`EvaluateCore`

`vignettes/EvaluationofCoreCollections.Rmd`

`EvaluationofCoreCollections.Rmd`

- Division of Germplasm Conservation, ICAR-National Bureau of Plant
Genetic Resources, New Delhi.
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant
Genetic Resources, New Delhi.
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic
Resources, New Delhi.
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington, Tamil Nadu.

- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic
Resources, New Delhi.

- Division of Germplasm Evaluation, ICAR-National Bureau of Plant
Genetic Resources, New Delhi.

A core collection is a *“limited set of accessions representing,
with minimum repetitiveness, the genetic diversity of a crop species and
its wild relatives”*(Frankel,
1984).

In case of several large and unwieldy germplasm collections conserved in genebanks, development of several such core collections has facilitated increasing the efficiency of their characterisation and in turn the utilisation.

There are different criteria available for evaluating the core
collections by comparing with the original collections from which they
have been sampled. The choice of the suitable evaluation criteria should
be dictated by the objectives of the core collection. Several such
criteria including the distance based metrics described in Odong et al. (2013) have been implemented in
`EvaluateCore`

and this document shows how to use them. This
document assumes a basic knowledge of `R`

programming
language.

The package can be installed using the following functions:

```
# Install from CRAN
install.packages('EvaluateCore', dependencies=TRUE)
# Install development version from Github
devtools::install_github("aravind-j/EvaluateCore")
```

Then the package can be loaded using the function

```
Registered S3 methods overwritten by 'vegan':
method from
plot.rda klaR
predict.rda klaR
print.rda klaR
```

```
--------------------------------------------------------------------------------
Welcome to EvaluateCore version 0.1.3.9000
# To know whats new in this version type:
news(package='EvaluateCore')
for the NEWS file.
# To cite the methods in the package type:
citation(package='EvaluateCore')
# To suppress this message use:
suppressPackageStartupMessages(library(EvaluateCore))
--------------------------------------------------------------------------------
```

The current version of the package is 0.1.3. The previous versions are as follows.

**Table 1.** Version history of
`EvaluateCore`

`R`

package.

Version | Date |
---|---|

0.1.1 | 2020-06-03 |

0.1.2 | 2021-06-12 |

To know detailed history of changes use
`news(package='EvaluateCore')`

.

**Table 2 :** Core evaluation methods implemented in
`EvaluateCore`

.

Metric | Criteria/Method | Function | Type of Variable | Type of Core | Type of comparison | Reference |
---|---|---|---|---|---|---|

Genetic distance | Average entry-to-nearest-entry distance (\(E-EN\)) | `dist.evaluate.core` |
Quantitative & Qualitative | CC–I | Multivariate | Odong et al. (2013) |

Genetic distance | Average accession-to-nearest-entry distance (\(A-EN\)) | `dist.evaluate.core` |
Quantitative & Qualitative | CC–X | Multivariate | Odong et al. (2013) |

Genetic distance | Average entry-to-entry distance (\(E-E\)) | `dist.evaluate.core` |
Quantitative & Qualitative | CC–X | Multivariate | Odong et al. (2013) |

Mean | Student-Newman-Keuls test | `snk.evaluate.core` |
Quantitative | CC–D | Univariate | Newman (1939); Keuls (1952) |

Median | Wilcoxon rank sum test or Mann-Whitney-Wilcoxon test or Mann-Whitney U test | `wilcox.evaluate.core` |
Quantitative | CC–D | Univariate | |

Mean | Student’s t test | `ttest.evaluate.core` |
Quantitative | CC–D | Univariate | |

Mean and Variance | Sign test | `signtest.evaluate.core` |
Quantitative | CC–D | Multivariate | |

Variance | Levene’s test | `levene.evaluate.core` |
Quantitative | CC–D | Univariate | |

Variability | Interquartile range | `iqr.evaluate.core` |
Quantitative | CC–D | Univariate | |

