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

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

Functions

ad4.mq Man page
ad4.mq.jack Man page
ad4.reml Man page
ad4.reml.jack Man page
adaa.mq Man page
adaa.mq.jack Man page
adaa.reml Man page
adaa.reml.jack Man page
adaa.simu Man page
adaa.simudata Man page
adaa.simu.jack Man page
adc4.mq Man page
adc4.mq.jack Man page
adc4.reml Man page
adc4.reml.jack Man page
adc.mq Man page
adc.mq.jack Man page
adc.reml Man page
adc.reml.jack Man page
adc.simu Man page
adc.simudata Man page
adc.simu.jack Man page
adm.mq Man page
adm.mq.jack Man page
ad.mq Man page
ad.mq.jack Man page
adm.reml Man page
adm.reml.jack Man page
adm.simu Man page
adm.simudata Man page
adm.simu.jack Man page
adrcdat Man page
adrc.mq Man page
adrc.mq.jack Man page
adrc.reml Man page
adrc.reml.jack Man page
ad.reml Man page
ad.reml.jack Man page
ad.simu Man page
ad.simudata Man page
ad.simu.jack Man page
cotf12 Man page
cotf2 Man page
maize Man page
qgtools Man page
qgtools-package Man page
stab.fw Man page
stab.mean Man page
stab.var Man page
wheat Man page

Files

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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