _! 0..9
+
+//////////////////////////////////////////////////////////////////////////////
+// numeric constants begin characters
+// note: characters shouldn't be delimited, except arrays
+// array of chars could be defined as from_char..to_char
+// number always starts with 0..9 except when NumConstBeg
+// defines other
+
+NumConstBegChars: 0..9
+
+
+//////////////////////////////////////////////////////////////////////////////
+// numeric constants characters
+// note: characters shouldn't be delimited, except arrays
+// array of chars could be defined as from_char..to_char
+// number always starts with 0..9 except when NumConstBeg
+// defines other
+
+NumConstChars: 0..9 -().E
+
+
+//////////////////////////////////////////////////////////////////////////////
+// escape character
+
+EscapeChar:
+
+
+//////////////////////////////////////////////////////////////////////////////
+// keyword table
+// note: delimited with spaces, lines could be wrapped
+// you may divide keywords into two groups which can be
+// highlighted differently
+
+// running switches
+
+KeyWords1: !ADJUST !AILOADINGS !AISINGULARITIES !ALPHA !AOD !ARCSIN
+ !ARGS !ASK !ASMV !ASUV !AVERAGE B !BINOMIAL !BLUP !BMP !BRIEF C !CINV
+ !COLFAC !COMPLOGLOG !CONTINUE !CONTRAST !CSV !CYCLE !DATAFILE !DDF
+ !DEBUG !DEC !DENSE !DEVIANCE !DF !DIAG !DISPLAY !DISP
+ !DOPART !DOPATH !EMFLAG !EPS !EXCEPT !EXTRA !FACPOINTS !FCON !FILTER
+ !FINAL !FLOAT !FORMAT !GAMMA !GIV !GKRIGE !GRAPHICS !GROUPS !G
+ !HARDCOPY !HPGL !IDENTITY !IGNORE!INBRED !INCLUDE !INTERACTIVE !JOIN
+ !KNOTS !LAST !LOGARITHM !LOGFILE !LOGIT !LOGIT !LOG !L !MAKE
+ !MATCH !MAXIT !MBF !MERGE !MGS !MVREMOVE !M !NEGBIN !NOCHECK
+ !NOGRAPHS !NOREORDER !NORMAL !NOSCRATCH !OFFSET !ONERUN !OWN !PARALLEL
+ !PEARSON !POISSON !POLPOINTS !PPOINTS !PRESENT !PRINT !PROBIT !PS !PVAL
+ !PVR !PVSFORM !PVW !PRWTS !P !QUIET !READ !RECODE !RENAME !REPEAT !REPORT
+ !RESIDUALS !RESPONSE !ROWFAC !RREC !RSKIP S !S2= !SAVE !SCALE !SCORE
+ !SCREEN !SECTION !SEED !SELECT !SELF !SETN !SETU !SKIP !SLNFORM
+ !SLOW !SMX !SORT !SPATIAL !SPLINE !SQRT !STEP !SUBSET !SUM
+ !TABFORM !TOLERANCE !TOTAL !TWOSTAGEWEIGHTS !TWOWAY !TXTFORM U
+ !UNIFORM !VCC !VGSECTORS !VRB !WMF !WORKSPACE !WORK !X !YHTFORM
+ !YSS !YVAR !Y ?
+ $A $B $C $D $E $F $G $H $I $J $1 $2 $3 $4 $5 $6 $7 $8 $9
+
+
+// model key words
+
+KeyWords2: !A !I !L !P !M !D !DATE !DMY !MDY !G !* !- !+ !/ !^ !^0
+ != !<> !> !< !== !<= !>=
+ !ABS !COS !DOM !SIN !EXP !Jddm !Jmmd !Jyyd !MAX !MIN !MOD !MM
+ !NA !REPLACE !RESCALE !SET !SUB !SEQ !V
+
+KeyWords3: a and at c con cos fac g giv h i ide inv l leg lin log
+ ma1 mbf mu mv out p pol pow qtl s sin spl sqrt uni units xfa
+ !bin !comp !logit !probit !total !r !f ~ Tr Trait
+ AEXP AGAU AINV ANTE AR AR2 AR3 ARMA CHOL CORB CORGB CORGH CORR
+ CORU DIAG EXP F FA FACV GAU GIV GIV1 GIV2 GIV3 GIV4 GIV5
+ GIV6 ID IDEN IDH IEUC IEXP IGAU ISP ISP2 LVR LVR2 MA MA2 MAT
+ OWN POW SAR SAR2 SPH SPH2 US XFA
+ !GF !GU !GP !GZ !S2
+
+//////////////////////////////////////////////////////////////////////////////
+// string delimiter: StringBegChar - string begin char
+// StringEndChar - string end char
+// MultilineStrings - enables multiline strings, as perl
+// has it
+
+StringBegChar: {
+StringEndChar: }
+MultilineStrings: 0
+
+
+//////////////////////////////////////////////////////////////////////////////
+// use preprocessor: 0 - no
+// 1 - yes
+// note: if yes, '#' and statements after it will be
+// highlighted with Preprocessor defined colors
+
+UsePreprocessor: 0
+
+
+//////////////////////////////////////////////////////////////////////////////
+// highlight line: 0 - no
+// 1 - yes
+// note: if yes, current line will be highlighted
+
+CurrLineHighlighted: 1
+
+
+//////////////////////////////////////////////////////////////////////////////
+// colors
+// note: first value is foreground, second is background color
+// and third (optional) represents font attribute:
+// B - bold
+// I - italic
+// U - underline
+// S - strike out
+// attributes can be combined: eg. B or BI
+// as value, it could be used any standard windows color:
+// clBlack, clMaroon, clGreen, clOlive, clNavy,
+// clPurple, clTeal, clGray, clSilver, clRed, clLime,
+// clYellow, clBlue, clFuchsia, clAqua, clLtGray,
+// clDkGray, clWhite, clScrollBar, clBackground,
+// clActiveCaption, clInactiveCaption, clMenu, clWindow,
+// clWindowFrame, clMenuText, clWindowText, clCaptionText,
+// clActiveBorder, clInactiveBorder, clAppWorkSpace,
+// clHighlight, clHighlightText, clBtnFace, clBtnShadow,
+// clGrayText, clBtnText, clInactiveCaptionText,
+// clBtnHighlight, cl3DDkShadow, cl3DLight, clInfoText,
+// clInfoBk
+// as value, it could be used hex numeric constant too:
+// $BBGGRR - BB: blue, GG: green, RR: red, eg: $FF6A00
+
+SpaceCol: clWindowText clWindow
+Keyword1Col: clMaroon clWindow B
+Keyword2Col: clGreen clWindow B
+Keyword3Col: clBlue clWindow
+IdentifierCol: clWindowText clWindow
+CommentCol: clGray clWindow
+NumberCol: clRed clWindow
+StringCol: clWindowText clWindow
+SymbolCol: clGray clWindow
+PreprocessorCol: clBlue clWindow
+SelectionCol: clWhite clNavy
+CurrentLineCol: clBlack $00C0FFFF
+
+OverrideTxtFgColor: 0
+BlockAutoindent: 0
+BlockBegStr:
+BlockEndStr:
+Keyword4Col: clWindowText clWindow
+Keyword5Col: clWindowText clWindow
+MatchedBracesCol: clWindowText clWindow