gen.var: Estimation of Genetic Parameters
In variability: Genetic Variability Analysis for Plant Breeding Research
Description
Usage
Arguments
Value
Examples
Description
Estimation of Genetic Parameters
Usage
1
Arguments
data
traits to be analyzed
genotypevector
vector containing genotypes
replicationvector
vector containig replications
Value
ANOVA, genotypic and phenotypic coefficient of variance, heritability, genetic advance and genetic advance as percentage of mean.
Examples
1
2
Example output
$DFF
$DFF[[1]]
Analysis of Variance Table
Response: data2
Df Sum Sq Mean Sq F value Pr(>F)
replication 2 186.5 93.249 4.907 0.009833 **
genotype 39 7414.4 190.113 10.004 < 2.2e-16 ***
Residuals 78 1482.2 19.003
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$DFF[[2]]
A
Maximum 145.0000
Minimum 95.0000
Grand Mean 127.4767
Standard Error of Mean (SEm) 2.5168
Critical Difference (CD) 5% 7.0861
Critical Difference (CD) 1% 9.3978
Environmental Variance 19.0032
Genotypic Variance 57.0364
Phenotypic Variance 76.0396
Environmental Coefficient of Variance 3.4197
Genotypic Coefficient of Variance 5.9244
Phenotypic Coefficient of Variance 6.8405
Heritability (Broad Sense) 0.7501
Genetic Advance 13.4741
Genetic Advance as percentage of mean 10.5699
$PH
$PH[[1]]
Analysis of Variance Table
Response: data2
Df Sum Sq Mean Sq F value Pr(>F)
replication 2 102.2 51.121 3.8416 0.02563 *
genotype 39 10034.5 257.296 19.3351 < 2e-16 ***
Residuals 78 1038.0 13.307
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$PH[[2]]
A
Maximum 123.6000
Minimum 65.4000
Grand Mean 94.7550
Standard Error of Mean (SEm) 2.1061
Critical Difference (CD) 5% 5.9297
Critical Difference (CD) 1% 7.8642
Environmental Variance 13.3072
Genotypic Variance 81.3296
Phenotypic Variance 94.6368
Environmental Coefficient of Variance 3.8498
Genotypic Coefficient of Variance 9.5175
Phenotypic Coefficient of Variance 10.2666
Heritability (Broad Sense) 0.8594
Genetic Advance 17.2221
Genetic Advance as percentage of mean 18.1754
$PL
$PL[[1]]
Analysis of Variance Table
Response: data2
Df Sum Sq Mean Sq F value Pr(>F)
replication 2 1.70 0.8511 4.2651 0.01746 *
genotype 39 442.44 11.3446 56.8524 < 2e-16 ***
Residuals 78 15.56 0.1995
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$PL[[2]]
A
Maximum 25.9000
Minimum 17.1000
Grand Mean 21.3142
Standard Error of Mean (SEm) 0.2579
Critical Difference (CD) 5% 0.7261
Critical Difference (CD) 1% 0.9630
Environmental Variance 0.1995
Genotypic Variance 3.7150
Phenotypic Variance 3.9145
Environmental Coefficient of Variance 2.0958
Genotypic Coefficient of Variance 9.0430
Phenotypic Coefficient of Variance 9.2826
Heritability (Broad Sense) 0.9490
Genetic Advance 3.8680
Genetic Advance as percentage of mean 18.1476
$PW
$PW[[1]]
Analysis of Variance Table
Response: data2
Df Sum Sq Mean Sq F value Pr(>F)
replication 2 179.2 89.61 6.7589 0.001963 **
genotype 39 17735.8 454.76 34.3014 < 2.2e-16 ***
Residuals 78 1034.1 13.26
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$PW[[2]]
A
Maximum 116.0000
Minimum 51.0000
Grand Mean 88.5833
Standard Error of Mean (SEm) 2.1022
Critical Difference (CD) 5% 5.9187
Critical Difference (CD) 1% 7.8497
Environmental Variance 13.2579
Genotypic Variance 147.1690
Phenotypic Variance 160.4269
Environmental Coefficient of Variance 4.1104
Genotypic Coefficient of Variance 13.6948
Phenotypic Coefficient of Variance 14.2984
Heritability (Broad Sense) 0.9174
Genetic Advance 23.9356
Genetic Advance as percentage of mean 27.0204
$HI
$HI[[1]]
Analysis of Variance Table
Response: data2
Df Sum Sq Mean Sq F value Pr(>F)
replication 2 177.2 88.602 5.3695 0.006535 **
genotype 39 6101.8 156.455 9.4815 < 2.2e-16 ***
