Nothing
traitstats.rbd<-function(Treatment,Replication,DataFile)
{
df_dataset<-DataFile
treatment<-as.factor(Treatment)
replication<-as.factor(Replication)
colnms<-colnames(df_dataset)
colcount=length(colnms)
colrangestart=3
t=length(levels(treatment))
r=length(levels(replication))
tlevels=levels(treatment)
rlevels=levels(replication)
TFT95<-qf(0.95,(t-1),(r-1)*(t-1))
TFT99<-qf(0.99,(t-1),(r-1)*(t-1))
TFT99.99<-qf(0.999,(t-1),(r-1)*(t-1))
TFR95<-qf(0.95,(r-1),(r-1)*(t-1))
TFR99<-qf(0.99,(r-1),(r-1)*(t-1))
TFR99.99<-qf(0.999,(r-1),(r-1)*(t-1))
TINV<-abs(qt(0.05/2,(r-1)*(t-1)))
sumvector<-c()
for (val in 3:colcount)
{
sumval<-sum(df_dataset[val])
sumvector<-c(sumvector,sumval)
}
matrow=colcount-2
rownames<-c()
colnames<-c()
for(i in 1:matrow)
{
rownames <- c(rownames,colnms[i+2])
}
for(i in 1:matrow)
{
colnames <- c(colnames,colnms[i+2])
}
RTS <- matrix( nrow = matrow,ncol = matrow, byrow = TRUE, dimnames = list(rownames, colnames))
tempvar=colcount-2
temprc=length(sumvector)
for(i in 1:tempvar)
{
varstart=i
for(j in varstart:tempvar)
{
if(i==j)
{
valTS=0
{
valTS= valTS+(sumvector[i]*sumvector[i])
}
RTS[i,j]<-valTS
}
else
{
valTS=0
valTS= valTS+(sumvector[i]*sumvector[j])
RTS[i,j]<-valTS
RTS[j,i]<-valTS
}
}
}
totvals=t*r
rtss<-c()
i=colrangestart
while(i<=colcount)
{
fsum<-c()
for(k in 1:totvals)
{
if(i<=colcount)
{
val1=df_dataset[k,i]*df_dataset[k,i]
fsum <-as.numeric(c(fsum,val1))
}
}
tss=sum(as.numeric(fsum))
rtss <-c(rtss,tss)
tempi=i
while(tempi<=colcount)
{
fsum<-c()
for(k in 1:totvals)
{
if(tempi<=colcount-1)
{
val1=df_dataset[k,i]*df_dataset[k,tempi+1]
fsum <-as.numeric(c(fsum,val1))
}
}
tempi=tempi+1
TSS=sum(fsum)
rtss <-c(rtss,TSS)
}
i=i+1
}
matrow=colcount-2
rownames<-c()
colnames<-c()
for(i in 1:matrow)
{
rownames <- c(rownames,colnms[i+2])
}
for(i in 1:matrow)
{
colnames <- c(colnames,colnms[i+2])
}
RTSS <- matrix( nrow = matrow,ncol = matrow, byrow = TRUE, dimnames = list(rownames, colnames))
tempvar=colcount-2
countchar=1
for(i in 1:tempvar)
{
varstart=i
for(j in varstart:tempvar)
{
if(rtss[countchar]==0)
countchar=countchar+1
{
val=rtss[countchar]
RTSS[i,j]<-val
RTSS[j,i]<-val
countchar=countchar+1
}
}
}
repsum<-c()
rcount=length(rlevels)
for(col in 3:colcount)
{
repcolsum<-c()
for (valRS in 1:rcount)
{
sumval<-sum(df_dataset[which(df_dataset[,2]==rlevels[valRS]),col])
repcolsum<-c(repcolsum,sumval)
}
repsum<-c(repsum,repcolsum)
}
rownames<-c()
colnames<-c()
repcount=length(rlevels)
for(i in 1:repcount)
{
rownames <- c(rownames,rlevels[i])
}
for(i in 1:matrow)
{
colnames <- c(colnames,colnms[i+2])
}
RRSS1 <- matrix( nrow = r,ncol = matrow, byrow = TRUE, dimnames = list(rownames, colnames))
incrementor=1
cc=colcount-2
for(i in 1:cc)
{
for(j in 1:r)
{
RRSS1[j,i]=repsum[incrementor]
incrementor=incrementor+1
}
}
matrow=colcount-2
rownames<-c()
colnames<-c()
for(i in 1:matrow)
{
rownames <- c(rownames,colnms[i+2])
}
for(i in 1:matrow)
{
colnames <- c(colnames,colnms[i+2])
}
RRSS <- matrix( nrow = matrow,ncol = matrow, byrow = TRUE, dimnames = list(rownames, colnames))
tempvar=colcount-2
for(i in 1:tempvar)
{
varstart=i
for(j in varstart:tempvar)
{
if(i==j)
{
valRS=0
for(k in 1:r)
{
valRS=valRS+(RRSS1[k,j]*RRSS1[k,j])
}
RRSS[i,j]<-valRS
}
else
{
valRS=0
for(k in 1:r)
{
valRS=valRS+(RRSS1[k,i]*RRSS1[k,j])
}
RRSS[i,j]<-valRS
RRSS[j,i]<-valRS
}
}
}
trsum<-c()
trtcount=length(tlevels)
for(col in 3:colcount)
{
trcolsum<-c()
for (val in 1:trtcount)
{
sumval<-sum(df_dataset[which(df_dataset[,1]==tlevels[val]),col])
trcolsum<-c(trcolsum,sumval)
}
trsum<-c(trsum,trcolsum)
}
rownames<-c()
colnames<-c()
for(i in 1:trtcount)
{
rownames <- c(rownames,tlevels[i])
}
for(i in 1:matrow)
{
colnames <- c(colnames,colnms[i+2])
}
RTSS1 <- matrix( nrow = t,ncol = matrow, byrow = TRUE, dimnames = list(rownames, colnames))
incrementor=1
cc=colcount-2
for(i in 1:cc)
{
for(j in 1:t)
{
RTSS1[j,i]=trsum[incrementor]
incrementor=incrementor+1
}
}
matrow=colcount-2
rownames<-c()
colnames<-c()
for(i in 1:matrow)
{
rownames <- c(rownames,colnms[i+2])
}
for(i in 1:matrow)
{
colnames <- c(colnames,colnms[i+2])
}
RTrSS <- matrix( nrow = matrow,ncol = matrow, byrow = TRUE, dimnames = list(rownames, colnames))
tempvar=colcount-2
temprc=length(tlevels)
for(i in 1:tempvar)
{
varstart=i
for(j in varstart:tempvar)
{
if(i==j)
{
valTS=0
for(k in 1:temprc)
{
valTS= valTS+(RTSS1[k,i]*RTSS1[k,i])
}
RTrSS[i,j]<-valTS
}
else
{
valTS=0
for(k in 1:temprc)
{
valTS= valTS+(RTSS1[k,j]*RTSS1[k,i])
}
RTrSS[i,j]<-valTS
RTrSS[j,i]<-valTS
}
}
}
matrow=colcount-2
rownames<-c()
colnames<-c()
for(i in 1:matrow)
{
rownames <- c(rownames,colnms[i+2])
}
for(i in 1:matrow)
{
colnames <- c(colnames,colnms[i+2])
}
CFM <- matrix( nrow = matrow,ncol = matrow, byrow = TRUE, dimnames = list(rownames, colnames))
CF<-c()
for(i in 1:i)
{
for(j in 1:j)
{
CF=c(RTS[i,j]/(t*r))
CFM[i,j]<-CF
}
}
matrow=colcount-2
rownames<-c()
colnames<-c()
for(i in 1:matrow)
{
rownames <- c(rownames,colnms[i+2])
}
for(i in 1:matrow)
{
colnames <- c(colnames,colnms[i+2])
}
TSS <- matrix( nrow = matrow,ncol = matrow, byrow = TRUE, dimnames = list(rownames, colnames))
TS<-c()
for(i in 1:i)
{
for(j in 1:j)
{
TS=c(RTSS[i,j]-CFM[i,j])
TSS[i,j]<-TS
}
}
matrow=colcount-2
rownames<-c()
colnames<-c()
for(i in 1:matrow)
{
rownames <- c(rownames,colnms[i+2])
}
for(i in 1:matrow)
{
colnames <- c(colnames,colnms[i+2])
}
TrSS <- matrix( nrow = matrow,ncol = matrow, byrow = TRUE, dimnames = list(rownames, colnames))
TrS<-c()
for(i in 1:i)
{
for(j in 1:j)
{
TrS=c((RTrSS[i,j]/(r))-CFM[i,j])
TrSS[i,j]<-TrS
}
}
matrow=colcount-2
rownames<-c()
colnames<-c()
for(i in 1:matrow)
{
rownames <- c(rownames,colnms[i+2])
}
for(i in 1:matrow)
{
colnames <- c(colnames,colnms[i+2])
}
RSS <- matrix( nrow = matrow,ncol = matrow, byrow = TRUE, dimnames = list(rownames, colnames))
RS<-c()
for(i in 1:i)
{
for(j in 1:j)
{
RS=c((RRSS[i,j]/(t))-CFM[i,j])
RSS[i,j]<-RS
}
}
matrow=colcount-2
rownames<-c()
colnames<-c()
for(i in 1:matrow)
{
rownames <- c(rownames,colnms[i+2])
}
for(i in 1:matrow)
{
colnames <- c(colnames,colnms[i+2])
}
ErSS <- matrix( nrow = matrow,ncol = matrow, byrow = TRUE, dimnames = list(rownames, colnames))
ErS<-c()
for(i in 1:i)
{
for(j in 1:j)
{
ErS=c(TSS[i,j]-TrSS[i,j]-RSS[i,j])
ErSS[i,j]<-ErS
}
}
matrow=colcount-2
rownames<-c()
colnames<-c()
for(i in 1:matrow)
{
rownames <- c(rownames,colnms[i+2])
}
for(i in 1:matrow)
{
colnames <- c(colnames,colnms[i+2])
}
TrMSS <- matrix( nrow = matrow,ncol = matrow, byrow = TRUE, dimnames = list(rownames, colnames))
TrMS<-c()
for(i in 1:i)
{
for(j in 1:j)
{
TrMS=c(TrSS[i,j]/(t-1))
TrMSS[i,j]<-TrMS
}
}
matrow=colcount-2
rownames<-c()
colnames<-c()
for(i in 1:matrow)
{
rownames <- c(rownames,colnms[i+2])
}
for(i in 1:matrow)
{
colnames <- c(colnames,colnms[i+2])
}
RMSS <- matrix( nrow = matrow,ncol = matrow, byrow = TRUE, dimnames = list(rownames, colnames))
RMS<-c()
for(i in 1:i)
{
for(j in 1:j)
{
RMS=c(RSS[i,j]/(r-1))
RMSS[i,j]<-RMS
}
}
matrow=colcount-2
rownames<-c()
colnames<-c()
for(i in 1:matrow)
{
rownames <- c(rownames,colnms[i+2])
}
for(i in 1:matrow)
{
colnames <- c(colnames,colnms[i+2])
}
ErMSS <- matrix( nrow = matrow,ncol = matrow, byrow = TRUE, dimnames = list(rownames, colnames))
ErMS<-c()
for(i in 1:i)
{
for(j in 1:j)
{
A<-(t-1)*(r-1)
ErMS=c(ErSS[i,j]/A)
ErMSS[i,j]<-ErMS
}
}
matrow=colcount-2
rownames<-c()
colnames<-c()
for(i in 1:matrow)
{
rownames <- c(rownames,colnms[i+2])
}
for(i in 1:matrow)
{
colnames <- c(colnames,colnms[i+2])
}
CalFT <- matrix( nrow = matrow,ncol = matrow, byrow = TRUE, dimnames = list(rownames, colnames))
calft<-c()
for(i in 1:i)
{
for(j in 1:j)
{
calft=c(TrMSS[i,j]/ErMSS[i,j])
CalFT[i,j]<-calft
}
}
matrow=colcount-2
rownames<-c()
colnames<-c()
for(i in 1:matrow)
{
rownames <- c(rownames,colnms[i+2])
}
for(i in 1:matrow)
{
colnames <- c(colnames,colnms[i+2])
}
CalFR <- matrix( nrow = matrow,ncol = matrow, byrow = TRUE, dimnames = list(rownames, colnames))
calfr<-c()
for(i in 1:i)
{
for(j in 1:j)
{
calfr=c(RMSS[i,j]/ErMSS[i,j])
CalFR[i,j]<-calfr
}
}
matrow=colcount-2
rownames<-c()
colnames<-c()
for(i in 1:matrow)
{
rownames <- c(rownames,colnms[i+2])
}
for(i in 1:matrow)
{
colnames <- c(colnames,colnms[i+2])
}
TSIGN <- matrix( nrow = matrow,ncol = matrow, byrow = TRUE, dimnames = list(rownames, colnames))
for(i in 1:i)
{
for(j in 1:j)
{
if(TFT99.99 < CalFT[i,j])
{
TSIGN[i,j]<-"***"
}
else
{
if(TFT99<CalFT[i,j])
{
TSIGN[i,j]<-"**"
}
else if(TFT95<CalFT[i,j])
{
TSIGN[i,j]<-"*"
}
else
{
TSIGN[i,j]<-"ns"
}
}
}
}
matrow=colcount-2
rownames<-c()
colnames<-c()
for(i in 1:matrow)
{
rownames <- c(rownames,colnms[i+2])
}
for(i in 1:matrow)
{
colnames <- c(colnames,colnms[i+2])
}
RSIGN <- matrix( nrow = matrow,ncol = matrow, byrow = TRUE, dimnames = list(rownames, colnames))
for(i in 1:i)
{
for(j in 1:j)
{
if(TFR99.99 < CalFR[i,j])
{
RSIGN[i,j]<-"***"
}
else
{
if(TFR99<CalFR[i,j])
{
RSIGN[i,j]<-"**"
}
else if(TFR95<CalFR[i,j])
{
RSIGN[i,j]<-"*"
}
else
{
RSIGN[i,j]<-"ns"
}
}
}
}
matrow=colcount-2
rownames<-c()
colnames<-c()
for(i in 1:matrow)
{
