https://github.com/zankrut20/selection.index

Analysis of Selection Index in Plant Breeding
https://github.com/zankrut20/selection.index

agriculture animal-science cran plant-breeding r rstudio selection-index selection-indices smith-selection-index

Last synced: about 2 months ago
JSON representation

Analysis of Selection Index in Plant Breeding

• Host: GitHub
• URL: https://github.com/zankrut20/selection.index
• Owner: zankrut20
• License: gpl-3.0
• Created: 2021-03-30T18:32:37.000Z (about 4 years ago)
• Default Branch: master
• Last Pushed: 2024-10-14T19:23:47.000Z (8 months ago)
• Last Synced: 2025-04-12T02:48:14.216Z (2 months ago)
• Topics: agriculture, animal-science, cran, plant-breeding, r, rstudio, selection-index, selection-indices, smith-selection-index
• Language: R
• Homepage: https://zankrut20.github.io/selection.index/
• Size: 1.37 MB
• Stars: 2
• Watchers: 0
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.Rmd
  • License: LICENSE.md

Awesome Lists containing this project

README

        
---

output: github_document

editor_options: 

  markdown: 

    wrap: 72

---

```{r, include = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "#>",

  fig.path = "man/figures/README-",

  out.width = "100%"

)

```

# selection.index

[![R-CMD-check](https://github.com/zankrut20/selection.index/workflows/R-CMD-check/badge.svg)](https://github.com/zankrut20/selection.index/actions)

[![CRAN checks](https://cranchecks.info/badges/summary/selection.index)](https://cran.r-project.org/web/checks/check_results_selection.index.html)

[![status](https://www.r-pkg.org/badges/version/selection.index)](https://CRAN.R-project.org/package=selection.index)

[![Dependencies](https://tinyverse.netlify.com/badge/selection.index)](https://cran.r-project.org/package=selection.index)

[![Total downloads](http://cranlogs.r-pkg.org/badges/grand-total/selection.index?color=blue)](https://cran.r-project.org/package=selection.index)

[![Last-Month downloads](http://cranlogs.r-pkg.org/badges/last-month/selection.index?color=green)](https://cran.r-project.org/package=selection.index)

[![Last-Week downloads](http://cranlogs.r-pkg.org/badges/last-week/selection.index?color=green)](https://cran.r-project.org/package=selection.index)

[![CodeFactor](https://www.codefactor.io/repository/github/zankrut20/selection.index/badge)](https://www.codefactor.io/repository/github/zankrut20/selection.index)

[![R-CMD-check](https://github.com/zankrut20/selection.index/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/zankrut20/selection.index/actions/workflows/R-CMD-check.yaml)

[![Codecov test coverage](https://codecov.io/gh/zankrut20/selection.index/branch/master/graph/badge.svg)](https://app.codecov.io/gh/zankrut20/selection.index?branch=master)

The goal of selection.index is to easily construct the selection index

and based on the these indices select the plant traits for the overall

improvement of the plant.

## Installation

You can install the released version of selection.index from

[CRAN](https://CRAN.R-project.org) with:

``` r

install.packages("selection.index")

```

from [github](https://github.com/zankrut20/selection.index) with:

``` r

devtools::install_github("zankrut20/selection.index")

```

## Example

This is a basic example which shows you how to solve a common problem:

Dataset `seldata` is included in package.

```{r example}

library(selection.index)

head(seldata)

```

### Genotypic Variance-Covariance Matrix

```{r}

genMat<- gen.varcov(data = seldata[,3:9], genotypes = seldata[,2],

                    replication = seldata[,1])

print(genMat)

```

### Phenotypic Variance-Covariance Matrix

```{r}

phenMat<- phen.varcov(data = seldata[,3:9], genotypes = seldata[,2],

                      replication = seldata[,1])

print(phenMat)

```

### Weight Matrix - Data is included in package `weight`

```{r}

weightMat <- weight.mat(weight)

weightMat

```

-   Genetic gain of Yield

```{r}

GAY<- gen.advance(phen_mat = phenMat[1,1], gen_mat = genMat[1,1],

                  weight_mat = weightMat[1,1])

print(GAY)

```

### Construction of selection index/indices

For the construction of selection index we requires **phenotypic &

genotypic variance-covariance matrix as well weight matrix.**


### Construction of all possible selection indices for a character combinations

```{r}

comb.indices(ncomb = 1, pmat = phenMat, gmat = genMat, wmat = weight[,2:3], wcol = 1, GAY = GAY)

```

### Construction of selection indices by removing desired single character from the combinations

```{r}

rcomb.indices(ncomb = 1, i = 1, pmat = phenMat, gmat = genMat, wmat = weight[,2:3], wcol = 1, GAY = GAY)

```