Re: [R] spatial analysis using quickPCNM

[Jeff Newmiller]

I don't know if I will be able to help solve your problem, but failure to 
follow the recommendations in the Posting Guide was probably getting you off in 
the wrong foot when you posted on the other (more appropriate?) mailing list, 
as it is here. 

A) Code is garbled. Post using plain text format... this is a setting you have 
to choose in your email program. 

B) Code is not reproducible. We cannot run your code to get your error due to 
missing library statements and no data. The Posting Guide and Google have 
suggestions for how you can make your example reproducible. 

C) Assuming you are using the PCNM package, the documentation found by Google 
(which you can probably read using ?quickPCNM) says quickPCNM expects a matrix, 
but it looks like you are giving it a data frame. Read your introductory R 
training materials (e.g. the Introduction to R document that ships with R) to 
understand the distinction.  But I have never used this function so this could 
be a red herring. 

Please go read the Posting Guide. 
-- 
Sent from my phone. Please excuse my brevity.

On January 23, 2017 6:42:28 AM PST, Andrew Halford  
wrote:
>Hi Listers,
>
>I posted this message to the R-sig-ecology group last Friday but have
>not
>had a response hence my post here.
>
>I have been trying to run spatial analyses on a fish community dataset.
>
>My fish dataset has 114 species(variables) x 45 sites
>My spatial dataset has the Lat and Long values for each site, converted
>to
>cartesian coordinates
>
>
>
>> fish <- read.table(file.choose())> latlong <-
>read.table(file.choose()) > fish.h <- decostand (fish, "hellinger")>
>fish.PCNM.quick <- quickPCNM(fish.h,latlong)
>
>Truncation level = 639.5348
>Time to compute PCNMs = 0.82  sec Error in if (temp2.test[1, 5] <=
>alpha) { : argument is of length zeroTiming stopped at: 1.06 0.05 1.19
>
>I do not understand the error message coming up and would appreciate
>some advice.
>
>Andy

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[R] spatial analysis using quickPCNM

[Andrew Halford]

Hi Listers,

I posted this message to the R-sig-ecology group last Friday but have not
had a response hence my post here.

I have been trying to run spatial analyses on a fish community dataset.

My fish dataset has 114 species(variables) x 45 sites
My spatial dataset has the Lat and Long values for each site, converted to
cartesian coordinates



> fish <- read.table(file.choose())> latlong <- read.table(file.choose()) > 
> fish.h <- decostand (fish, "hellinger")> fish.PCNM.quick <- 
> quickPCNM(fish.h,latlong)

Truncation level = 639.5348
Time to compute PCNMs = 0.82  sec Error in if (temp2.test[1, 5] <=
alpha) { : argument is of length zeroTiming stopped at: 1.06 0.05 1.19

I do not understand the error message coming up and would appreciate
some advice.

Andy


-- 
Andrew Halford Ph.D
Research Scientist (Kimberley Marine Parks)
Dept. Parks and Wildlife
Western Australia

Ph: +61 8 9219 9795
Mobile: +61 (0) 468 419 473

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