Dear all,
I have a data frame
a - data.frame(cbind(x=c('a','a','a','b','c'),
y=c('a','b','c','d','e'),z=c(1,2,3,4,5)))
a
x y z
1 a a 1
2 a b 2
3 a c 3
4 b d 4
5 c e 5
and a matrix
mm - matrix(0,5,5)
colnames(mm) - c('a','b','c','d','e')
rownames(mm) - c('a','b','c','d','e')
mm
a b c d e
Dear all,
Suppose I plot two normal distributions (A and B) side by side and add
vertical line which hipotheticaly represent alpha value; e.g.:
x - seq(-3.5,5, length=1000)
y - dnorm(x)
# Plot distribution A
plot(y~x, type='l',axes=F,xlab=,ylab=,lwd=2)
# Plot distribution B
y2 - dnorm(x-1.5)
Roy Spitz pravi:
Hello
I have 2 rows in a matrix and I want to calculate the Gower Distance between
the 2 , how can I do it?
I searched and found nothing that can help me, and my program doesn't know
the gdist function and I couldn't find it on the R help site.
Can anyone help me
Simon Blomberg wrote:
Hi all,
We've just had a paper accepted for publication in Nature. We used R for
95% of our analyses (one of my co-authors sneaked in some GenStat when I
wasn't looking.). The preprint is available from the Nature web site, in
the open peer-review trial section. I
What's wrong with cross-tabs?
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Hi,
I have a matrix containing ID numbers in each column. I would like to
program function which calculate common number of ID numbers between
each pair of columns.
Suppose:
5 6 7
1 5 3
6 7 2
Then the result should be:
0 2 0
2 0 1
0 1 0
The main problem is how to implement intersect()
inner - function(a,b=a,f=crossprod)
apply(b,2,function(x)apply(a,2,function(y)f(x,y)))
inner(mm, f = function(x,y) length(intersect(x,y))) * !diag(ncol(mm))
On 7/15/06, Andrej Kastrin [EMAIL PROTECTED] wrote:
Hi,
I have a matrix containing ID numbers in each column. I would like
Dear useRs,
I use dics.ef function from dprep package to discretize continuous
variable using intervals of equal frequencies. Dataset to be discretized
include 4 continuous and 2 discrete variables in the following order:
Continuous Countinuous Countinuous Discrete Discrete Continuous
The
richard mendes wrote:
Hello R list members,
I'm a bio informatics student from the Leiden university
(netherlands). We were asked to make a program with different
clustering methods. The problem we are experiencing is the following.
we have a matrix with data like the following
Spencer Graves wrote:
I know of no software for time series clustering in R. Google
produced some interesting hits for time series clustering. If you
find an algorithm you like, the author might have software.
Alternatively, the algorithm might be a modification of something
Dear useRs,
I have two different length vectors: one column (1...m) and one row
vector (1...n):
20
40
20
60
5 4 2
Now I have to calculate ratios between column vector elements and each
row vector elements:
4 5 10
8 10 20
4 5 20
15 12 30
Thank's in advance for any suggestions,
Andrej
Der useRs,
I'm working on meta analysis using rmeta package. Using code below I
plot the forest plot:
library(rmeta)
data (catheter)
a-meta.MH (n.trt, n.ctrl, col.trt, col.ctrl, data=catheter, names=Name,
subset=c(13,6,5,3,7,12,4,11,1,8,10,2))
summary(a) # odds ratio values and confidence
andrew mcsweeny wrote:
Hi:
I'm clustering a microarray dataset with a large # of samples. I would
like your opinion on the best way to automatically determine the optimal # of
clusters. Currently I am using the cluster package, clustering with
clara, examining the average
Uwe Ligges wrote:
[EMAIL PROTECTED] wrote:
Hi,
I would like to know how to configure R so that I can enter some values
and compute the Muximum likelihood estimation of my data.
Maximum likelihood estimation of what?
