qgtools: Tools for Quantitative Genetics Data Analyses

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Two linear mixed model approaches: REML(restricted maximum likelihood) and MINQUE (minimum norm quadratic unbiased estimation) approaches and several resampling techniques are integrated for various quantitative genetics analyses. With these two types of approaches, various unbalanced data structures, missing data, and any irregular genetic mating designs can be analyzed and statistically tested. This package also offers fast computations for many large data sets. Other functions will be added to this R tool in the future.

Author
Jixiang Wu (South Dakota State University), Johnie N. Jenkins and Jack C. McCarty (USDA-ARS)
Date of publication
2014-09-17 18:12:26
Maintainer
Jixiang Wu <qgtools@gmail.com>
License
GPL-2
Version
1.0

View on CRAN

Man pages

ad4.mq
Additive-dominance (AD) model with MINQUE analysis for...
ad4.mq.jack
Additive-dominance (AD) model, multi-parent mating designs,...
ad4.reml
Additive-dominance (AD) model with REML analysis for...
ad4.reml.jack
Additive-dominance (AD) model, multi-parent mating designs,...
adaa.mq
ADAA model with MINQUE analysis
adaa.mq.jack
ADAA model with MINQUE and jacknife analyses
adaa.reml
Additive-dominance (AD) with additive-additive interaction...
adaa.reml.jack
ADAA model with REML and jacknife analyses
adaa.simu
An R function for AD model simulation.
adaa.simudata
An R function to generate an ADAA model simulated data set
adaa.simu.jack
An R function for AD model simulation
adc4.mq
ADC model with MINQUE analysis for multi-parent mating...
adc4.mq.jack
ADC model, multi-parent mating designs, MINQUE, and jackknife
adc4.reml
ADC model with REML analysis for multi-parent mating designs
adc4.reml.jack
ADC model, multi-parent mating designs, REML, and jackknife
adc.mq
An ADC with MINQUE analysis
adc.mq.jack
An ADC model with MINQUE analyses and jackknife tests
adc.reml
ADC model with REML analysis
adc.reml.jack
ADC model with REML analysis and jackknife resampling test
adc.simu
An R function for ADC model simulation.
adc.simudata
An R function to generate an ADC model simulated data set
adc.simu.jack
An R function for ADC model simulation
adm.mq
An ADM model with MINQUE analysis
adm.mq.jack
ADM model awith MINQUE analysis and jackknife test
ad.mq
Additive-dominance (AD) model with MINQUE analysis
ad.mq.jack
Additive-dominance (AD) model with MINQUE analysis and...
adm.reml
ADM model with REML analysis
adm.reml.jack
ADM model awith REML analysis and jackknife test
adm.simu
An R function for ADM model simulation.
adm.simudata
An R function to generate an ADM model simulated data set
adm.simu.jack
An R function for ADM model simulation
adrcdat
F2 spring wheat data with row and column
adrc.mq
AD model with row and column effects
adrc.mq.jack
AD model with row and column effects analyzed by MINQUE and...
adrc.reml
AD model with row and column effects analyzed by REML...
adrc.reml.jack
AD model with row and column effects analyzed by MINQUE and...
ad.reml
Additive-dominance (AD) model with REML analysis
ad.reml.jack
AD model with REML analysis and jackknife resampling test
ad.simu
An R function for AD model simulation.
ad.simudata
An R function to generate an AD model simulated data set
ad.simu.jack
An R function for AD model simulation
cotf12
Cotton F1 and F2 data
cotf2
A cotton F2 data set from a 2*6 factorial genetic mating...
maize
Maize variety trial
qgtools-package
Tools for Quantitative Genetics Analyses
stab.fw
Resgression based stability analysis
stab.mean
Group mean and rank calculator
stab.var
Within-group variance calculation with resampling techniques
wheat
Multi-parental mating design data

Files in this package

qgtools
qgtools/NAMESPACE
qgtools/data
qgtools/data/adrcdat.rda
qgtools/data/cotf12.rda
qgtools/data/cotf2.rda
qgtools/data/wheat.rda
qgtools/data/maize.rda
qgtools/R
qgtools/R/stab.fw.R
qgtools/R/stab.mean.R
qgtools/R/lmm.mq.perm.R
qgtools/R/Umatrix.R
qgtools/R/lmm.reml.jack.R
qgtools/R/qgmod.R
qgtools/R/minquefunction4.r
qgtools/R/lmm.mq.jack.R
qgtools/R/qgtoolsfunctions.r
qgtools/R/qgmod.perm.R
qgtools/R/lmm.mq.R
qgtools/R/stab.var.R
qgtools/R/generateu.R
qgtools/R/remlfunctions.R
qgtools/R/qgmod.jack.R
qgtools/R/lmm.mq.simu.R
qgtools/R/stabilityfunctions.r
qgtools/R/lmm.reml.R
qgtools/MD5
qgtools/DESCRIPTION
qgtools/man
qgtools/man/adc4.mq.jack.Rd
qgtools/man/ad4.reml.Rd
qgtools/man/adc.simudata.Rd
qgtools/man/adaa.mq.jack.Rd
qgtools/man/adc.reml.jack.Rd
qgtools/man/adm.reml.Rd
qgtools/man/ad4.mq.Rd
qgtools/man/stab.mean.Rd
qgtools/man/adrc.reml.jack.Rd
qgtools/man/wheat.Rd
qgtools/man/adc.mq.jack.Rd
qgtools/man/adaa.reml.Rd
qgtools/man/adaa.mq.Rd
qgtools/man/adc.simu.jack.Rd
qgtools/man/stab.fw.Rd
qgtools/man/adaa.simu.Rd
qgtools/man/adaa.reml.jack.Rd
qgtools/man/adrc.mq.Rd
qgtools/man/qgtools-package.Rd
qgtools/man/adm.mq.Rd
qgtools/man/adrc.mq.jack.Rd
qgtools/man/ad.mq.Rd
qgtools/man/adaa.simudata.Rd
qgtools/man/adm.reml.jack.Rd
qgtools/man/ad4.reml.jack.Rd
qgtools/man/ad.simudata.Rd
qgtools/man/adc4.mq.Rd
qgtools/man/adm.simu.Rd
qgtools/man/maize.Rd
qgtools/man/cotf12.Rd
qgtools/man/adc.simu.Rd
qgtools/man/ad4.mq.jack.Rd
qgtools/man/adc.mq.Rd
qgtools/man/adc4.reml.jack.Rd
qgtools/man/ad.simu.jack.Rd
qgtools/man/ad.reml.jack.Rd
qgtools/man/adc4.reml.Rd
qgtools/man/adrc.reml.Rd
qgtools/man/ad.mq.jack.Rd
qgtools/man/adm.simu.jack.Rd
qgtools/man/cotf2.Rd
qgtools/man/ad.simu.Rd
qgtools/man/ad.reml.Rd
qgtools/man/adm.mq.jack.Rd
qgtools/man/adrcdat.Rd
qgtools/man/stab.var.Rd
qgtools/man/adaa.simu.jack.Rd
qgtools/man/adm.simudata.Rd
qgtools/man/adc.reml.Rd