Re: [R-sig-eco] error message with function rda of package vegan
Feel free to send your data to me, off list. I'll take a look at what might be
going on inside vegan.
Gavin
Sent from my HTC
- Reply message -
From: "Duarte Viana"
Date: Mon, Jun 11, 2012 20:47
Subject: [R-sig-eco] error message with function rda of package vegan
To: "Sarah Goslee"
Cc: "r-sig-ecology@r-project.org"
Hi,
Thank you for your reply. It's not easy to give you a reproducible
example, because this is a very specific case (something in my data ,
I believe). The only way is to send the data and try yourself. If
someone is willing to do that, I would be grateful.
I can send the response matrix and the explanatory matrix, and all one
has to do is load library vegan, load the data, and run the rda
function:
library(vegan)
resp<-read.table("resp.txt", head=F, sep="\t")
expl<-read.table("expl.txt", head=F, sep="\t")
myrda<-rda(resp, expl)
Thanks,
Duarte
On Mon, Jun 11, 2012 at 6:42 PM, Sarah Goslee wrote:
> Hi,
>
> On Mon, Jun 11, 2012 at 12:35 PM, Duarte Viana wrote:
>> Hello all,
>>
>> Apologies for cross postings.
>>
>> I am running the function "rda" of the vegan library, like I did many
>> times without having troubles, and I get the following error message:
>> "Error in if (rank) { : argument is not interpretable as logical".
>>
>> I am just testing a response matrix against a single explanatory
>> matrix, which is the result of a model matrix with 4 dummy variables
>> (coding for a factor of 5 levels).
>>
>> myrda<-rda(resp, expl)
>>
>> When I, for instance, change the response matrix, it goes well.
>>
>> Does anyone know what might be happening?
>
> Not without a reproducible example, I'm afraid.
>
> Sarah
>
> --
> Sarah Goslee
> http://www.functionaldiversity.org
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[R-sig-eco] error message with function rda of package vegan
Hi,
Thank you for your reply. It's not easy to give you a reproducible
example, because this is a very specific case (something in my data ,
I believe). The only way is to send the data and try yourself. If
someone is willing to do that, I would be grateful.
I can send the response matrix and the explanatory matrix, and all one
has to do is load library vegan, load the data, and run the rda
function:
library(vegan)
resp<-read.table("resp.txt", head=F, sep="\t")
expl<-read.table("expl.txt", head=F, sep="\t")
myrda<-rda(resp, expl)
Thanks,
Duarte
On Mon, Jun 11, 2012 at 6:42 PM, Sarah Goslee wrote:
> Hi,
>
> On Mon, Jun 11, 2012 at 12:35 PM, Duarte Viana wrote:
>> Hello all,
>>
>> Apologies for cross postings.
>>
>> I am running the function "rda" of the vegan library, like I did many
>> times without having troubles, and I get the following error message:
>> "Error in if (rank) { : argument is not interpretable as logical".
>>
>> I am just testing a response matrix against a single explanatory
>> matrix, which is the result of a model matrix with 4 dummy variables
>> (coding for a factor of 5 levels).
>>
>> myrda<-rda(resp, expl)
>>
>> When I, for instance, change the response matrix, it goes well.
>>
>> Does anyone know what might be happening?
>
> Not without a reproducible example, I'm afraid.
>
> Sarah
>
> --
> Sarah Goslee
> http://www.functionaldiversity.org
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Re: [R-sig-eco] error message with function rda of package vegan
Hi,
On Mon, Jun 11, 2012 at 12:35 PM, Duarte Viana wrote:
> Hello all,
>
> Apologies for cross postings.
>
> I am running the function "rda" of the vegan library, like I did many
> times without having troubles, and I get the following error message:
> "Error in if (rank) { : argument is not interpretable as logical".
>
> I am just testing a response matrix against a single explanatory
> matrix, which is the result of a model matrix with 4 dummy variables
> (coding for a factor of 5 levels).
>
> myrda<-rda(resp, expl)
>
> When I, for instance, change the response matrix, it goes well.
>
> Does anyone know what might be happening?
Not without a reproducible example, I'm afraid.
Sarah
--
Sarah Goslee
http://www.functionaldiversity.org
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R-sig-ecology@r-project.org
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[R-sig-eco] error message with function rda of package vegan
Hello all,
Apologies for cross postings.
I am running the function "rda" of the vegan library, like I did many
times without having troubles, and I get the following error message:
"Error in if (rank) { : argument is not interpretable as logical".
I am just testing a response matrix against a single explanatory
matrix, which is the result of a model matrix with 4 dummy variables
(coding for a factor of 5 levels).
myrda<-rda(resp, expl)
When I, for instance, change the response matrix, it goes well.
Does anyone know what might be happening?
Thanks,
Duarte
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R-sig-ecology@r-project.org
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[R-sig-eco] cozigam
hi i try to find regression between clupeidae,with temperature,salinity and depth. the response variable is inclued many zero ( 86 from 133 observed) therefore i used this code : res <- cozigam(Clupeidae~s(temperature,salinity)+s(depth), constraint = "proportional", family = gaussian) the result: iteration = 2norm = 1.001743 iteration = 3norm = 0.3377464 iteration = 4norm = 9.172232e-05 == estimated alpha = -0.5337883 ( 0.1789113 ) estimated delta = -0.0009891505 ( NaN ) == Warning message: In sqrt(V.theta[2, 2]) : NaNs produced what is exactly meaning? thanks for your help -- Mahnaz [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