I do not know the definition of Maximum likelihood estimation
Dear useRs,
shame on me, but I have no idea how to apply two arguments function on
my data. I have 2 vectors, 'n' and 'm' and the function below:
n - c(10,30,50,1000)
m - c(10,50,100,200)
MonteCarlo - function(n,m){
temp - NULL
for(i in 1:m){
temp - c(temp,walk(n)) # walk is external
Dead R useRs,
I wrote function, which plot dotchart from given matrix, compute mean
from diagonal elements and plot it with abline. In addition, if
particular element of matrix is greater then mean value (i.e.
mead.diagonal), it should be plot in red, otherwise in green color.
graph -
Dear useRs,
I have 4×4 symmetrical matrix ; then I use
image(log(my.matrix)) to visualise it.
Is there any 'simple' way to add text labels into each cell lie on
diagonal of the image plot? Thanks for any pointers...
Cheers, Andrej
__
Dear R useRs,
is there any simple, build in function to match specific regular
expression in data file and write it to a vector. I have the following
text file:
*NEW RECORD
*ID-001
*AB-text
*NEW RECORD
*ID-002
*AB-text
etc.
Now I have to match all ID fields and print them to a vector:
001
-', '', result)
[1] 001 002
On 1/28/06, *Andrej Kastrin* [EMAIL PROTECTED]
mailto:[EMAIL PROTECTED] wrote:
Dear R useRs,
is there any simple, build in function to match specific regular
expression in data file and write it to a vector. I have the
following
text file
Dear R useRs,
I have big (23000 rows), vertical bar delimited file:
e.g.
A1|Text a,Text b, Text c|345
A2|Text bla|456
...
..
.
Try using
A - read.table('filename.txt', header=FALSE,sep='\|')
process stop at line 11975 with warning message:
number of items read is not a multiple of
Dear R useRs,
what's the most elegant way to modify distance between x-axis and it's
title. I didn't find any parameter to do that...
Thank's in advance,
cheers, Andrej
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Vincent Deng wrote:
Dear R-helpers,
Can anybody suggest me some common packages for standard microarray
analysis, either from CRAN or Bioconductor?
Many thanks...
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Dear R useRs,
I have a vector with positive and negative numbers:
A=c(0,1,2,3,0,4,5)
Now if i-th element in vector A is 0, then i-th element in vector B
is a+1
else i-th element in vector b=a (or 0)
vector A: 0 1 2 3 0 4 5
vector B: 0 2 3 4 0 5 6
What's the right way to do this. I still
Dear R useRs,
I have a problem to add title to the following graphics;
Tukey=TukeyHSD(aov(CA~C), C,ordered=TRUE))
plot (Tukey, main=My first graph)
actually, it draw a graph, but it also display:
parameter main could not be set in high-level plot() function.
If I execute:
Dear useRs,
I am having difficulty to plot graphics with mfrow command, where both
axis are equal length. Below is sample code, which plots rectangles
instead of squares:
par (mfrow=c(3,3))
qqnorm(a)
qqnorm(b)
...
..
Thanks in advance for any pointers or notes.
Andrej Kastrin wrote:
Dear useRs,
I am having difficulty to plot graphics with mfrow command, where both
axis are equal length. Below is sample code, which plots rectangles
instead of squares:
par (mfrow=c(3,3))
qqnorm(a)
qqnorm(b)
...
..
Thanks in advance for any pointers or notes
Dear useRs,
I'm working on multiple comparison design on two factor (2 × 3 levels)
ANOVA. Each of the tests I have tried (Tukey, multcomp package) seem to
do only with one factor at a time.
fm1 - aov(breaks ~ wool * tension, data = warpbreaks)
tHSD - TukeyHSD(fm1, tension, ordered = FALSE)
Dear R users,
is there any simple low-level function that split single-line graph
labels and produce something like (e.g. for x axis):
100300500 700...
200400 600
Cheers, Andrej
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