R help - Aug 2005 - invalid 'mode' of argument?

Dear Colleagues,

 

As a novice I was trying to calculate Shannon diversity index using
diversity function in vegan package and kept having same error message.

 

Error in sum(..., na.rm = na.rm) : invalid 'mode' of argument

 

My dataset is from microarray and have abundant missing values, so I
tried labeling them as NA and 0, but still same error message.

 

Shannon index is negative sum of proportion times log of proportion, so
I put 1 for missing values to avoid log 0, but still same error message.

 

What do you think I'm missing here?

 

Many thanks in advance.

 

Sanghoon Kang.

 


	[[alternative HTML version deleted]]

On Wed, 2005-08-10 at 08:13 -0400, Kang, Sang-Hoon wrote:
> As a novice I was trying to calculate Shannon diversity index using
> diversity function in vegan package and kept having same error message.
> Error in sum(..., na.rm = na.rm) : invalid 'mode' of argument
> 
This error (which is from sum()) seems to come if you have non-numeric
data (factors, character variables etc.). Check that your data are
strictly numeric. Some of the most common cases I've seen are that row
or column names are not read as row and column names but as data rows or
columns. 
> 
> My dataset is from microarray and have abundant missing values, so I
> tried labeling them as NA and 0, but still same error message.
> Shannon index is negative sum of proportion times log of proportion, so
> I put 1 for missing values to avoid log 0, but still same error message.
> 
You shouldn't forge your data: the function handles zeros.

PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

cheers, jari oksanen
-- 
Jari Oksanen -- Dept Biology, Univ Oulu, 90014 Oulu, Finland
email jari.oksanen at oulu.fi, homepage http://cc.oulu.fi/~jarioksa/