lineXtester: Line x Tester Analysis

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/lineXtester.R

Description

It makes the Line x Tester Genetic Analysis. It also estimates the general and specific combinatory ability effects and the line and tester genetic contribution.

Usage

1

Arguments

replications

Replications

lines

Lines

testers

Testers

y

Variable, response

Details

ANOVA with parents and crosses
ANOVA for line X tester analysis
ANOVA for line X tester analysis including parents
GCA Effects: Lines Effects, Testers Effects and SCA Effects.
Standard Errors for Combining Ability Effects.
Genetic Components.
...
Proportional contribution of lines, testers and their interactions to total variance

Value

return anova(formula = Y ~ Replications + Treatments).
where the Treatments contains parents, crosses and crosses vs Parents.
The crosses contains Lines, Testers and its interaction .

Author(s)

Felipe de Mendiburu

References

Biometrical Methods in Quantitative Genetic Analysis, Singh, Chaudhary. 1979. Hierarchial and factorial mating designs for quantitative genetic analysis in tetrasomic potato. R. Ortis; A.Golmirzaie. Theor Appl Genet (2002) 104:675-679

See Also

AMMI

Examples

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# see structure line by testers
library(agricolae)
# example 1
data(heterosis)
site1<-subset(heterosis,heterosis[,1]==1)
output1<-with(site1,lineXtester(Replication, Female, Male, v2))
# example 2
data(LxT)
str(LxT)
output2<-with(LxT,lineXtester(replication, line, tester, yield))

Example output

ANALYSIS LINE x TESTER:  v2 

ANOVA with parents and crosses 
==============================
                     Df       Sum Sq     Mean Sq F value Pr(>F)
Replications          2  0.002674074 0.001337037   0.088 0.9159
Treatments           35 29.135740741 0.832449735  54.763 0.0000
Parents              11 21.221688889 1.929244444 126.917 0.0000
Parents vs. Crosses   1  1.692474074 1.692474074 111.341 0.0000
Crosses              23  6.221577778 0.270503382  17.795 0.0000
Error                70  1.064059259 0.015200847               
Total               107 30.202474074                           

ANOVA for line X tester analysis 
================================
                Df    Sum Sq    Mean Sq F value Pr(>F)
Lines            7 4.3497111 0.62138730   9.078 0.0003
Testers          2 0.9135444 0.45677222   6.673 0.0092
Lines X Testers 14 0.9583222 0.06845159   4.503 0.0000
Error           70 1.0640593 0.01520085               

ANOVA for line X tester analysis including parents 
==================================================
                     Df       Sum Sq     Mean Sq F value Pr(>F)
Replications          2  0.002674074 0.001337037   0.088 0.9159
Treatments           35 29.135740741 0.832449735  54.763 0.0000
Parents              11 21.221688889 1.929244444 126.917 0.0000
Parents vs. Crosses   1  1.692474074 1.692474074 111.341 0.0000
Crosses              23  6.221577778 0.270503382  17.795 0.0000
Lines                 7  4.349711111 0.621387302   9.078 0.0003
Testers               2  0.913544444 0.456772222   6.673 0.0092
Lines X Testers      14  0.958322222 0.068451587   4.503 0.0000
Error                70  1.064059259 0.015200847               
Total               107 30.202474074                           

GCA Effects: 
===========
Lines Effects:
Achirana     LT-8     MF-I    MF-II  Serrana    TPS-2   TPS-25    TPS-7 
   0.143   -0.346   -0.134   -0.169    0.394   -0.016    0.321   -0.194 

Testers Effects:
TPS-13 TPS-67  TS-15 
 0.104  0.052 -0.156 

SCA Effects: 
===========
          Testers
Lines      TPS-13 TPS-67  TS-15
  Achirana -0.010  0.002  0.008
  LT-8      0.186 -0.042 -0.144
  MF-I     -0.059  0.070 -0.011
  MF-II    -0.021  0.055 -0.034
  Serrana  -0.241  0.008  0.233
  TPS-2    -0.044  0.101 -0.057
  TPS-25    0.136 -0.259  0.123
  TPS-7     0.054  0.064 -0.118

Standard Errors for Combining Ability Effects: 
=============================================
S.E. (gca for line)   : 0.04109724
S.E. (gca for tester) : 0.02516682
S.E. (sca effect)     : 0.0711825
S.E. (gi - gj)line    : 0.05812027
S.E. (gi - gj)tester  : 0.03559125
S.E. (sij - skl)tester: 0.1006673 

