Exam5.2 {eda4treeR} R Documentation

Example 5.2 from Experimental Design & Analysis for Tree Improvement

Description

Exam5.2 presents the height of 37 seedlots from 6 sites.

Author(s)

2. Sami Ullah (samiullahuos@gmail.com)

References

1. Williams, E.R., Matheson, A.C. and Harwood, C.E. (2002).Experimental Design and Analysis for Tree Improvement. CSIRO Publishing.

DataExam5.2

Examples

data(DataExam5.2)
library(tidyverse)
library(ggplot2)

fm5.7 <- aov(formula = height~env*gen
,data    = DataExam5.2
#, subset
#, weights
#, na.action
, method = "qr"
, model = TRUE
, x = FALSE
, y = FALSE
, qr = TRUE
, singular.ok = TRUE
, contrasts = NULL
)

anova(fm5.7)

fm5.9  <-    aov(formula = height~env*gen
,data    = DataExam5.2
#, subset
#, weights
#, na.action
, method = "qr"
, model = TRUE
, x = FALSE
, y = FALSE
, qr = TRUE
, singular.ok = TRUE
, contrasts = NULL
)
anova(fm5.9)
b<-anova(fm5.9)
Res                     <- length(b[["Sum Sq"]])
df                      <- 384
MSS                     <- 964
b[["Df"]][Res]          <- df
b[["Sum Sq"]][Res]      <- MSS*df
b[["Mean Sq"]][Res]     <- b[["Sum Sq"]][Res]/b[["Df"]][Res]
b[["F value"]][1:Res-1] <- b[["Mean Sq"]][1:Res-1]/b[["Mean Sq"]][Res]
b[["Pr(>F)"]][Res-1]     <- df(b[["F value"]][Res-1],b[["Df"]][Res-1],b[["Df"]][Res])
b

X1<- DataExam5.2 %>%
group_by(env) %>%
summarize(SiteMean=mean(height))

Data5.2new<-merge(DataExam5.2,X1, by.x="env",by.y="env")
RegCoeff <- function(Data5.2new)
{
fm     <- lm(formula = height ~ SiteMean
,data    = Data5.2new)
setNames(data.frame(t(coef(fm)))
,c("intercept", "slope"))
}
RegCoeff1     <- Data5.2new %>%
group_by(gen) %>%
do(RegCoeff(.))
SeedLot.Mean <- DataExam5.2 %>%
group_by(gen) %>%
summarize(mean(height))
Tab5.14    <- data.frame(RegCoeff1,Mean=SeedLot.Mean$'mean(height)') Tab5.14 ggplot(Tab5.14,aes(x=Mean,y=slope))+ geom_point(size=2)+ theme_bw()+ geom_text(aes(label=gen),hjust=0, vjust=0)+ labs(x="Seed Lot Mean",y="Regression Coefficient") Code<-c("a","a","a","a","b","b","b","b","c","d","d","d","d","e","f","g", "h","h","i","i","j","k","l","m","n","n","n","o","p","p","q","r", "s","t","t","u","v") Tab5.14$Code<-Code
ggplot(Tab5.14,aes(x=Mean,y=slope))+
geom_point(size=2)+
theme_bw()+
geom_text(aes(label=Code),hjust=-0.5, vjust=-0.5)+
labs(x="Seed Lot Mean",y="Regression Coefficient")


[Package eda4treeR version 0.3.0 Index]