[R] Formatted Data File Question for Clustering -Quickie Project
I am trying to learn how to format Ascii data files for scan or read
into R.
Precisely for a quickie project, I found some code (at end of this
email) to do exactly what I need:
To cluster and graph a dendrogram from package (stats).
I am stuck on how to format a text file to run the script.
I looked at the dataset USArrests (which would be replaced by my data
and labels) using UltraEdit. That data appears to be in binary format
and I would simply like a readable ASCII text file.
How can I:
A) format this data to a file for the script below?
B) I would like to use squared Euclidean distance, can hclust support
this?
Thanks,
Neil Gottlieb
Here is sub-set example of my data set, return series to cluster: 13
cases by 36 observations):
Month Convertible Arbitrage Dedicated Short BiasEmerging
Markets
1/31/1994 0.004 -0.016 0.105
2/28/1994 0.002 0.020 -0.011
3/31/1994 -0.010 0.072 -0.046
4/30/1994 -0.025 0.013 -0.084
5/31/1994 -0.010 0.023 -0.007
6/30/1994 0.002 0.064 0.005
7/31/1994 0.001 -0.012 0.058
8/31/1994 0.000 -0.057 0.164
9/30/1994 -0.012 0.016 0.052
10/31/1994 -0.014 -0.004 -0.035
11/30/1994 -0.002 0.030 -0.014
12/31/1994 -0.019 -0.002 -0.042
1/31/1995 -0.006 0.013 -0.100
2/28/1995 0.012 -0.022 -0.079
3/31/1995 0.013 0.004 -0.055
4/30/1995 0.023 -0.004 0.073
5/31/1995 0.017 -0.013 0.013
6/30/1995 0.019 -0.069 0.008
7/31/1995 0.009 -0.059 0.022
8/31/1995 0.008 0.008 0.010
9/30/1995 0.011 -0.029 0.019
10/31/1995 0.013 0.064 -0.057
11/30/1995 0.023 -0.010 -0.031
12/31/1995 0.014 0.049 0.007
1/31/1996 0.021 0.006 0.079
2/29/1996 0.012 -0.056 -0.006
3/31/1996 0.015 -0.009 -0.009
4/30/1996 0.013 -0.066 0.051
5/31/1996 0.016 0.000 0.045
6/30/1996 0.015 0.051 0.054
7/31/1996 0.014 0.098 -0.027
8/31/1996 0.013 -0.034 0.036
9/30/1996 0.011 -0.059 0.016
10/31/1996 0.014 0.043 0.017
11/30/1996 0.014 -0.029 0.026
Code Example from Help files:
hc <- hclust(dist(USArrests), "ave")
(dend1 <- as.dendrogram(hc)) # "print()" method
str(dend1) # "str()" method
str(dend1, max = 2) # only the first two sub-levels
op <- par(mfrow= c(2,2), mar = c(5,2,1,4))
plot(dend1)
## "triangle" type and show inner nodes:
plot(dend1, nodePar=list(pch = c(1,NA), cex=0.8, lab.cex = 0.8),
type = "t", center=TRUE)
plot(dend1, edgePar=list(col = 1:2, lty = 2:3), dLeaf=1, edge.root =
TRUE)
plot(dend1, nodePar=list(pch = 2:1,cex=.4*2:1, col = 2:3), horiz=TRUE)
dend2 <- cut(dend1, h=70)
plot(dend2$upper)
## leafs are wrong horizontally:
plot(dend2$upper, nodePar=list(pch = c(1,7), col = 2:1))
## dend2$lower is *NOT* a dendrogram, but a list of .. :
plot(dend2$lower[[3]], nodePar=list(col=4), horiz = TRUE, type = "tr")
## "inner" and "leaf" edges in different type & color :
plot(dend2$lower[[2]], nodePar=list(col=1),# non empty list
edgePar = list(lty=1:2, col=2:1), edge.root=TRUE)
par(op)
str(d3 <- dend2$lower[[2]][[2]][[1]])
nP <- list(col=3:2, cex=c(2.0, 0.75), pch= 21:22, bg= c("light blue",
"pink"),
lab.cex = 0.75, lab.col = "tomato")
plot(d3, nodePar= nP, edgePar = list(col="gray", lwd=2), horiz = TRUE)
addE <- function(n) {
if(!is.leaf(n)) {
attr(n, "edgePar") <- list(p.col="plum")
attr(n, "edgetext") <- paste(attr(n,"members"),"members")
}
n
}
d3e <- dendrapply(d3, addE)
plot(d3e, nodePar= nP)
plot(d3e, nodePar= nP, leaflab = "textlike")
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Re: [R] Formatted Data File Question for Clustering -Quickie Project
if you look at
the data USArrests by doing
> data(USArrets)
> USArrets
you will see that it is a data.frame.
