Package: gpyramid 0.0.1

Shoji Taniguchi

gpyramid: Identify Efficient Crossing Schemes for Gene Pyramiding

Calculates the cost of crossing in terms of the number of individuals and generations, which is theoretically formulated by Servin et al. (2004) <doi:10.1534/genetics.103.023358>. This package has been designed for selecting appropriate parental genotypes and find the most efficient crossing scheme for gene pyramiding, especially for plant breeding.

Authors:Shoji Taniguchi [aut, cre], The National Agriculture and Food Research Organization [cph]

gpyramid_0.0.1.tar.gz
gpyramid_0.0.1.tar.gz(r-4.7-any)gpyramid_0.0.1.tar.gz(r-4.6-any)
gpyramid_0.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
gpyramid/json (API)

# Install 'gpyramid' in R:
install.packages('gpyramid', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.00 score 151 downloads 7 exports 20 dependencies

Last updated from:2e20ecc001. Checks:4 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK99
source / vignettesOK153
linux-release-x86_64OK126
wasm-releaseOK106

Exports:allCrossescalcCostcalcCostAllfindPsetgetFromAllutil_haploutil_recom_mat

Dependencies:apeclidigestdplyrgenericsgluelatticelifecyclemagrittrnlmepillarpkgconfigR6Rcpprlangtibbletidyselectutf8vctrswithr

Introduction
0. Introduction to gpyramid package | 1. Set up | 2. Prepare data | 2.1 Gene data | 2.2 Position data | 2.3 Preprosessing | Generate haplotype dataframe from row data | Generate recombination probability matrix from raw data | 3. Find parent sets from candidate lines (cultivars) | 4. Calculate the number of necessary individuals and generations | 4.1 Fig 4a (Servin et al., 2004) | 4.2 Fig 4b (Servin et al., 2004) | 4.3 Fig 4c (Servin et al., 2004)
Rendered fromIntroduction.Rmdusingknitr::rmarkdown

Last update: 2025-12-12
Started: 2025-12-12

Tutorial of R package gpyramid
1. Set up | 2. Prepare data | 2.1 Gene data | 2.2 Position data | 2.3 Preprosessing | Generate haplotype dataframe from row data | Generate recombination probability matrix from raw data | 3. Find parent sets from candidate lines (cultivars) | 4. Calculate the number of necessary individuals and generations | 4.1 Calculate cost of all the crossing schemes | 4.2 Plot cost of each crossing scheme | 4.3 Select the most cost-effective crossing strategy | 4.4 Another example
Rendered fromTutorial.Rmdusingknitr::rmarkdown

Last update: 2025-12-12
Started: 2025-12-12