Range | Coincidence rate of range | `cr.evaluate.core` |
Quantitative | CC–D | Multivariate | |

Variance | Variable rate of coefficient of variation | `vr.evaluate.core` |
Quantitative | CC–D | Multivariate | |

Probability distribution | Quantile-quantile plots | `qq.evaluate.core` |
Quantitative | CC–D | Univariate | |

Probability distribution | Kullback-Leibler distance | `pdfdist.evaluate.core` |
Quantitative | CC–D | Univariate | |

Probability distribution | Kolmogorov-Smirnov distance | `pdfdist.evaluate.core` |
Quantitative | CC–D | Univariate | |

Probability distribution | Anderson-Darling distance | `pdfdist.evaluate.core` |
Quantitative | CC–D | Univariate | |

Probability distribution | Box-and-whisker plot | `box.evaluate.core` |
Quantitative | CC–D | Univariate | |

Mean | Percentage of significant differences of mean | `percentdiff.evaluate.core` |
Quantitative | CC–D | Multivariate | |

Variance | Percentage of significant differences of variance | `percentdiff.evaluate.core` |
Quantitative | CC–D | Multivariate | |

Mean | Average of absolute differences between means | `percentdiff.evaluate.core` |
Quantitative | CC–D | Multivariate | |

Variance | Average of absolute differences between variances | `percentdiff.evaluate.core` |
Quantitative | CC–D | Multivariate | |

Euclidean distance | Percentage difference between the mean squared Euclidean distance | `percentdiff.evaluate.core` |
Quantitative | CC–D | Multivariate | |

Probability distribution | Principal component analysis | `pca.evaluate.core` |
Quantitative | CC–D | Multivariate | |

Frequency distribution | Bar plot | `bar.evaluate.core` |
Qualitative | CC–D | Univariate | |

Frequency distribution | Chi-squared test for homogeneity | `chisquare.evaluate.core` |
Qualitative | CC–D | Univariate | |

Frequency distribution | Class coverage | `coverage.evaluate.core` |
Qualitative | CC–I | Univariate | |

Diversity | Shannon-Weaver diversity index | `shannon.evaluate.core` |
Qualitative | CC–I | Univariate | |

Diversity | Maximum Shannon-Weaver diversity index | `shannon.evaluate.core` |
Qualitative | CC–I | Univariate | |

Diversity | Shannon Equitability index | `shannon.evaluate.core` |
Qualitative | CC–I | Univariate | |

Phenotypic correlation | Pearson correlation coefficients | `corr.evaluate.core` |
Quantitative & Qualitative | CC-D | Multivariate | |

Correlation matrix | Mantel correlation coefficient | `corr.evaluate.core` |
Quantitative & Qualitative | CC-D | Multivariate | |

Frequency distribution | Stacked frequency distribution histogram | `freqdist.evaluate.core` |
Quantitative & Qualitative | CC-D | Univariate |

Frankel, O. H. (1984). “Genetic perspective of germplasm
conservation,” in *Genetic Manipulations:
Impact on Man and Society*,
eds. W. Arber, K. Limensee, W. J. Peacock, and P. Stralinger (Cambridge
University Press: Cambridge, UK), 161–170.

Keuls, M. (1952). The use of the „studentized range” in connection with
an analysis of variance. *Euphytica* 1, 112–122. doi:10.1007/BF01908269.

Newman, D. (1939). The distribution of range in samples from a normal
population, expressed in terms of an independent estimate of standard
deviation. *Biometrika* 31, 20–30. doi:10.1093/biomet/31.1-2.20.

Odong, T. L., Jansen, J., Eeuwijk, F. A. van, and Hintum, T. J. L. van
(2013). Quality of core collections for effective utilisation of genetic
resources review, discussion and interpretation. *Theoretical and
Applied Genetics* 126, 289–305. doi:10.1007/s00122-012-1971-y.