phyloclim help

From what I have gathered, the maxent argument is a list of four elements:

app <- file.path("C:\\Documents and Settings\\hendrb\\Desktop\\R\\maxent.jar")
samples <- file.path("C:\\Documents and Settings\\hendrb\\Desktop\\R\\allspecies_swd.csv")
background <- file.path("C:\\Documents and Settings\\hendrb\\Desktop\\R\\background_swd.csv")
projections <- file.path("C:\\Documents and Settings\\hendrb\\Desktop\\R")
maxent <- list(app, samples, background, projections)

niche.equivalency.test(spec, n = 10, maxent, mx = 2000)

Hi all ?

My apologies if this is a redundant message.  I am a newbie to R and  
have had a terrible time trying to figure out how to set up an  
analysis.  I have installed and loaded the appropriate package  
(phyloclim), but I'm not sure I have defined the arguments correctly.

The usage for the command I?m trying to perform is:

niche.equivalency.test(spec, n, maxent, mx = 2000)

I am comfortable with the arguments "spec", "n", and "mx" but have  
had problems with "maxent"

maxent         is a list containing the location of the MAXENT  
application and its input files (see below)

From what I have gathered, the maxent argument is a list of four  
elements:

app                       the path to the MAXENT application (MAXENT  
is a JAVA program)

samples               the path to a SWD-formatted file with sample  
points (e.g., samples.csv)

background         the path to a SWD-formatted file with background  
points (e.g., background.csv)

projections       the path to a folder containing environmental GIS  
layers to be used for projection of the MAXENT models

Suppose all of these files are placed into the directory ?C: 
\Documents and Settings\hendrb\Desktop\R?.   Can anyone determine if  
I'm on the right track with the following syntax or am I way off?

app <- file.path("C:\\Documents and Settings\\hendrb\\Desktop\\R\ 
\maxent.jar")
samples <- file.path("C:\\Documents and Settings\\hendrb\\Desktop\\R 
\\allspecies_swd.csv")
background <- file.path("C:\\Documents and Settings\\hendrb\\Desktop 
\\R\\background_swd.csv")
projections <- file.path("C:\\Documents and Settings\\hendrb\ 
\Desktop\\R")
maxent <- list(app, samples, background, projections)

When I try to execute the command niche.equivalency.test based on  
the above information, I get the following statement:

niche.equivalency.test(spec, n = 10, maxent, mx = 2000)

Error in read.table(file = file, header = header, sep = sep, quote =  
quote,  :
  'file' must be a character string or connection

I'm incredibly confused by all of this and sincerely appreciate any  
help you can provide.

Regards,

Brent
	

On Jun 13, 2012, at 6:29 PM, Brent Hendrixson wrote:

Hi all ?

My apologies if this is a redundant message.  I am a newbie to R and  
have had a terrible time trying to figure out how to set up an  
analysis.  I have installed and loaded the appropriate package  
(phyloclim), but I'm not sure I have defined the arguments correctly.

The usage for the command I?m trying to perform is:

niche.equivalency.test(spec, n, maxent, mx = 2000)

You might give the name of the package. (I'm not likely to have any  
experience with that package, but it might ring a bell so someone with  
the right background.)

I am comfortable with the arguments "spec", "n", and "mx" but have  
had problems with "maxent"

maxent         is a list containing the location of the MAXENT  
application and its input files (see below)

From what I have gathered, the maxent argument is a list of four  
elements:

app                       the path to the MAXENT application (MAXENT  
is a JAVA program)

samples               the path to a SWD-formatted file with sample  
points (e.g., samples.csv)

background         the path to a SWD-formatted file with background  
points (e.g., background.csv)

projections       the path to a folder containing environmental GIS  
layers to be used for projection of the MAXENT models

Suppose all of these files are placed into the directory ?C: 
\Documents and Settings\hendrb\Desktop\R?.   Can anyone determine if  
I'm on the right track with the following syntax or am I way off?

app <- file.path("C:\\Documents and Settings\\hendrb\\Desktop\\R\ 
\maxent.jar")
samples <- file.path("C:\\Documents and Settings\\hendrb\\Desktop\\R 
\\allspecies_swd.csv")
background <- file.path("C:\\Documents and Settings\\hendrb\\Desktop 
\\R\\background_swd.csv")
projections <- file.path("C:\\Documents and Settings\\hendrb\ 
\Desktop\\R")
maxent <- list(app, samples, background, projections)

When I try to execute the command niche.equivalency.test based on  
the above information, I get the following statement:

niche.equivalency.test(spec, n = 10, maxent, mx = 2000)

Error in read.table(file = file, header = header, sep = sep, quote =  
quote,  :
  'file' must be a character string or connection

Right. So what is the object named "spec"? The R interpreter is  
expecting a file name or a connection object.

