Please forgive me if this question has been answered somewhere else, but
for the life of me I couldn't find an answer (although i have found that
others have asked similar questions.)

If anyone replies, PLEASE keep in mind that I am a soil ecologist with
absolutely no background or experience in object-oriented programming,
which is perhaps why I have not been able to take advantage of existing
help on this subject. If there are answers, I simply do not understand them!

*What I need to do:*
I am trying to generate a table of correlations (26 parameters in columns,
60 data rows.) I need Spearman's rho, the significance level p, and I need
to apply the Bonferroni correction. I also need to export it into Excel in
a nice matrix-y table format.

*What I am able to do:*
I am able to do parts of what I want: with cor() I can generate a Spearman
correlation (but it's very ugly and hard to read or export nicely).
With cor.test I can generate a result when I use only 2 parameters (eg.
soilMois and BD), but I need to produce a table with all parameters
compared to each other.

Ex:     result<-cor.test(AprCorKR$SoilMois, AprCorKR$BD,method="spearman",
adjust.method="Bonferroni")

Warning message:

In cor.test.default(AprCorKR$SoilMois, AprCorKR$BD,  :

  Cannot compute exact p-values with ties


        Spearman's rank correlation rho

data:  AprCorKR$SoilMois and AprCorKR$BD
S = 49274.48, p-value = 0.003705
alternative hypothesis: true rho is not equal to 0
sample estimates:
       rho
-0.3691158

(By the way, I understand the warning message.)

*What I am unable to do:*
Use the function cor.test to generate the output of all my parameters with
respect to one another.

Examples below are of various ways of writing what I want to R:
> result<-cor.test(AprCorKR$[2:26], AprCorKR$[2:26],method="spearman",
adjust.method="Bonferroni")
Error: unexpected '[' in "result<-cor.test(AprCorKR$["
>
> result<-cor.test(AprCorKR$[2,26], AprCorKR$[2,26],method="spearman",
adjust.method="Bonferroni")
Error: unexpected '[' in "result<-cor.test(AprCorKR$["
> result<-cor.test(c([2:26]), c([2:26]),data=AprCorKR,method="spearman",
adjust.method="Bonferroni")
Error: unexpected '[' in "result<-cor.test(c(["
> result<-cor.test(vars=2:26, vars=2:26,data=AprCorKR,method="spearman",
adjust.method="Bonferroni")
Error in cor.test.default(vars = 2:26, vars = 2:26, data = AprCorKR, method
= "spearman",  :
  argument "x" is missing, with no default
> result<-cor.test(vars=2:26,data=AprCorKR,method="spearman",
adjust.method="Bonferroni")
Error in cor.test.default(vars = 2:26, data = AprCorKR, method =
"spearman",  :
  argument "x" is missing, with no default
> result<-cor.test(data=AprCorKR,vars=2:26,method="spearman",
adjust.method="Bonferroni")
Error in cor.test.default(data = AprCorKR, vars = 2:26, method =
"spearman",  :
  argument "x" is missing, with no default

*What I know:*
I have no missing values, no values of zero, and no typos that I am aware
of. I can display all my data correctly in R (and R seems to read it
correctly, based on what I am already able to do.)

A former colleague wrote a small line of code that does what I am trying to
do but I can't get it to work on my newer version of R. I have R 2.14.2 and
I don't know what version he was using.
His code for this: *result<-cor_test(data="**mydata*
",vars=2:26,adjust.method="Bonferroni")

(I include below his entire German instructions. But the code he wrote to
do this job is very short, and I would like to duplicate it if I can. It
provides the results I need in a form I can use.)

* *An additional note:
I have multtest loaded, and in my version cor.test is not written as
cor_test with an underscore but rather with a period. In the version of R
that I am using, there is no such thing as "correlation.r".

*
*


("Alb_Gesamtdat_10-03-10_bd_NA.txt") und das R-Skript ("correlation.r")
liegen und das Paket 'multtest' ist installiert
(www.r-project.org<file:///C:/Users/Regan/Documents/SCALEMIC/NewRStats/www.r-project.org>->
CRAN

-> Mirror -> Packages)



> source("correlation.r")



> result <- cor_test( data="Alb_Gesamtdat_10-03-10_bd_NA.txt",

> vars=5:23,

adjust.method="Bonferroni" )



Es werden bei diesem Funktionsaufruf automatisch 3 Dateien angelegt:

  - spearman_correlation_coefficients_complete_data.txt

  - spearman_correlation_raw_pvalues_complete_data.txt

  - spearman_correlation_Bonferroni_corrected_pvalues_complete_data.txt





Thanks to anyone who can help me with this!


Kind regards,

Kathy Regan
-- 
Kathleen Regan

University of Hohenheim

Institute of Soil Science and Land Evaluation

Soil Biology Section

Emil-Wolff-Str. 27

D-70593 Stuttgart-Hohenheim

"Traveler, there is no road. We make the road by walking."

phone: +49(0)711 459 23118

fax: +49(0)711 459 23117
E-mail:kath.regan@gmail.com

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