Genetic Components: 
==================
Cov H.S. (line)   : 0.0614373
Cov H.S. (tester) : 0.01618003
Cov H.S. (average): 0.004651843
Cov F.S. (average): 0.1223343
F = 0, Adittive genetic variance: 0.01860737
F = 1, Adittive genetic variance: 0.009303686
F = 0, Variance due to Dominance: 0.03550049
F = 1, Variance due to Dominance: 0.01775025 

Proportional contribution of lines, testers 
 and their interactions to total variance 
===========================================
Contributions of lines  : 69.91331
Contributions of testers: 14.68349
Contributions of lxt    : 15.4032 
'data.frame':	92 obs. of  4 variables:
 $ replication: int  1 2 3 4 1 2 3 4 1 2 ...
 $ line       : int  1 1 1 1 1 1 1 1 1 1 ...
 $ tester     : int  6 6 6 6 7 7 7 7 8 8 ...
 $ yield      : num  74.4 70.9 60.9 68 91.8 ...

ANALYSIS LINE x TESTER:  yield 

ANOVA with parents and crosses 
==============================
                    Df      Sum Sq    Mean Sq F value Pr(>F)
Replications         3    83.00012   27.66671   0.304 0.8224
Treatments          22 32553.20239 1479.69102  16.249 0.0000
Parents              7  6299.88519  899.98360   9.883 0.0000
Parents vs. Crosses  1    53.66287   53.66287   0.589 0.4455
Crosses             14 26199.65433 1871.40388  20.551 0.0000
Error               66  6010.03298   91.06111               
Total               91 38646.23549                          

ANOVA for line X tester analysis 
================================
                Df    Sum Sq    Mean Sq F value Pr(>F)
Lines            4 10318.361 2579.59035   1.457 0.3009
Testers          2  1718.926  859.46289   0.485 0.6327
Lines X Testers  8 14162.367 1770.29590  19.441 0.0000
Error           66  6010.033   91.06111               

ANOVA for line X tester analysis including parents 
==================================================
                    Df      Sum Sq    Mean Sq F value Pr(>F)
Replications         3    83.00012   27.66671   0.304 0.8224
Treatments          22 32553.20239 1479.69102  16.249 0.0000
Parents              7  6299.88519  899.98360   9.883 0.0000
Parents vs. Crosses  1    53.66287   53.66287   0.589 0.4455
Crosses             14 26199.65433 1871.40388  20.551 0.0000
Lines                4 10318.36140 2579.59035   1.457 0.3009
Testers              2  1718.92577  859.46289   0.485 0.6327
Lines X Testers      8 14162.36716 1770.29590  19.441 0.0000
Error               66  6010.03298   91.06111               
Total               91 38646.23549                          

GCA Effects: 
===========
Lines Effects:
      1       2       3       4       5 
 -9.960  -0.718  23.817 -13.870   0.732 

Testers Effects:
     6      7      8 
 0.292  6.404 -6.697 

SCA Effects: 
===========
     Testers
Lines       6       7       8
    1  -8.019  24.959 -16.940
    2 -12.546   5.717   6.828
    3  -9.461  -4.918  14.378
    4  33.136 -14.321 -18.815
    5  -3.111 -11.438  14.548

Standard Errors for Combining Ability Effects: 
=============================================
S.E. (gca for line)   : 2.75471
S.E. (gca for tester) : 2.133789
S.E. (sca effect)     : 4.771297
S.E. (gi - gj)line    : 3.895748
S.E. (gi - gj)tester  : 3.017633
S.E. (sij - skl)tester: 6.747633 

Genetic Components: 
==================
Cov H.S. (line)   : 67.4412
Cov H.S. (tester) : -45.54165
Cov H.S. (average): 2.680894
Cov F.S. (average): 411.3472
F = 0, Adittive genetic variance: 10.72357
F = 1, Adittive genetic variance: 5.361787
F = 0, Variance due to Dominance: 839.6174
F = 1, Variance due to Dominance: 419.8087 

Proportional contribution of lines, testers 
 and their interactions to total variance 
===========================================
Contributions of lines  : 39.38358
Contributions of testers: 6.560872
Contributions of lxt    : 54.05555 

agricolae documentation built on Sept. 13, 2017, 1:03 a.m.