I'm incredibly confused by all of this and sincerely appreciate any  
help you can provide.

Regards,

Brent
	

David Winsemius, MD
West Hartford, CT

Hi David -

Thanks for the response.

On Jun 13, 2012, at 6:29 PM, Brent Hendrixson wrote:

Hi all ?

My apologies if this is a redundant message.  I am a newbie to R and
have had a terrible time trying to figure out how to set up an
analysis.  I have installed and loaded the appropriate package
(phyloclim), but I'm not sure I have defined the arguments  
correctly.

The usage for the command I?m trying to perform is:

niche.equivalency.test(spec, n, maxent, mx = 2000)

You might give the name of the package. (I'm not likely to have any
experience with that package, but it might ring a bell so someone  
with
the right background.)

The package is "phyloclim" (evolutionary biology).

I am comfortable with the arguments "spec", "n", and "mx" but have
had problems with "maxent"

maxent         is a list containing the location of the MAXENT
application and its input files (see below)

From what I have gathered, the maxent argument is a list of four
elements:

app                       the path to the MAXENT application (MAXENT
is a JAVA program)

samples               the path to a SWD-formatted file with sample
points (e.g., samples.csv)

background         the path to a SWD-formatted file with background
points (e.g., background.csv)

projections       the path to a folder containing environmental GIS
layers to be used for projection of the MAXENT models

Suppose all of these files are placed into the directory ?C:
\Documents and Settings\hendrb\Desktop\R?.   Can anyone determine  
if
I'm on the right track with the following syntax or am I way off?

app <- file.path("C:\\Documents and Settings\\hendrb\\Desktop\\R\
\maxent.jar")
samples <- file.path("C:\\Documents and Settings\\hendrb\\Desktop\ 
\R
\\allspecies_swd.csv")
background <- file.path("C:\\Documents and Settings\\hendrb\ 
\Desktop
\\R\\background_swd.csv")
projections <- file.path("C:\\Documents and Settings\\hendrb\
\Desktop\\R")
maxent <- list(app, samples, background, projections)

When I try to execute the command niche.equivalency.test based on
the above information, I get the following statement:

niche.equivalency.test(spec, n = 10, maxent, mx = 2000)

Error in read.table(file = file, header = header, sep = sep, quote =
quote,  :
 'file' must be a character string or connection

Right. So what is the object named "spec"? The R interpreter is
expecting a file name or a connection object.

The object "spec" is a vector of mode = character and length = 2 (it  
contains the names of two different species that I'm comparing).  I  
did define it correctly (to my knowledge).  It looks like:

spec <- c("aphonopelma_mojave", "aphonopelma_newmojave")

I'm just unsure if everything else for the "maxent" argument is  
defined correctly and whether I have set up the list appropriately.   
If the syntax is okay, then I just need to check the files.   
Unfortunately, the error message does not indicate which file is  
throwing stuff off...

Looking at the package documentation I see this:

maxent: A list containing the location of the MAXENT application and
its input ?les (see
details).

Maybe I was wrong about 'spec' and the malformed argument is 'maxent'.
If I had been constructing it I would have created a _named_ list:

maxent <- list( app =app,
samples =samples,
background, # cannot tell if a csv file meets the
requiremtn
# "The path to a SWD-formatted ?le with
background points."
projections =projections) # that value .../R looks
pretty suspicious, too.

Hi David -

Looking at the package documentation I see this:

maxent: A list containing the location of the MAXENT application and
its input ?les (see
details).

Maybe I was wrong about 'spec' and the malformed argument is  
'maxent'.
If I had been constructing it I would have created a _named_ list:

maxent <- list( app =app,
samples =samples,
background, # cannot tell if a csv file meets the
requiremtn
# "The path to a SWD-formatted ?le with
background points."
projections =projections) # that value .../R looks
pretty suspicious, too.

