Nothing
pint.boot <-
function (traits,replicates=1000,verbose =FALSE){
X<-traits
nas<-length(unique(which(is.na(X),arr.ind=T)[,1]))
if(nas>0)
{
warning(paste("Rows containing missing data (",nas, if(nas==1) " row", if(nas>1) " rows",") has been removed to perform the analysis",sep=""))
X<-na.exclude(traits)
}
Y<-replicates
INT = list()
INTC = list()
length (INT) = Y
for (i in 1:Y){
cor_X<-cor(X[sample(nrow(X), replace=TRUE),])
d<-eigen(cor_X, only.values=TRUE)$values
p <- length (d)
n <- nrow(X)
Int<-sum((d-1)^2)/(p)
INT[i]<-Int
Int.c<-(Int-((p-1)/n))
INTC[i]<-Int.c
if(i==1) cat("\nStarting bootstrap...........\n")
if(i==round(Y/4)) cat("\nPerforming bootstrap......25%\n")
if(i==round(Y/2)) cat("\nPerforming bootstrap......50%\n")
if(i==round(3*Y/4)) cat("\nPerforming bootstrap......75%\n")
if(i==Y) cat("\nBootstrap finished.......100%\n")
}
Intphen1 <-as.numeric(INT)
Intphen2 <-as.numeric(INTC)
pref0="Mean = "
pref1="Median ="
pref2="SD = "
pref3="SE = "
se1<-(sd(Intphen1)/sqrt(nrow(X)))
se2<-(sd(Intphen2)/sqrt(nrow(X)))
pref4="Lower IC 99% = "
pref5="Higher IC 99% = "
pref6="Lower IC 95% = "
pref7="Higher IC 95% = "
pref8="Number of replicates = "
#Igual que antes:
names<-matrix(c(pref0,pref1,pref2,pref3,pref4,pref5,pref6,pref7,pref8))
outs<-cbind(
c(
round(mean(Intphen1), 3),
round(median(Intphen1), 3),
round(sd(Intphen1), 3),
round(se1, 3),
round(quantile(Intphen1, probs=0.5/100), 3),
round(quantile(Intphen1, probs=99.5/100), 3),
round(quantile(Intphen1, probs=2.5/100), 3),
round(quantile(Intphen1, probs=97.5/100), 3),
length(INT)
)
,
c(
round(mean(Intphen2), 3),
round(median(Intphen2), 3),
round(sd(Intphen2), 3),
round(se2, 3),
round(quantile(Intphen2, probs=0.5/100), 3),
round(quantile(Intphen2, probs=99.5/100), 3),
round(quantile(Intphen2, probs=2.5/100), 3),
round(quantile(Intphen2, probs=97.5/100), 3),
length(INT)
)
)
row.names(outs)<-names
colnames(outs)<-c("PINT","PINT.C")
if(verbose==TRUE)
{
outs<-list(outs)
outs[[2]]<-Intphen1
outs[[3]]<-Intphen2
names(outs)<-c("Summary","Resampled PINT","Resampled PINT.C")
}
outs
}
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