rownames <- c(rownames,colnms[i+2])
}
for(i in 1:matrow)
{
colnames <- c(colnames,colnms[i+2])
}
SEm <- matrix( nrow = matrow,ncol = matrow, byrow = TRUE, dimnames = list(rownames, colnames))
sem<-c()
for(i in 1:i)
{
E=(ErMSS[i,i]/r)
sem=c(sqrt(E))
SEm[i,i]<-sem
}
matrow=colcount-2
rownames<-c()
colnames<-c()
for(i in 1:matrow)
{
rownames <- c(rownames,colnms[i+2])
}
for(i in 1:matrow)
{
colnames <- c(colnames,colnms[i+2])
}
SEd <- matrix( nrow = matrow,ncol = matrow, byrow = TRUE, dimnames = list(rownames, colnames))
sed<-c()
for(i in 1:i)
{
E=((2*ErMSS[i,i])/r)
sed=c(sqrt(E))
SEd[i,i]<-sed
}
matrow=colcount-2
rownames<-c()
colnames<-c()
for(i in 1:matrow)
{
rownames <- c(rownames,colnms[i+2])
}
for(i in 1:matrow)
{
colnames <- c(colnames,colnms[i+2])
}
TM <- matrix( nrow = matrow,ncol = matrow, byrow = TRUE, dimnames = list(rownames, colnames))
traittotal=sumvector
tm<-c()
for(i in 1:i)
{
for(j in i:i)
{
tm<-traittotal[i]/(t*r)
TM[i,j]<-c(tm)
}
}
for(i in 1:i)
{
for(j in 1:j)
{
tm<-c(TM[i,i]+TM[j,j])/2
TM[i,j]<-tm
TM[j,i]<-tm
}
}
matrow=colcount-2
rownames<-c()
colnames<-c()
for(i in 1:matrow)
{
rownames <- c(rownames,colnms[i+2])
}
for(i in 1:matrow)
{
colnames <- c(colnames,colnms[i+2])
}
MIN <- matrix( nrow = matrow,ncol = matrow, byrow = TRUE, dimnames = list(rownames, colnames))
mind<-c()
for(i in 1:i)
{
mind<-c(min(df_dataset[i+2]))
MIN[i,i]<-mind
}
matrow=colcount-2
rownames<-c()
colnames<-c()
for(i in 1:matrow)
{
rownames <- c(rownames,colnms[i+2])
}
for(i in 1:matrow)
{
colnames <- c(colnames,colnms[i+2])
}
MAX <- matrix( nrow = matrow,ncol = matrow, byrow = TRUE, dimnames = list(rownames, colnames))
maxd<-c()
for(i in 1:i)
{
maxd<-c(max(df_dataset[i+2]))
MAX[i,i]<-maxd
}
matrow=colcount-2
rownames<-c()
colnames<-c()
for(i in 1:matrow)
{
rownames <- c(rownames,colnms[i+2])
}
for(i in 1:matrow)
{
colnames <- c(colnames,colnms[i+2])
}
CV <- matrix( nrow = matrow,ncol = matrow, byrow = TRUE, dimnames = list(rownames, colnames))
cv<-c()
for(i in 1:i)
{
B<-sqrt(ErMSS[i,i])
cv<-c((B/TM[i,i])*100)
CV[i,i]<-cv
}
rownames<-c("Number of Replication","Number of Treatment","Treatment Mean Sum of Square","Replication Mean Sum of Square","Error Mean Sum of Square","Trait Mean","Minimum","Maximum","CV","StdError(m)","StdError(d)")
colnames<-c()
for(i in 1:matrow)
{
colnames <- c(colnames,colnms[i+2])
}
ANOVA <- matrix( nrow = 11,ncol = matrow, byrow = TRUE, dimnames = list(rownames, colnames))
j=length((colnames))
for(i in 1:11)
{
for(j in 1:j)
{
ANOVA[1,j]<-r
ANOVA[2,j]<-t
ANOVA[3,j]<-paste(round(TrMSS[j,j],digits = 4),TSIGN[j,j])
ANOVA[4,j]<-paste(round(RMSS[j,j],digits = 4),RSIGN[j,j])
ANOVA[5,j]<-round(ErMSS[j,j],digits=4)
ANOVA[6,j]<-round(TM[j,j],digits=4)
ANOVA[7,j]<-round(MIN[j,j],digits=4)
ANOVA[8,j]<-round(MAX[j,j],digits=4)
ANOVA[9,j]<-round(CV[j,j],digits=4)
ANOVA[10,j]<-round(SEm[j,j],digits=4)
ANOVA[11,j]<-round(SEd[j,j],digits=4)
}
}
ANOVA<-noquote(ANOVA)
ANOVA
return(ANOVA)
}
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