R help - Jul 2010 - cca in vegan (formula instead of community matrix data)

Dear List,

I tried to do cca based on species data and environmental variables (formula
instead of community data).
However, there was an error saying row sums must be >0.
I searched the previous related messages but found few solutions.
Please kindly help and thank you in advance.


code
This is vegan 1.17-3
Warning message:
package 'vegan' was built under R version 2.10.1

rm(list=ls())
library(vegan)

datam <-read.csv("c:/migration/M_R_20100707_winterM.csv",header=T,
row.names=1)
dim(datam)
datam[1,]

m.cca  <-
 cca(datam$WinterM_ratio~datam$topo_mean+datam$coast+datam$prec_max
+datam$temp_min+datam$evi_min,  datam)

error in  cca.default(d$X, d$Y, d$Z) :
  All row sums must be >0 in the community data matrix

	[[alternative HTML version deleted]]

As it says, (at least) one of your rows is all zeros.  CCA cannot handle such
sites.

You might want to try something like this:

m.cca  <-
 cca(WinterM_ratio ~ topo_mean + coast + prec_max + 
 temp_min + evi_min,  data = datam, 
 subset = rowSums(WinterM_ratio) > 0) ### Note.

(Note that you do not need to put a "datam$" in front of the terms in
your formula.)


-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
On Behalf Of elaine kuo
Sent: Saturday, 17 July 2010 2:45 PM
To: r-help at r-project.org
Subject: [R] cca in vegan (formula instead of community matrix data)

Dear List,

I tried to do cca based on species data and environmental variables (formula
instead of community data).
However, there was an error saying row sums must be >0.
I searched the previous related messages but found few solutions.
Please kindly help and thank you in advance.


code
This is vegan 1.17-3
Warning message:
package 'vegan' was built under R version 2.10.1

rm(list=ls())
library(vegan)

datam <-read.csv("c:/migration/M_R_20100707_winterM.csv",header=T,
row.names=1)
dim(datam)
datam[1,]

m.cca  <-
 cca(datam$WinterM_ratio~datam$topo_mean+datam$coast+datam$prec_max
+datam$temp_min+datam$evi_min,  datam)

error in  cca.default(d$X, d$Y, d$Z) :
  All row sums must be >0 in the community data matrix

	[[alternative HTML version deleted]]

______________________________________________
R-help at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

On Sat, 2010-07-17 at 12:44 +0800, elaine kuo wrote:
> Dear List,
> 
> I tried to do cca based on species data and environmental variables
(formula
> instead of community data).
> However, there was an error saying row sums must be >0.
> I searched the previous related messages but found few solutions.
> Please kindly help and thank you in advance.
You have samples that have no species observed at all. As such is it
impossible to anything with these samples. Remove them and then fit your
model

datam <- with(datam, datam[rowSums(WinterM_ratio) > 0, ])
m.cca <- cca(WinterM_ratio ~ topo_mean + coast + prec_max +
             temp_min + evi_min,  datam)

However, I have one question for you; is WinterM_ratio a univariate
response (single column)? If it is, why do you want to analyse it using
CCA? CCA is generally used for multivariate species responses.

Finally; you might want to do something about that warning message.
Either your R is out of date or your package library is. If you are
using R2.11-x then run this:

update.packages(checkBuilt = TRUE)

to update the packages to the newest version of R; there have been lots
of changes in the way help is processed / made available that might not
be available if using packages built under earlier versions of R.

HTH

G
> 
> 
> code
> This is vegan 1.17-3
> Warning message:
> package 'vegan' was built under R version 2.10.1
> 
> rm(list=ls())
> library(vegan)
> 
> datam
<-read.csv("c:/migration/M_R_20100707_winterM.csv",header=T,
> row.names=1)
> dim(datam)
> datam[1,]
> 
> m.cca  <-
>  cca(datam$WinterM_ratio~datam$topo_mean+datam$coast+datam$prec_max
> +datam$temp_min+datam$evi_min,  datam)
> 
> error in  cca.default(d$X, d$Y, d$Z) :
>   All row sums must be >0 in the community data matrix
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
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