Your advice definitely helped - THANK YOU!  However, I'm now getting  
another error that seems to be tied to the maxent java program  
itself.  Here's the syntax I have used for the  
niche.equivalency.test (recall that it consists of 4 elements: spec,  
n, maxent, mx=2000)

spec <- c("aphonopelma_mojave", "aphonopelma_newmojave")

app <- file.path("C:\\Documents and Settings\\hendrb\\Desktop\\R\ 
\maxent.jar")

samples <- file.path("C:\\Documents and Settings\\hendrb\\Desktop\\R\ 
\samples.csv")

background <- file.path("C:\\Documents and Settings\\hendrb\\Desktop\ 
\R\\background.csv")

projections <- file.path("C:\\Documents and Settings\\hendrb\\Desktop 
\\R")

maxent <- list(app=app, samples=samples, background=background,  
projections=projections)

After I defined each of those, I tried to execute the command as  
follows:

niche.equivalency.test(spec, n=100, maxent, mx=2000)

And here was the message I received:

Unable to access jarfile C:\Documents

Error in file(file, "r") : cannot open the connection
In addition: Warning messages:
1: running command 'java -mx2000m -jar C:\Documents and Settings 
\hendrb\Desktop\R\maxent.jar -e R.phyloclim.temp/background.csv -s  
R.phyloclim.temp/samples.csv -j C:\Documents and Settings\hendrb 
\Desktop\R -o R.phyloclim.temp/out -r removeduplicates nopictures  
outputformat=raw autorun' had status 1
2: In file(file, "r") :
  cannot open file 'aphonopelma_mojave_C:\Documents and Settings 
\hendrb\Desktop\R.asc': Invalid argument

Like I mentioned, it seems that this particular error is unrelated  
to R code but I'm unsure why the jarfile (maxent.jar) cannot be  
accessed.

Any thoughts?

The above command did produce a new file that serves as the input  
for the jarfile.

Thanks again for your help!

Brent
		 	   		

CC: r-help at r-project.org
From: dwinsemius at comcast.net
To: behendrixson at hotmail.com
Subject: Re: [R] phyloclim help
Date: Fri, 15 Jun 2012 16:45:51 -0400


On Jun 15, 2012, at 3:43 PM, Brent Hendrixson wrote:

Hi David -

Looking at the package documentation I see this:

maxent: A list containing the location of the MAXENT application and
its input ?les (see
details).

Maybe I was wrong about 'spec' and the malformed argument is
'maxent'.
If I had been constructing it I would have created a _named_ list:

maxent <- list( app =app,
samples =samples,
background, # cannot tell if a csv file meets the
requiremtn
# "The path to a SWD-formatted ?le with
background points."
projections =projections) # that value .../R looks
pretty suspicious, too.

Your advice definitely helped - THANK YOU! However, I'm now getting
another error that seems to be tied to the maxent java program
itself. Here's the syntax I have used for the
niche.equivalency.test (recall that it consists of 4 elements: spec,
n, maxent, mx=2000)

spec <- c("aphonopelma_mojave", "aphonopelma_newmojave")

app <- file.path("C:\\Documents and Settings\\hendrb\\Desktop\\R\
\maxent.jar")

samples <- file.path("C:\\Documents and Settings\\hendrb\\Desktop\\R\
\samples.csv")

background <- file.path("C:\\Documents and Settings\\hendrb\\Desktop\
\R\\background.csv")

projections <- file.path("C:\\Documents and Settings\\hendrb\\Desktop
\\R")

maxent <- list(app=app, samples=samples, background=background,
projections=projections)

After I defined each of those, I tried to execute the command as
follows:

niche.equivalency.test(spec, n=100, maxent, mx=2000)

And here was the message I received:

Unable to access jarfile C:\Documents

That hanging "Documents" being listed as the file target makes me
think that the file specification is creating errors due to spaces in
Windows directories. In Windows it is often the case that backslashes
need to be doubled or replaced with forward slashes.I see that you
already know that, but would have tried the forward slash gambit as
well. (I am not sure why you are passing hte results of file.path(...)
when you already have a complete file name. I would also try just
giving it a file specification with just a character argument.)

Error in file(file, "r") : cannot open the connection
In addition: Warning messages:
1: running command 'java -mx2000m -jar C:\Documents and Settings
\hendrb\Desktop\R\maxent.jar -e R.phyloclim.temp/background.csv -s
R.phyloclim.temp/samples.csv -j C:\Documents and Settings\hendrb
\Desktop\R -o R.phyloclim.temp/out -r removeduplicates nopictures
outputformat=raw autorun' had status 1
2: In file(file, "r") :
cannot open file 'aphonopelma_mojave_C:\Documents and Settings
\hendrb\Desktop\R.asc': Invalid argument

Like I mentioned, it seems that this particular error is unrelated
to R code but I'm unsure why the jarfile (maxent.jar) cannot be
accessed.

Any thoughts?

The above command did produce a new file that serves as the input
for the jarfile.

Thanks again for your help!

Brent

David Winsemius, MD
West Hartford, CT