Residuals 78 1287.1 16.501
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$HI[[2]]
A
Maximum 71.0500
Minimum 26.4900
Grand Mean 48.7279
Standard Error of Mean (SEm) 2.3453
Critical Difference (CD) 5% 6.6031
Critical Difference (CD) 1% 8.7573
Environmental Variance 16.5012
Genotypic Variance 46.6514
Phenotypic Variance 63.1526
Environmental Coefficient of Variance 8.3364
Genotypic Coefficient of Variance 14.0170
Phenotypic Coefficient of Variance 16.3086
Heritability (Broad Sense) 0.7387
Genetic Advance 12.0931
Genetic Advance as percentage of mean 24.8176
$TW
$TW[[1]]
Analysis of Variance Table
Response: data2
Df Sum Sq Mean Sq F value Pr(>F)
replication 2 5.82 2.908 0.7236 0.4882
genotype 39 1504.66 38.581 9.5986 <2e-16 ***
Residuals 78 313.52 4.019
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$TW[[2]]
A
Maximum 30.0000
Minimum 10.0000
Grand Mean 17.2417
Standard Error of Mean (SEm) 1.1575
Critical Difference (CD) 5% 3.2589
Critical Difference (CD) 1% 4.3221
Environmental Variance 4.0194
Genotypic Variance 11.5205
Phenotypic Variance 15.5399
Environmental Coefficient of Variance 11.6280
Genotypic Coefficient of Variance 19.6860
Phenotypic Coefficient of Variance 22.8636
Heritability (Broad Sense) 0.7413
Genetic Advance 6.0202
Genetic Advance as percentage of mean 34.9166
$MILL
$MILL[[1]]
Analysis of Variance Table
Response: data2
Df Sum Sq Mean Sq F value Pr(>F)
replication 2 1599.6 799.82 23.0429 1.369e-08 ***
genotype 39 5347.4 137.11 3.9503 1.233e-07 ***
Residuals 78 2707.4 34.71
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$MILL[[2]]
A
Maximum 100.4700
Minimum 39.9300
Grand Mean 66.8238
Standard Error of Mean (SEm) 3.4015
Critical Difference (CD) 5% 9.5768
Critical Difference (CD) 1% 12.7011
Environmental Variance 34.7099
Genotypic Variance 34.1345
Phenotypic Variance 68.8444
Environmental Coefficient of Variance 8.8165
Genotypic Coefficient of Variance 8.7431
Phenotypic Coefficient of Variance 12.4166
Heritability (Broad Sense) 0.4958
Genetic Advance 8.4747
Genetic Advance as percentage of mean 12.6822
$HRR
$HRR[[1]]
Analysis of Variance Table
Response: data2
Df Sum Sq Mean Sq F value Pr(>F)
replication 2 115.4 57.719 2.8886 0.06163 .
genotype 39 10221.9 262.101 13.1169 < 2e-16 ***
Residuals 78 1558.6 19.982
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$HRR[[2]]
A
Maximum 79.0300
Minimum 22.9500
Grand Mean 43.8299
Standard Error of Mean (SEm) 2.5808
Critical Difference (CD) 5% 7.2662
Critical Difference (CD) 1% 9.6368
Environmental Variance 19.9818
Genotypic Variance 80.7063
Phenotypic Variance 100.6881
Environmental Coefficient of Variance 10.1988
Genotypic Coefficient of Variance 20.4967
Phenotypic Coefficient of Variance 22.8938
Heritability (Broad Sense) 0.8015
Genetic Advance 16.5686
Genetic Advance as percentage of mean 37.8020
$GY
$GY[[1]]
Analysis of Variance Table
Response: data2
Df Sum Sq Mean Sq F value Pr(>F)
replication 2 326.9 163.47 6.5602 0.002326 **
genotype 39 23259.1 596.39 23.9338 < 2.2e-16 ***
Residuals 78 1943.6 24.92
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$GY[[2]]
A
Maximum 114.5000
Minimum 34.7000
Grand Mean 65.3112
Standard Error of Mean (SEm) 2.8820
Critical Difference (CD) 5% 8.1143
Critical Difference (CD) 1% 10.7615
Environmental Variance 24.9182
Genotypic Variance 190.4898
Phenotypic Variance 215.4080
Environmental Coefficient of Variance 7.6431
Genotypic Coefficient of Variance 21.1324
Phenotypic Coefficient of Variance 22.4721
Heritability (Broad Sense) 0.8843
Genetic Advance 26.7367
Genetic Advance as percentage of mean 40.9374
variability documentation built on Oct. 24, 2020, 9:10 a.m.
