qgtools: Tools for Quantitative Genetics Data Analyses

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.

AuthorJixiang Wu (South Dakota State University), Johnie N. Jenkins and Jack C. McCarty (USDA-ARS)
Date of publication2014-09-17 18:12:26
MaintainerJixiang Wu <qgtools@gmail.com>
LicenseGPL-2
Version1.0

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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

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