help, please! matrix operations inside 3 nested loops
Hi
all problems solved. thank you for your help!
for the sake of completeness, here my solution:
#1) read in data:
daten<-read.table('K:/Analysen/STRUCTURE/test.txt', header=TRUE,
sep="\t")
daten<-as.data.frame(daten)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^ not needed, daten is already data frame
#2) create empty matrix:
indxind<-matrix(0,nrow=617, ncol=617)
#indxind[1:20,1:19]
#3) compare cells to each other, score:
#for the whole dataset: s in 3:34, z1 in 1:617, z2 in 1:617
z1<-1 #running variable for rows in daten
z2<-1 #running variable for rows in daten
l1<-1 #running variable for rows in indxind
l2<-1 #running variable for rows in indxind
for (s in 3:6) { #walks though the matrix colum by colum, starting at
colum 3
while (z1<11) { #for each current colum, take one row
(z1)...
while (z2<11) { #...and compare it to
another row (z2) of the current colum
if (z1!=z2) {
l1
topf<-indxind[l1,l2]
if
(daten[z1,s]==daten[z2,s]) topf<-topf+1 #actually, 2 rows make up 1
individual,
if
(daten[z1,s]==daten[z2+1,s]) topf<-topf+1 #therefore i compare 2
rows
if
(daten[z1+1,s]==daten[z2,s]) topf<-topf+1 #with another 2 rows
if
(daten[z1+1,s]==daten[z2+1,s]) topf<-topf+1
indxind[l1,l2]<-topf
}
z2<-z2+2
l2<-l2+1
}
z2<-1
l2<-1
z1<-z1+2
l1<-l1+1
}
z1<-1
l1<-1
}
#4) check:
indxind[1:5,1:5]
I believe that above cycles can be simplified, maybe by changing your daten to three dimensional array or some clever **ply construction but if your loops works it is not probably worth en effort. Regards Petr
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