It can be a little tricky. Are the R image files being output at all?

I e-mailed the authors. They sent me a zipped folder containing R functions compatible with the latest R version. Graphics get embedded nicely now.

Hi Uzay, I have same problem with R-lequine. Can u send me this zipped file u got.

it could help me ([email protected])!

Mohamed, please check your e-mail.

I am sorry Uzay, but I got nothing on my email. Could you please re send it?

Thank u in advance!

Hello all,

I downloaded the latest version of R functions form the Arlequin website and updated the files in my Arlequin program folder; files are for R version 3.01, although I'm using R 3.1.0. I also downloaded R 3.0.1 and specified that version's Rcmd file in the configuration, but I can't get the graphs to work at all (not in R 3.1.0 either).

Anyone else having this problem and hopefully a solution?

Hi Silke, I use Arlequin 3.5.1.3 and can send you the associated R functions if you give me your mail.

Hi Uzay, I am using Arlequin 3.5.1.3 and cannot get graphics to work. Could you please send me the associated R functions ([email protected])

Hi Uzay, I just got the R functions from another source...and it works fine, guess i was using the wrong functions!!??

Outdated R functions! I am glad things are working for most of you. Silke (one of the users posted before) is unfortunately still having problems. Moses can you help her? Perhaps your version works for her? 

Hi Uzay, I am having the same problem! Could you please email me the R functions ([email protected]) thanks!

i am have the same problem!!! Could you plese me the R function ([email protected]).Thank you!

Hello,

Same here! Could someone send me the R-functions too? Thanks in advance :) Carina

[email protected]

Hello,

Same problem.

R-functions are at the web site of Arlequin (http://cmpg.unibe.ch/software/arlequin35/Arl35Downloads.html) at R functions topics following the different systems.

I attached here also.

Thanks Gael Lecellier. I can see the figures now.

hello again,

I am still confused about how R is called from Arlequin. I gather that in the Arlequin configuration tab you have to specify the path to the Rcmd.exe executable? After running an analysis, when I click the Rcmd button it doesn't do anything except a black box appears for a second. I also get parsing errors with the XML output. Am i doing this in the right order? many thanks in advance,

carina

Hi carina,

What I did is the following: I installed the package provided two answers before by Gael Lecellier, then I unzipped them in the arlequin directory and substituted the old ones. Then I ran this Rcmd button to have this black window for some seconds. Finally you open the results from the Arlequin GUI and you will find the figures there.

regards

Nawar

Hi Nawar,

I am still not seeing any figures, I did replace the new files in the Arlequin directory but, as Carina said, I get the 1second black box and that's it. If you have that black box thingy as well, then where do you find the figures?

Silke

Hi Silke, 

You find them when you open the results directly from Arlequin user interface "view results" after running the Rcmd and getting this black window from some seconds. Please be Sure that you had correctly located the Rcmd.exe file for Arlequin. 

Regards

Nawar

Hi both,

I have done all those steps and when I click "view results" after clicking the Rcmd the results browser just gives me ax XML parsing error message again! I have linked to the Rcmd.exe file in the R folder. Not sure again what I am doing wrong :(

thanks

Carina

Hi Carina,

Did you try to change your default browser?. Especially if you are using MOZILLA, you need some more configurations. I will recommend using google chrome or internet explorer for this time.

Regards

Nawar

Hi Nawar,

thanks again for your reply. I am using Firefox but they recommend using it in the Arlequin manual...unless I should change some settings? I just tried Chrome and it gave an error message and IE just couldn't cope and crashed!

all the best,

carina

Hi Carina,

Yes, one has to change one option in the security settings when you use mozilla as follows:

1) Type about:config in Firefox address bar

2) Change security.fileuri.strict_origin_policy to false

Bests

Nawar

Hi Nawar,

I have changed those settings and tried again and still no luck :(

thanks

carina

Hi Carina, 

Then I have no clue what could be the problem.... Better contact the developing team. Good luck. 

Regards 

Nawar

thanks for all the help Nawar! I will get in touch with them.

best,

carina

Hi , I followed all instructions of manual but I have the same problem : the graphics don´t embedded in the XML output . Can anybody help me with this? . Please ,send me the folder of R-functions that you mentioned , my email is [email protected]

Thanks in advance

Hi, I have the same problem with Arlequin, do you have solutions to R graphics in XML output? Thanks

Faye if you could send me your e-mail I can send you the R funtions folder I use. [email protected]

Hi Uzay,

you can send me the R function folder in [email protected].

thanks you in advance

regards

Hi Uzay and Faye, could I have the R functions that you use to parse XML files from Arlequin as well? My email is: [email protected]

Thank you!

Hi Uzay and Faye, could I have the R functions that you use to parse XML files from Arlequin as well? My email is: [email protected]

Hi Uzay and Fay,

Would you mind sending me the R functions you used to parse XML files from Arlequin as well? I'm having similar problems. My email: [email protected]. Thanks!

I am having the same issue with R graphics not embedding in XML files. I am running R 3.1.2 and the latest Arlequin ver 3.5.1.2. I have downloaded the r graphics package from the Arlequin website, however it is only for R version 3.0.1. Any solutions? Thanks  

Hi Bridie, are you running Arlequin on a MacOS or Windows? I could not run the R-functions on a Mac, then I emulated a Windows session and could get the graphs done.  

Hi Ana, Thanks for the suggestion, however I am running on Windows. Still not sure what the issue is?

Hi Bridie, are you sure that you are pointing the correct path to run R in the arlequin settings?

Hi Uzay,

you can send me the R function folder in [email protected]

Anwesha Saha, the Rcmd.exe should be in R/R3.2.0/bin/*/Rcmd.exe

* stands for either i386 or x64, depending if your OS is 32-bit or 64-bit.

About viewing the results on the browser:

I am having the same issue with Internet Explorer. I tried seeing the results on Google Chrome but had no success. When I switched to Firefox I was able to properly see the results with the embedded graphics. The PDF manual tells you how to solve the styling issue on Firefox, I am now looking for solutions in the other browsers. If you have Firefox, type about:config in the address bar, then search for security.fileuri.strict_origin_policy  and change the value to FALSE

Dear Uzay, 

I have the same problem with R function in Arlequin (3.5.1.3). May you please send me also the associated R functions? my Email: [email protected] ).

Thanks for your help

I followed the instruction of Ana Carolina Arcanjo. Use firefox, and the latest R package, with latest arlequin, and everthing is ok. By the way if you finish project, you must press the stop button. I use windows 7 64bit.

Dear all, 

For those of you still dealing with this problem, here is what did to finally see the graphics on the XML file after running an analysis on Arlequin.

First of all, I will give you the setup of my system/computer.

I use a Mac Pro Mid 2012 with OS 10.10.3 (Yosemite). However, I am running Arlequin version 3.5.2.1 (just downloaded it) through Parallel desktop 9 for Mac. I have Windows XP running on my Parallel. The internet explorer 8 is my default browser.

I did added the version of Arlequin because with the previous one (3.5.1.3) it didn't work at all. Now, make sure you really have the latest version, you should get this info from: menu help-> about Arlequin, once you have the software opened. I had something that said 3.5.2.1 in the software name/top bar, but instead it was a previous version according to the help menu (perhaps I didn't dowloaded the right version since the beginning).

So, how can you make sure you have the latest version on your computer? on version 3.5.2.1 you should see available the option: Use 64bit external arlecore.... exactly like the first screenshot from Arlequin's website: http://cmpg.unibe.ch/software/arlequin35/img/Configuration.PNG

In the previous version, this option was not available.

I also downgraded my R version to 3.0.1 (http://cran.r-project.org/bin/windows/base/old/3.1.0/) because the R-Functions folder for Arlequin were written on that version of R (you might try with your current version before install/uninstall R, because perhaps this might not be the real issue).

Even though this R version is older, it does give you the application for 32 and 64 bits. My mac is 64 bit, however, I was not able to get the graphics (they are not written to the graphics folder) using the Rcmd for 64bit. So, I gave the path to 32 bits instead (on your computer, it should more or less look like: C:\Program Files\R\R-3.0.1\bin\i386)

The option Use 64 bit external arlecore... should be also unchecked.

How can I make sure R is properly working through Arlequin. If you have the XML output checked, you can request the graphics via Rcmd. You will see the DOS window for a few seconds just like everyone has mentioned/described. If your internet explorer browser open the XML file without a problem, you should see the graphics already with all the extra information from the analyses you requested Arlequin to do it.

However, if you still have a problem reading the file, you can check the graphics folder that is created by Arlequin. If R is working properly, you should expect some PNG files in that folder. Otherwise, you are still having problems with the communication between R and Arlequin. If you see those files, but cannot open the XML, then perhaps is a problem with your browser (it was not on my case).

I also tried to open the XML via firefox (version 36.0.4) and it worked just fine (I did changed the config of firefox following the Arlequin's manual thought). Not sure, if it would work without changing that.

In my opinion, the error message I was getting when the analysis was finished (when the XML is supposed to be opened) was due to the fact I had the wrong Arlequin version, as simple as that!

Hope this can help others.

Cheers,

Tiago

I followed your steps Tiago and finally I got the graphics straight!

I'm running a Win7 (64-bit).

What I did:

- Updated Arlequin to v3.5.2.1 and activated the option (tested and still nothing)

- Downgraded R to v3.0.1 (parallel installation, you know) and guided Arlequin to the x64

- Called Rcmd AFTER running the analysis (I think that was a key point btw).

Thanks for your comprehensive answer and abraços from RS, Tiago!

Tiago you're the man!!!!! :) :) :)

Oh dear, am still having the same problems!

I have Arlequin, 3.5.2.1, R version 3.0.1, Windows 7 64-bit and am directing the Rcmd to the x64 bin folder for R-3.0.1. When I click the XML box an error opens in my browser (Firefox) "XML Parsing Error: not well-formed" when I run Arlequin. Even if I try clicking the Rcmd button on Arlequin after an analysis has run, the black box appears for a second but then disappears. I can't see any graphics file in the folder I am working from. Frustrating!!

It seems Arlequin can't keep up with new versions of R. You might want to scan the thread and see which R version works with which Arlequin version. I can send you my  R library but it appears that my version doesn't work in newer Arlequin versions as well. Yes frustrating but this is a free software...

Uzay, I was following the threads extensively and used exactly the software versions recommended by Tiago and Guillermo i.e. R v3.0.1, Arlequin v3.5.2.1 and linking to Rcmd in the 32 or 64 bit bins depending on the OS...as you can see in my own message...I understand it is free software :)

hi guys,

this thing with rmcd in arlequin just took whole my day, as Carina I also can not just get those png files from R. any suggestions? my pc 64bit, did all the required things though!

Hi Shahzad,

I installed R, set a path to rmcd from arlequin, then also did a path for text editor. The R functions folder inside arlequin software is there. I run the software, then called rmcd function, just only a black screen then nothing, I do not get the point. Can you please step by step explain it?

can somebody send me Arlequin v3.5.2.1 version? from Arlequins web page, it has been updated to 3.5, email is [email protected]

Dear fellows,

it is about 2 days since I lost myself in the Arlequin XML files in order to get some fancy R graphics, since these visualizations help more to interpret than just staring at the data.

Here is the deal;

1. download the Arlequin 3.5 (it does not matter which version), if you want to involve R with XML outputs in your data analysis, just download beyond Arlequin 3.11 where you can call Rmcd function which is near to the Start button. Since Arlequin 3.11 and older version do not have Rmcd button to fly with fancy outputs :)

2. install the R, it does not matter which version (there are some speculations that Arlequin best adapts with older R versions, they say that reason maybe the software was written in older scripts, but it is not like that!)

3. in arlequin confugartion, select the XML output (you can and welcome to use other options, so don't stick to my order), and also set text editor exe file

4. run the analysis, then call the Rmcd, in the meantime if your browser like mozilla automatically opens the results. If mozilla does not automatically open, then read the Arlequin manual how to manage. Watch out for PC operating system 32 or 64 bit

5. As Tiago said before, if your Arlequin adapts to R, it will automaically open a folder named 'Graphics' nearby to your Arlequin XML and other results. At least you can enjoy the R graphics you get as jpeg or png extension

Remark!!!

One thing to do is - in the attached Rfunctions file, there stands 3 folders (Rfunctions, rParsingSettings and rParsingSettiings.r.Rout). Just copy and paste 'rParsingSettings and rParsingSettiings.r.Rout' inside Rfunctions folder. And that is!!!

rParsingSettings and rParsingSettiings.r.Rout' should be together standing with Rfunctions in order to get some nice graphics. Because there some certain scripts which displays like Matrix of pairwise Fst.

