Data

Tools

Indexes

Applications

Experiments

Open Source Science

selection.index

Analysis of Selection Index in Plant Breeding

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

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.9%) to scientific vocabulary

Keywords

agriculture animal-science cran plant-breeding r rstudio selection-index selection-indices smith-selection-index
Last synced: 6 months ago · JSON representation

Repository

Analysis of Selection Index in Plant Breeding

Basic Info
Statistics
  • Stars: 3
  • Watchers: 0
  • Forks: 4
  • Open Issues: 0
  • Releases: 7
Topics
agriculture animal-science cran plant-breeding r rstudio selection-index selection-indices smith-selection-index
Created almost 5 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog License

README.Rmd 

---
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)
```

Owner

  • Name: Zankrut Goyani
  • Login: zankrut20
  • Kind: user
  • Location: Surat

GitHub Events

Total
  • Watch event: 1
  • Fork event: 1
Last Year
  • Watch event: 1
  • Fork event: 1

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 95
  • Total Committers: 2
  • Avg Commits per committer: 47.5
  • Development Distribution Score (DDS): 0.011
Past Year
  • Commits: 1
  • Committers: 1
  • Avg Commits per committer: 1.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Zankrut Goyani 6****0 94
Zankrut Goyani 1****i 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 8
  • Total pull requests: 3
  • Average time to close issues: 14 days
  • Average time to close pull requests: 7 minutes
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.33
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • zankrut20 (8)
Pull Request Authors
  • zankrut20 (3)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 355 last-month
  • Total docker downloads: 21,613
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 7
  • Total maintainers: 1
cran.r-project.org: selection.index

Analysis of Selection Index in Plant Breeding

  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 355 Last month
  • Docker Downloads: 21,613
Rankings
Forks count: 21.9%
Dependent packages count: 29.8%
Stargazers count: 35.2%
Dependent repos count: 35.5%
Average: 36.1%
Downloads: 58.2%
Maintainers (1)
zankrut20@gmail.com
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 2.10 depends
  • utils * imports
  • knitr * suggests
  • markdown * suggests
  • rmarkdown * suggests
  • testthat >= 3.0.0 suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/r.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact main composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.4.1 composite
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/pr-commands.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/pr-fetch v2 composite
  • r-lib/actions/pr-push v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/test-coverage.yaml actions
  • actions/checkout v3 composite
  • actions/upload-artifact v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite