statgenSTA v1.0.2

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by Bart-Jan van Rossum View Source

Single Trial Analysis (STA) of Field Trials

Phenotypic analysis of field trials using mixed models with and without spatial components. One of a series of statistical genetic packages for streamlining the analysis of typical plant breeding experiments developed by Biometris. Some functions have been created to be used in conjunction with the R package 'asreml' for the 'ASReml' software, which can be obtained upon purchase from 'VSN' international (<http://www.vsni.co.uk/software/asreml-r>).

Readme

statgenSTA

R package for single trial analysis

Implemented functionality

The following functionality has been implemented:

Single trial analysis
- Single trial analysis using SpATS, asreml or lme4
- Computation of statistics e.g. BLUEs, BLUPs, SE of BLUEs, SE of BLUPs and heritability based on the fitted models.
Plotting and reporting (.pdf and .tex) functions for most raw and fitted data.

Functions in statgenSTA

Name	Description
TDMaize	Field data for a maize experiment in Tlaltizapan, Mexico
as.data.frame.extract	Coerce extracted heritabilities to data.frame
STAtoCross	Convert STA to Cross
summary.TD	Summarizing objects of class TD
plot.STA	Plot function for class STA
plot.TD	Plot function for class TD
STAtoTD	Convert STA to TD
extract	Extract statistics from Fitted Models
fitTD	Fit Single Trial Mixed Model
TDHeat05	Field data for a wheat experiment in Mexico
TD	S3 class TD
wheatChl	Field data for a wheat experiment in Chili
report	Base method for creating a report
report.STA	Report method for class STA
outlierSTA	Identifying outliers in objects of class STA
getMeta	Get and set metadata for TD objects
summary.STA	Summarizing objects of class STA
statgenSTA-package	statgenSTA: Single Trial Analysis (STA) of Field Trials
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Vignettes of statgenSTA

Name
bibliography.bib
statgenSTA.Rmd
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Details

Type	Package
Date	2020-01-09
License	GPL
Encoding	UTF-8
LazyData	true
RoxygenNote	7.0.2
SystemRequirements	pdflatex
VignetteBuilder	knitr
NeedsCompilation	no
Packaged	2020-01-09 09:05:07 UTC; rossu027
Repository	CRAN
Date/Publication	2020-01-14 11:30:02 UTC

suggests	asreml (>= 3.0) , rmarkdown , testthat , tibble
imports	emmeans , ggplot2 (>= 3.0) , ggrepel , gridExtra , knitr , lme4 , mapproj , maps , methods , qtl , reshape2 , scales , SpATS (>= 1.0-10) , xtable
depends	R (>= 3.3)
Contributors	Ron Wehrens, Willem Kruijer, Martin Boer, Fred van Eeuwijk, Marcos Malosetti, Daniela Bustos-Korts, Emilie Millet, Joao Paulo, Maikel Verouden, Choazhi Zheng