Package: pedtricks 0.5.0

pedtricks: Visualize, Summarize and Simulate Data from Pedigrees

Sensitivity and power analysis, for calculating statistics describing pedigrees from wild populations, and for visualizing pedigrees. This is a reboot of the methods developed by Morrissey and Wilson (2010) <doi:10.1111/j.1755-0998.2009.02817.x>.

Authors:Julien Martin [aut, cre], Matthew Wolak [aut], Susan Johnston [aut], Joel Pick [aut], Michael Morrissey [aut]

pedtricks_0.5.0.tar.gz
pedtricks_0.5.0.zip(r-4.7)pedtricks_0.5.0.zip(r-4.6)pedtricks_0.5.0.zip(r-4.5)
pedtricks_0.5.0.tgz(r-4.6-any)pedtricks_0.5.0.tgz(r-4.5-any)
pedtricks_0.5.0.tar.gz(r-4.7-any)pedtricks_0.5.0.tar.gz(r-4.6-any)
pedtricks_0.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
pedtricks/json (API)
NEWS

# Install 'pedtricks' in R:

install.packages('pedtricks', repos = c('https://juliengamartin.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/juliengamartin/pedtricks/issues

Pkgdown/docs site:https://juliengamartin.github.io

Datasets:

gryphons - Example dataset for pedtricks examples and tutorial
WarblerG - Seychelles Warbler Genotypes

On CRAN:

4.19 score 4 stars 13 scripts 157 downloads 20 exports 55 dependencies

Last updated from:7cd0cf4747. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	164
source / vignettes	OK	184
linux-release-x86_64	OK	166
macos-release-arm64	OK	148
macos-oldrel-arm64	OK	219
windows-devel	OK	130
windows-release	OK	120
windows-oldrel	OK	134
wasm-release	OK	120

Exports:convert_ped draw_ped draw_pedA drawPedigree extractA fix_ped fixPedigree genome_sim genomesim ggpedigree h2_samp_var makemakePedigreeFactor makePedigreeNumeric micro_sim microsim ped_stats pedigreeStat pedStatSummary phen_sim phensim

Dependencies:ape cli coda combinat corpcor cpp11 cubature digest dplyr evaluate farver gdata generics genetics ggplot2 glue gtable gtools highr igraph isoband kinship2 knitr labeling lattice lifecycle magrittr MASS Matrix MCMCglmm mvtnorm nadiv nlme pillar pkgconfig purrr quadprog R6 RColorBrewer Rcpp rlang S7 scales stringi stringr tensorA tibble tidyr tidyselect utf8 vctrs viridisLite withr xfun yaml

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Converts a pedigree with individuals specified as factors to a numeric pedigree	convert_ped
Produce a graphical representation of a pedigree	draw_ped
Produce a graphical representation of the relatedness matrix of a pedigree	draw_pedA
Manipulating pedigrees to prepare them for requirements of subsequent analyses Prepares a pedigree to conform with requirements of many softwares used in quantitative genetic analysis, as well as for many of the functions in pedtricks.	fix_ped
A function to simulate QTL and/or SNP data.	genome_sim
ggpedigree: Plotting tool for simple and complex pedigrees.	ggpedigree
Example dataset for pedtricks examples and tutorial	gryphons
Calculates expected sampling variance of a given $h^2$ from the A matrix of a pedigree, based on the method of Visscher and Goddard 2015 Genetics	h2_samp_var
Simulates microsatellite data across a pedigree.	micro_sim
Calculates a range of statistics of pedigrees	pedigreeStats ped_stats
A function to simulated phenotypic data	phen_sim
Plot output from ped_stats	plot.ped_stats
Post-processes output from ped_stats	summary.ped_stats
Seychelles Warbler Genotypes	WarblerG