Finally, do not stick to Mozilla firefox as a browser!!! I tried with old daddy Internet Explorer. It works, you can go with Chrome or Opera. There are no rules.

All the best with Arlequin and R analysis

Cheers

Nurlan

Thanks Nurlan! I hope your detailed note helps a whole new generation of Arlequin users... :)

please I have the same problem now could help me to resolve it

Hi all,

Thanks for this thread! I have everything running but I encountered a problem: I am looking for mismatch distribution for both spatial and demographic expansion models. Because just a few of my populations can't converge for the demographic expansion model, Arlequin can't finish the analysis and therefore I can't run R to give me the nice graphs... Do you know if it's possible to configure Arlequin to stop the analysis whenever it does not converge or to obtain graphs from the unfinished file? 

Cheers!

Hello,

I was wondering if there is a way to change the colors of the R graphics produced inside Arlequin 35.

Thanks

I solved the problem by deleting all the output from previous runs.

The generation of the graphics and embedding them in the XML does not seem to work with more recent versions of R (e.g., v3.4.0). I reinstalled v.3.0.1 of R and then things seemed to work fine.

 Hi Uzay, I am using Arlequin 3.5 . May you please send me the associated R functions ([email protected]).

Regards 

Hello Uzay, I'm having the same problem here (Arlequin 3.5). The graphs doesn't appear in the output folder. Could you send me the updated R functions??? hoping that would solve the problem... ([email protected])

Thank you!!

Regards!!

Hello ! I am using Arlequin 3.5 and have the same problems as above people. If anyone using this Arlequin version received Rcmd functions that work can you share them please ? greatly appreciated . eugenia

([email protected])

Update: I tried fixing the issue with the "rParsingSettings" and "rParsingSettings.r.Rout" fix mentioned above and it did not resolve my issue. However, I have fixed the issue by installing the older version of R as recommended above by Tiago José Pereira. It did install with a 64 bit Rcmd version, therefore I did not have to uncheck the "Use 64 bit external arlecore program for computations"

I am running Windows 7 Home Premium SP1 64 bit. I lost 2 days on this as well. I hope this helps the next person.

-Cheers!

I was also having this problem but I did as Stephen suggested, i.e. downloaded the older version of R and it ran! Yipee :-)

Thanks so much for all of your advice, I used it all.

I also installed the older version of R and problem solved! Thanks!

Definitely is just to install R 3.0.1 and solved problem!

Hi, I was able to get the graphics (only png format), but when I try with a different project it doesn´t work despite having the same configuration. The analysis performed well but the graphics folder is empty.

Any idea? Will be much appreciated.

Hello! I am using Arlequin 3.5 and the graphics folder is empty (R v3.0.1 and x32). I followed the advices from Tiago and I still can't generate the graphs. Any ideas how this continue to happen?

Thanks

Hello Uzay, I'm having the same problem here (Arlequin 3.5.2.2). The graphs doesn't appear in the output folder. Could you send me the updated R functions??? hoping that would solve the problem... ([email protected])

Thanks!

Hi fellows,

I have the same problem. Arlequin does not produce any graph. Everything has been configured well according to the quide and sill nothing. I have been changing versions of R-software (old and new). Arlequin creates only the folder for graphs but wothout anything inside. I did not work on Arlequin software for few years but when i was working i did not have such problem. Now new computer and big problem. Can anyone help? Please.

Hi Luana Joana Barreto Cabral ,

I cannot access the google drive link in your video for Rfunctions. Could you make it accessible please.

Thanks,

Prashanna

Thanks Luana

Downgrading R version worked for me.

Hi Uzay, I am using Arlequin 3.5 . Can you please send me the associated R functions ([email protected])

Thanks and Best regards

A super old thread but hoping someone has a foolproof answer by now... My graphics folder is still empty and I've replaced the Rfunctions folder but no luck

Latest version of Arlequin with R 2.11/2.12/2.13 versions will solve the XML visualization issue. I spent a hell lot of time on it! Sharing it here for everyone's convenience. Thank you.