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Description Usage Arguments Value Examples
Description
Estimation of Genetic Parameters
Usage
1 |
Arguments
data |
traits to be analyzed |
genotypevector |
vector containing genotypes |
replicationvector |
vector containig replications |
Value
ANOVA, genotypic and phenotypic coefficient of variance, heritability, genetic advance and genetic advance as percentage of mean.
Examples
1 2 |
Example output
$DFF
$DFF[[1]]
Analysis of Variance Table
Response: data2
Df Sum Sq Mean Sq F value Pr(>F)
replication 2 186.5 93.249 4.907 0.009833 **
genotype 39 7414.4 190.113 10.004 < 2.2e-16 ***
Residuals 78 1482.2 19.003
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$DFF[[2]]
A
Maximum 145.0000
Minimum 95.0000
Grand Mean 127.4767
Standard Error of Mean (SEm) 2.5168
Critical Difference (CD) 5% 7.0861
Critical Difference (CD) 1% 9.3978
Environmental Variance 19.0032
Genotypic Variance 57.0364
Phenotypic Variance 76.0396
Environmental Coefficient of Variance 3.4197
Genotypic Coefficient of Variance 5.9244
Phenotypic Coefficient of Variance 6.8405
Heritability (Broad Sense) 0.7501
Genetic Advance 13.4741
Genetic Advance as percentage of mean 10.5699
$PH
$PH[[1]]
Analysis of Variance Table
Response: data2
Df Sum Sq Mean Sq F value Pr(>F)
replication 2 102.2 51.121 3.8416 0.02563 *
genotype 39 10034.5 257.296 19.3351 < 2e-16 ***
Residuals 78 1038.0 13.307
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$PH[[2]]
A
Maximum 123.6000
Minimum 65.4000
Grand Mean 94.7550
Standard Error of Mean (SEm) 2.1061
Critical Difference (CD) 5% 5.9297
Critical Difference (CD) 1% 7.8642
Environmental Variance 13.3072
Genotypic Variance 81.3296
Phenotypic Variance 94.6368
Environmental Coefficient of Variance 3.8498
Genotypic Coefficient of Variance 9.5175
Phenotypic Coefficient of Variance 10.2666
Heritability (Broad Sense) 0.8594
Genetic Advance 17.2221
Genetic Advance as percentage of mean 18.1754
$PL
$PL[[1]]
Analysis of Variance Table
Response: data2
Df Sum Sq Mean Sq F value Pr(>F)
replication 2 1.70 0.8511 4.2651 0.01746 *
genotype 39 442.44 11.3446 56.8524 < 2e-16 ***
Residuals 78 15.56 0.1995
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$PL[[2]]
A
Maximum 25.9000
Minimum 17.1000
Grand Mean 21.3142
Standard Error of Mean (SEm) 0.2579
Critical Difference (CD) 5% 0.7261
Critical Difference (CD) 1% 0.9630
Environmental Variance 0.1995
Genotypic Variance 3.7150
Phenotypic Variance 3.9145
Environmental Coefficient of Variance 2.0958
Genotypic Coefficient of Variance 9.0430
Phenotypic Coefficient of Variance 9.2826
Heritability (Broad Sense) 0.9490
Genetic Advance 3.8680
Genetic Advance as percentage of mean 18.1476
$PW
$PW[[1]]
Analysis of Variance Table
Response: data2
Df Sum Sq Mean Sq F value Pr(>F)
replication 2 179.2 89.61 6.7589 0.001963 **
genotype 39 17735.8 454.76 34.3014 < 2.2e-16 ***
Residuals 78 1034.1 13.26
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$PW[[2]]
A
Maximum 116.0000
Minimum 51.0000
Grand Mean 88.5833
Standard Error of Mean (SEm) 2.1022
Critical Difference (CD) 5% 5.9187
Critical Difference (CD) 1% 7.8497
Environmental Variance 13.2579
Genotypic Variance 147.1690
Phenotypic Variance 160.4269
Environmental Coefficient of Variance 4.1104
Genotypic Coefficient of Variance 13.6948
Phenotypic Coefficient of Variance 14.2984
Heritability (Broad Sense) 0.9174
Genetic Advance 23.9356
Genetic Advance as percentage of mean 27.0204
$HI
$HI[[1]]
Analysis of Variance Table
Response: data2
Df Sum Sq Mean Sq F value Pr(>F)
replication 2 177.2 88.602 5.3695 0.006535 **
genotype 39 6101.8 156.455 9.4815 < 2.2e-16 ***
