R help - Dec 2023 - regarding CCA plot

Hii rstudio members
I am learning rstudio, For my manuscript I am trying to plot CCA using
species and environmental data. But I am getting error like
Error in cca.default(sptrans, envtrans) :

  all row sums must be >0 in the community data matrix


*My code is like *
library(vegan)
library(ggplot2)
library(dplyr)
rassspec<-read.csv("C:/Users/hp/Desktop/R_data/rassspec.csv",
header=T,
stringsAsFactors=T)
rassevee<-read.csv("C:/Users/hp/Desktop/R_data/rassenv.csv",
header=T,
stringsAsFactors=T)
sptrans <- decostand(rassspec, "hellinger")
envtrans <- decostand(rassevee, "hellinger")

vare.cca <- cca(sptrans, envtrans)


Any kind of help will be appreciable
Thanking you
regards

Shailendra Pal

Research Scholar
Plant Ecology Lab
(Prof. S.C. Garkoti)
School of Environmental Sciences
JNU, New Delhi
110067

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Dear Shailendra Pal,

Welcome to the R-help mailing list! Most of us are not members of
RStudio in any way. Your problem is also purely about programming in R,
so you've come to the right place. You have also done the right thing
by showing us the code.

On Fri, 8 Dec 2023 16:08:51 +0530
shailendra pal <palshailendra9 at gmail.com> wrote:
> vare.cca <- cca(sptrans, envtrans)
> Error in cca.default(sptrans, envtrans) :
>   all row sums must be >0 in the community data matrix
One of the most important tools provided by R is its online help
system. Use it to look up the documentation for the function you're
having problems with. You can prepend a question mark to most function
calls and get a help page in response; failing that, help('cca') should
also work. Here's what it says:
>> ## Default S3 method:
>> cca(X, Y, Z, ...)
>> X Community data matrix.
>> Y Constraining matrix, typically of environmental variables
In other words, the "community data matrix" mentioned in the error
message is your `sptrans` data.frame. The function complains that at
least some of the rows don't have a positive sum, which is a
requirement of the method. Can you spot the problem by looking at the
data or using rowSums()? 

-- 
Best regards,
Ivan

Dear Shailendra,

For me the problem is not related to R or Rstudio or even vegan. The CCA
analysis can not be done with denuded site, as the sum will be zero.

"all row sums must be >0 in the community data matrix"

Best regards,

GCC

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Em s?b., 9 de dez. de 2023 ?s 06:50, shailendra pal <
palshailendra9 at gmail.com> escreveu:
> Hii rstudio members
> I am learning rstudio, For my manuscript I am trying to plot CCA using
> species and environmental data. But I am getting error like
> Error in cca.default(sptrans, envtrans) :
>
>   all row sums must be >0 in the community data matrix
>
>
> *My code is like *
> library(vegan)
> library(ggplot2)
> library(dplyr)
> rassspec<-read.csv("C:/Users/hp/Desktop/R_data/rassspec.csv",
header=T,
> stringsAsFactors=T)
> rassevee<-read.csv("C:/Users/hp/Desktop/R_data/rassenv.csv",
header=T,
> stringsAsFactors=T)
> sptrans <- decostand(rassspec, "hellinger")
> envtrans <- decostand(rassevee, "hellinger")
>
> vare.cca <- cca(sptrans, envtrans)
>
>
> Any kind of help will be appreciable
> Thanking you
> regards
>
> Shailendra Pal
>
> Research Scholar
> Plant Ecology Lab
> (Prof. S.C. Garkoti)
> School of Environmental Sciences
> JNU, New Delhi
> 110067
>
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>
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