so by analogy you could do the following:
Probably you have this data in Excel (I guess from the format in your mail).
Have the data in a sheet as:
convertsshortBais
19940131 0.004 -0.0016
19940228 ...
save this sheet as tab limited txt file.
then use
mydata <- read.table("yourdata.txt")
now you can use the data.frame mydata in the cluster analysis.
I would suggest you read the intro to R.
You can also use
read.csv see
?read.table
for more info, read R import/export on
http://finzi.psych.upenn.edu/R/doc/manual/R-data.html
good luck.
AA.
- Original Message -
From: <[EMAIL PROTECTED]>
To:
Sent: Wednesday, June 13, 2007 11:46 AM
Subject: [R] Formatted Data File Question for Clustering -Quickie Project
>I am trying to learn how to format Ascii data files for scan or read
> into R.
>
> Precisely for a quickie project, I found some code (at end of this
> email) to do exactly what I need:
> To cluster and graph a dendrogram from package (stats).
>
> I am stuck on how to format a text file to run the script.
> I looked at the dataset USArrests (which would be replaced by my data
> and labels) using UltraEdit. That data appears to be in binary format
> and I would simply like a readable ASCII text file.
>
> How can I:
> A) format this data to a file for the script below?
> B) I would like to use squared Euclidean distance, can hclust support
> this?
>
> Thanks,
> Neil Gottlieb
>
> Here is sub-set example of my data set, return series to cluster: 13
> cases by 36 observations):
> Month Convertible Arbitrage Dedicated Short Bias Emerging
> Markets
> 1/31/1994 0.004 -0.016 0.105
> 2/28/1994 0.002 0.020 -0.011
> 3/31/1994 -0.010 0.072 -0.046
> 4/30/1994 -0.025 0.013 -0.084
> 5/31/1994 -0.010 0.023 -0.007
> 6/30/1994 0.002 0.064 0.005
> 7/31/1994 0.001 -0.012 0.058
> 8/31/1994 0.000 -0.057 0.164
> 9/30/1994 -0.012 0.016 0.052
> 10/31/1994 -0.014 -0.004 -0.035
> 11/30/1994 -0.002 0.030 -0.014
> 12/31/1994 -0.019 -0.002 -0.042
> 1/31/1995 -0.006 0.013 -0.100
> 2/28/1995 0.012 -0.022 -0.079
> 3/31/1995 0.013 0.004 -0.055
> 4/30/1995 0.023 -0.004 0.073
> 5/31/1995 0.017 -0.013 0.013
> 6/30/1995 0.019 -0.069 0.008
> 7/31/1995 0.009 -0.059 0.022
> 8/31/1995 0.008 0.008 0.010
> 9/30/1995 0.011 -0.029 0.019
> 10/31/1995 0.013 0.064 -0.057
> 11/30/1995 0.023 -0.010 -0.031
> 12/31/1995 0.014 0.049 0.007
> 1/31/1996 0.021 0.006 0.079
> 2/29/1996 0.012 -0.056 -0.006
> 3/31/1996 0.015 -0.009 -0.009
> 4/30/1996 0.013 -0.066 0.051
> 5/31/1996 0.016 0.000 0.045
> 6/30/1996 0.015 0.051 0.054
> 7/31/1996 0.014 0.098 -0.027
> 8/31/1996 0.013 -0.034 0.036
> 9/30/1996 0.011 -0.059 0.016
> 10/31/1996 0.014 0.043 0.017
> 11/30/1996 0.014 -0.029 0.026
>
> Code Example from Help files:
> hc <- hclust(dist(USArrests), "ave")
> (dend1 <- as.dendrogram(hc)) # "print()" method
> str(dend1) # "str()" method
