Exam5.1 {eda4treeR} R Documentation

## Example 5.1 from Experimental Design & Analysis for Tree Improvement

### Description

Exam5.1 presents the height of 27 seedlots from 4 sites.

### Author(s)

1. Muhammad Yaseen (myaseen208@gmail.com)

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.

### Examples

data(DataExam5.1)
library(tidyverse)
library(ggplot2)

fm5.4 <- lm(formula = Ht~Site*SeedLot
,data    = DataExam5.1
#, subset
#, weights
#, na.action
, method = "qr"
, model = TRUE
, x = FALSE
, y = FALSE
, qr = TRUE
, singular.ok = TRUE
, contrasts = NULL
)

anova(fm5.4)

DataExam5.1 %>%
dplyr::group_by(Site) %>%
dplyr::summarize(Mean=mean(Ht))

DataExam5.1 %>%
dplyr::group_by(SeedLot) %>%
dplyr::summarize(Mean=mean(Ht))

b<-anova(fm5.4)
Res                     <- length(b[["Sum Sq"]])
df                      <- 208
MSS                     <- 1040
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

RegCoeff <- function(DataExam5.1)
{
fm     <- lm(formula = Ht ~ SiteMean
,data    = DataExam5.1)
setNames(data.frame(t(coef(fm)))
,c("intercept", "slope"))
}
X1       <- DataExam5.1%>%group_by(Site)%>%summarize(sitemean=mean(Ht))
X2       <- filter(DataExam5.1, SeedLot=="13653")
X3       <- filter(DataExam5.1, SeedLot=="13871")
dffig5.1 <-merge(rbind(X2,X3),X1)
ggplot(dffig5.1, aes(x=sitemean, y=Ht, color=SeedLot, shape=SeedLot)) +
geom_point() +
geom_smooth(method=lm, se=FALSE, fullrange=TRUE)+
theme_classic()+
labs(y="Seedlot mean",x="Sitemean")

RegCoeff     <- DataExam5.1 %>%
group_by(SeedLot) %>%
do(RegCoeff(.))

SeedLot.Mean <- DataExam5.1 %>%
group_by(SeedLot) %>%
summarize(mean(Ht))

Tab5.10    <- data.frame(RegCoeff,Mean=SeedLot.Mean\$'mean(Ht)')
Tab5.10
ggplot(Tab5.10,aes(x=Mean,y=slope))+
geom_point(size=2)+
theme_bw()+
labs(x="Seed Lot Mean",y="Regression Coefficient")

[Package eda4treeR version 0.3.0 Index]