Raj at 05:19, 28 October 2016

2016-10-28T05:19:13Z

← Older revision		Revision as of 05:19, 28 October 2016
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	==r-BLUP==		==r-BLUP==

Raj: /* r-BLUP */

2013-08-06T09:09:11Z

r-BLUP

← Older revision		Revision as of 09:09, 6 August 2013
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	==r-BLUP==		==r-BLUP==


			<source line>

	# computation of BLUP's, using seedling dry weight data as example		# computation of BLUP's, using seedling dry weight data as example
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	plot(gmean, pred.tray)		plot(gmean, pred.tray)


			</source>

Raj: Created page with ":Category:R ==r-BLUP== # computation of BLUP's, using seedling dry weight data as example library(lme4) d <- read.table('SeedlingDryWeight2.txt',as.is=T, header=T) # ..."

2013-08-06T09:07:11Z

Created page with "Category:R ==r-BLUP== # computation of BLUP's, using seedling dry weight data as example library(lme4) d <- read.table('SeedlingDryWeight2.txt',as.is=T, header=T) # ..."

New page

[[:Category:R]]

==r-BLUP==

# computation of BLUP's, using seedling dry weight data as example

library(lme4)

d <- read.table('SeedlingDryWeight2.txt',as.is=T, header=T)

# create factors
d$g <- as.factor(d$Genotype)
d$t <- as.factor(d$Tray)
d$s <- as.factor(d$Seedling)

# fit the mixed effects model model
temp <- lmer(SeedlingWeight~g+(1|t),data=d)

# BLUPs
blup <- ranef(temp)

# look at ranef() output to see its structure
str(blup)

# there are options to ranef(drop=T) to simplify structure of output

# compare BLUP to genotype averages
gmean <- tapply(d$SeedlingWeight,d$t,mean)

plot(gmean,blup$t$'(Intercept)')

# BLUPs + fixed effects
# there is no predict() for an lmer object
# these are the equivalents

betau <- coef(temp)
# values are beta + u for each row

trayX <- cbind(rep(1,8), rep(c(0,1),c(4,4)))
# model.matrix with one row per tray
pred.tray <- apply(betau$t*trayX,1,sum)

plot(gmean, pred.tray)

BLUP - Revision history

Raj at 05:19, 28 October 2016

Raj: /* r-BLUP */

Raj: Created page with ":Category:R ==r-BLUP== # computation of BLUP's, using seedling dry weight data as example library(lme4) d <- read.table('SeedlingDryWeight2.txt',as.is=T, header=T) # ..."