> str(dend1, max = 2) # only the first two sub-levels
>
> op <- par(mfrow= c(2,2), mar = c(5,2,1,4))
> plot(dend1)
> ## "triangle" type and show inner nodes:
> plot(dend1, nodePar=list(pch = c(1,NA), cex=0.8, lab.cex = 0.8),
> type = "t", center=TRUE)
> plot(dend1, edgePar=list(col = 1:2, lty = 2:3), dLeaf=1, edge.root =
> TRUE)
> plot(dend1, nodePar=list(pch = 2:1,cex=.4*2:1, col = 2:3), horiz=TRUE)
>
> dend2 <- cut(dend1, h=70)
> plot(dend2$upper)
> ## leafs are wrong horizontally:
> plot(dend2$upper, nodePar=list(pch = c(1,7), col = 2:1))
> ## dend2$lower is *NOT* a dendrogram, but a list of .. :
> plot(dend2$lower[[3]], nodePar=list(col=4), horiz = TRUE, type = "tr")
> ## "inner" and "leaf" edges in different type & color :
> plot(dend2$lower[[2]], nodePar=list(col=1),# non empty list
> edgePar = list(lty=1:2, col=2:1), edge.root=TRUE)
> par(op)
> str(d3 <- dend2$lower[[2]][[2]][[1]])
>
> nP <- list(col=3:2, cex=c(2.0, 0.75), pch= 21:22, bg= c("light blue",
> "pink"),
> lab.cex = 0.75, lab.col = "tomato")
> plot(d3, nodePar= nP, edgePar = list(col="gray", lwd=2), horiz = TRUE)
> addE <- function(n) {
> if(!is.leaf(n)) {
>attr(n, "edgePar") <- list(p.col="plum")
>attr(n, "edgetext") <- paste(attr(n,"members"),"members")
> }
> n
> }
> d3e <- dendrapply(d3, addE)
> plot(d3e, nodePar= nP)
> plot(d3e, nodePar= nP, leaflab = "textlike")
> -
Re: [R] Formatted Data File Question for Clustering -Quickie Project
The "R Data Import/Export" guide was mentioned already, it contains
everything you should know about data exchange between R and other software.
In case it says nothing about dates, try as.Date() and strftime().
For your example below,
as.Date("1/31/1994",format="%m/%d/%Y")
works.
ngottlieb wrote:
>
> I am trying to learn how to format Ascii data files for scan or read
> into R.
>
> Precisely for a quickie project, I found some code (at end of this
> email) to do exactly what I need:
> To cluster and graph a dendrogram from package (stats).
>
> I am stuck on how to format a text file to run the script.
> I looked at the dataset USArrests (which would be replaced by my data
> and labels) using UltraEdit. That data appears to be in binary format
> and I would simply like a readable ASCII text file.
>
> How can I:
> A) format this data to a file for the script below?
> B) I would like to use squared Euclidean distance, can hclust support
> this?
>
> Thanks,
> Neil Gottlieb
>
> Here is sub-set example of my data set, return series to cluster: 13
> cases by 36 observations):
> Month Convertible Arbitrage Dedicated Short BiasEmerging
> Markets
> 1/31/1994 0.004 -0.016 0.105
> 2/28/1994 0.002 0.020 -0.011
> 3/31/1994 -0.010 0.072 -0.046
>
> [skip]
>
--
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and provide commented, minimal, self-contained, reproducible code.
