R help - Jul 2003 - correlation, import of large tables, test for point-biserial c.c.?

Dear R help community,

I want to calculate correlations between environment parameters and species
abundance data. When I use the cor() for my table (121 columns 91 rows) R
generates a dataset with the correlations between all columns; 

1) How can I limit the calculations to the correlations of only the first
column with every other ? (Or:) How can I extract the line/row in question from
the cor() dataset produced by R ?

2) I assume that with one continuous factor and the other binary (0/1), 
cor() gives the point-biserial correlation coefficient, but how can I find the
method used by R ?

3) I was not able to import (from "Excel") the whole 121x67 table, for
instance I divided it into pieces. Is there a simple solution to import the
whole
file ?

4) In the end I want to test the correlation coefficients. Where do I find
an appropriated test for the point biserial correlation ? Can R calculate the
coefficient and test it for all data in one step ?

I just started working & learning with R, but even after reading the R-help
and Introduction to R, I still have big difficulties, so
Thanks in advance for your help !!

Arne Saatkamp

Arne Saatkamp
Inst. f. Biol. II - Abt. f. Geobotanik
Sch?nzlestr. 1
79104 Freiburg
Germany

-- 


Jetzt ein- oder umsteigen und USB-Speicheruhr als Pr?mie sichern!

1) Calculating a 121 x 121 correlation matrix and then extracting the relevant
correlating is extremely inefficient and slow. Instead try this :

data  <- as.matrix( data )                           # data is your 91 x 121
matrix or dataframe
colInterest   <- data[ ,1]
apply( data, 2, function(x) cor(x , colInterest) )


Here you take each column of data (at which point it becomes a vector called x)
and calculates its correlation. apply() is an efficient form of for() loop.


3) I have imported files of much bigger dimensions without any problem. First of
all ensure that the data is in tab delimited or comma seperated not .xls. Next
use read.delim or read.csv to read in the file.

If the file is only partially loaded or garbled up, then check for special
characters. Most often the culprit is the comment character #. Sometimes % @ etc
can also cause a problem.

I have no idea about the other questions. If you type in help.start(), you will
get a help page where you can do a keyword search etc.


-----Original Message-----
From: ArneSaatkamp at gmx.de [mailto:ArneSaatkamp at gmx.de] 
Sent: Friday, July 11, 2003 10:01 PM
To: r-help at stat.math.ethz.ch
Subject: [R] correlation, import of large tables,test for point-biserial c.c.?


Dear R help community,

I want to calculate correlations between environment parameters and species
abundance data. When I use the cor() for my table (121 columns 91 rows) R
generates a dataset with the correlations between all columns;

1) How can I limit the calculations to the correlations of only the first column
with every other ? (Or:) How can I extract the line/row in question from the
cor() dataset produced by R ?

2) I assume that with one continuous factor and the other binary (0/1), 
cor() gives the point-biserial correlation coefficient, but how can I find the
method used by R ?

3) I was not able to import (from "Excel") the whole 121x67 table, for
instance I divided it into pieces. Is there a simple solution to import the
whole file ?

4) In the end I want to test the correlation coefficients. Where do I find an
appropriated test for the point biserial correlation ? Can R calculate the
coefficient and test it for all data in one step ?

I just started working & learning with R, but even after reading the R-help
and Introduction to R, I still have big difficulties, so Thanks in advance for
your help !!

Arne Saatkamp

Arne Saatkamp
Inst. f. Biol. II - Abt. f. Geobotanik
Sch?nzlestr. 1
79104 Freiburg
Germany

-- 


Jetzt ein- oder umsteigen und USB-Speicheruhr als Pr?mie sichern!

______________________________________________
R-help at stat.math.ethz.ch mailing list
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Did you look at "?cor"?

The documentation observes that cor accepts an optional second argument. 
  The following works:
 > df1 <- data.frame(a=1:8, b=rep(c(-1, 1), 4),
+  c=rep(c(-1, 1), each=4))
 > cor(df1[,1], df1[, -1])
              b         c
[1,] 0.2182179 0.8728716
 >
hope this helps.  spencer graves

ArneSaatkamp at gmx.de wrote:
> Dear R help community,
> 
> I want to calculate correlations between environment parameters and species
> abundance data. When I use the cor() for my table (121 columns 91 rows) R
> generates a dataset with the correlations between all columns; 
> 
> 1) How can I limit the calculations to the correlations of only the first
> column with every other ? (Or:) How can I extract the line/row in question
from
> the cor() dataset produced by R ?
> 
> 2) I assume that with one continuous factor and the other binary (0/1), 
> cor() gives the point-biserial correlation coefficient, but how can I find
the
> method used by R ?
> 
> 3) I was not able to import (from "Excel") the whole 121x67
table, for
> instance I divided it into pieces. Is there a simple solution to import the
whole
> file ?
> 
> 4) In the end I want to test the correlation coefficients. Where do I find
> an appropriated test for the point biserial correlation ? Can R calculate
the
> coefficient and test it for all data in one step ?
> 
> I just started working & learning with R, but even after reading the
R-help
> and Introduction to R, I still have big difficulties, so
> Thanks in advance for your help !!
> 
> Arne Saatkamp
> 
> Arne Saatkamp
> Inst. f. Biol. II - Abt. f. Geobotanik
> Sch?nzlestr. 1
> 79104 Freiburg
> Germany
>