Residuals 78 1287.1 16.501
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$HI[[2]]
A
Maximum 71.0500
Minimum 26.4900
Grand Mean 48.7279
Standard Error of Mean (SEm) 2.3453
Critical Difference (CD) 5% 6.6031
Critical Difference (CD) 1% 8.7573
Environmental Variance 16.5012
Genotypic Variance 46.6514
Phenotypic Variance 63.1526
Environmental Coefficient of Variance 8.3364
Genotypic Coefficient of Variance 14.0170
Phenotypic Coefficient of Variance 16.3086
Heritability (Broad Sense) 0.7387
Genetic Advance 12.0931
Genetic Advance as percentage of mean 24.8176
$TW
$TW[[1]]
Analysis of Variance Table
Response: data2
Df Sum Sq Mean Sq F value Pr(>F)
replication 2 5.82 2.908 0.7236 0.4882
genotype 39 1504.66 38.581 9.5986 <2e-16 ***
Residuals 78 313.52 4.019
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$TW[[2]]
A
Maximum 30.0000
Minimum 10.0000
Grand Mean 17.2417
Standard Error of Mean (SEm) 1.1575
Critical Difference (CD) 5% 3.2589
Critical Difference (CD) 1% 4.3221
Environmental Variance 4.0194
Genotypic Variance 11.5205
Phenotypic Variance 15.5399
Environmental Coefficient of Variance 11.6280
Genotypic Coefficient of Variance 19.6860
Phenotypic Coefficient of Variance 22.8636
Heritability (Broad Sense) 0.7413
Genetic Advance 6.0202
Genetic Advance as percentage of mean 34.9166
$MILL
$MILL[[1]]
Analysis of Variance Table
Response: data2
Df Sum Sq Mean Sq F value Pr(>F)
replication 2 1599.6 799.82 23.0429 1.369e-08 ***
genotype 39 5347.4 137.11 3.9503 1.233e-07 ***
Residuals 78 2707.4 34.71
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$MILL[[2]]
A
Maximum 100.4700
Minimum 39.9300
Grand Mean 66.8238
Standard Error of Mean (SEm) 3.4015
Critical Difference (CD) 5% 9.5768
Critical Difference (CD) 1% 12.7011
Environmental Variance 34.7099
Genotypic Variance 34.1345
Phenotypic Variance 68.8444
Environmental Coefficient of Variance 8.8165
Genotypic Coefficient of Variance 8.7431
Phenotypic Coefficient of Variance 12.4166
Heritability (Broad Sense) 0.4958
Genetic Advance 8.4747
Genetic Advance as percentage of mean 12.6822
$HRR
$HRR[[1]]
Analysis of Variance Table
Response: data2
Df Sum Sq Mean Sq F value Pr(>F)
replication 2 115.4 57.719 2.8886 0.06163 .
genotype 39 10221.9 262.101 13.1169 < 2e-16 ***
Residuals 78 1558.6 19.982
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$HRR[[2]]
A
Maximum 79.0300
Minimum 22.9500
Grand Mean 43.8299
Standard Error of Mean (SEm) 2.5808
Critical Difference (CD) 5% 7.2662
Critical Difference (CD) 1% 9.6368
Environmental Variance 19.9818
Genotypic Variance 80.7063
Phenotypic Variance 100.6881
Environmental Coefficient of Variance 10.1988
Genotypic Coefficient of Variance 20.4967
Phenotypic Coefficient of Variance 22.8938
Heritability (Broad Sense) 0.8015
Genetic Advance 16.5686
Genetic Advance as percentage of mean 37.8020
$GY
$GY[[1]]
Analysis of Variance Table
Response: data2
Df Sum Sq Mean Sq F value Pr(>F)
replication 2 326.9 163.47 6.5602 0.002326 **
genotype 39 23259.1 596.39 23.9338 < 2.2e-16 ***
Residuals 78 1943.6 24.92
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
$GY[[2]]
A
Maximum 114.5000
Minimum 34.7000
Grand Mean 65.3112
Standard Error of Mean (SEm) 2.8820
Critical Difference (CD) 5% 8.1143
Critical Difference (CD) 1% 10.7615
Environmental Variance 24.9182
Genotypic Variance 190.4898
Phenotypic Variance 215.4080
Environmental Coefficient of Variance 7.6431
Genotypic Coefficient of Variance 21.1324
Phenotypic Coefficient of Variance 22.4721
Heritability (Broad Sense) 0.8843
Genetic Advance 26.7367
Genetic Advance as percentage of mean 40.9374
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