[R-sig-phylo] RMesquite package

[Ayelet Salman]

Dear r-SIG-phylo members,

I have tried to call the RMesquite package from R but got an error that it
is not available.
Do you know how to download and install RMesquite (on windows or server)?

Any other idea how to use Mesquite or the pairwise comparison tool
(Maddison 2000) on a large scale data?

Best,
Ayelet

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[Hilmar Lapp]

Hi Ayelet,

Instructions for installing RMesquite are on the project’s homepage:
http://rmesquite.r-forge.r-project.org

Let us know if the information there doesn’t answer your question.

-hilmar

Post by Ayelet Salman
Dear r-SIG-phylo members,
I have tried to call the RMesquite package from R but got an error that it
is not available.
Do you know how to download and install RMesquite (on windows or server)?
Any other idea how to use Mesquite or the pairwise comparison tool
(Maddison 2000) on a large scale data?
Best,
Ayelet
[[alternative HTML version deleted]]
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[Hilmar Lapp]

Ayelet - If you provide the exact error that prevents you from loading RMesquite, I can try to see what the underlying cause might be. I can’t help you with using Mesquite itself , but others on the list may, which is why I’m copying the list.

Jeannine - I don’t know right now which version(s) of R won’t work with RMesquite. But the rJava package that it’s dependent on has I believe undergone some changes recently, so I’m not surprised if recent versions of R don’t work. (Can you report the error you were getting?)

I think if there’s some continued interest for this package what would be best is to migrate it to being hosted on Github. At the time that would have made integration with the R package management difficult, which is why we chose R-Forge, but I think now if anything it’s the opposite. And Github is what I (and probably most others here) use all the time, so would be vastly preferable for maintenance for that reason alone. I’ll look into that later this month (unless someone wants to beat me to it).

-hilmar

Sent from away

On Sep 23, 2017, at 3:31 AM, Ayelet Salman <***@gmail.com<mailto:***@gmail.com>> wrote:

Dear Hilmar,

I wasn't able to load RMesquite,
I will very much appreciate your help with the Mesquite software
Could you please guide me how to us Mesquite tools on batch data?

e.g. applying the pairwise comparison tool on trees and character data, for several different genera.
Currently I am loading the tree and data for every genera separately, and appling the pairwise comparison test for every genera. How can I save time and apply these same steps on the different genera data?

Thanks,
Ayelet

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On Wed, Sep 13, 2017 at 5:28 PM, Hilmar Lapp <***@duke.edu<mailto:***@duke.edu>> wrote:
Hi Ayelet,

Instructions for installing RMesquite are on the project’s homepage:
http://rmesquite.r-forge.r-project.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__rmesquite.r-2Dforge.r-2Dproject.org&d=DwMFaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y&m=XtWaA86jwYiS-E38jiKUh2-Wy8M5rAzczsBO5xyAJ8I&s=D2Hm5Yrj5iT0hEg8gG21JtHki93r-kOPIVgtUq7LA9g&e=>

Let us know if the information there doesn’t answer your question.

-hilmar

Post by Ayelet Salman
Dear r-SIG-phylo members,
I have tried to call the RMesquite package from R but got an error that it
is not available.
Do you know how to download and install RMesquite (on windows or server)?
Any other idea how to use Mesquite or the pairwise comparison tool
(Maddison 2000) on a large scale data?
Best,
Ayelet
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[Ayelet Salman]

Dear Hilmar, Jeannine and r-sig-phylo members,

Here's the error I get when trying to load RMesquite package on R, from
RStudio with R version 3.4.2
(the same error occurs when I try to load it on Linux with R versions: 215,
301, 310, 322, 342)

install.packages("RMesquite", repos="http://R-Forge.R-project.org")

Installing package into ‘D:/My Documents/R/win-library/3.4’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘RMesquite’ is not available (for R version 3.4.1)

install.packages("RMesquite")

Installing package into ‘D:/My Documents/R/win-library/3.4’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘RMesquite’ is not available (for R version 3.4.1)

Thanks for the help
Best,
Ayelet

Ayelet - If you provide the exact error that prevents you from loading
RMesquite, I can try to see what the underlying cause might be. I can’t
help you with using Mesquite itself , but others on the list may, which is
why I’m copying the list.
Jeannine - I don’t know right now which version(s) of R won’t work with
RMesquite. But the rJava package that it’s dependent on has I believe
undergone some changes recently, so I’m not surprised if recent versions of
R don’t work. (Can you report the error you were getting?)
I think if there’s some continued interest for this package what would be
best is to migrate it to being hosted on Github. At the time that would
have made integration with the R package management difficult, which is why
we chose R-Forge, but I think now if anything it’s the opposite. And Github
is what I (and probably most others here) use all the time, so would be
vastly preferable for maintenance for that reason alone. I’ll look into
that later this month (unless someone wants to beat me to it).
-hilmar
Sent from away
Dear Hilmar,
I wasn't able to load RMesquite,
I will very much appreciate your help with the Mesquite software
Could you please guide me how to us Mesquite tools on batch data?
e.g. applying the pairwise comparison tool on trees and character data,
for several different genera.
Currently I am loading the tree and data for every genera separately, and
appling the pairwise comparison test for every genera. How can I save time
and apply these same steps on the different genera data?
Thanks,
Ayelet
<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.avast.com_sig-2Demail-3Futm-5Fmedium-3Demail-26utm-5Fsource-3Dlink-26utm-5Fcampaign-3Dsig-2Demail-26utm-5Fcontent-3Dwebmail&d=DwMFaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y&m=XtWaA86jwYiS-E38jiKUh2-Wy8M5rAzczsBO5xyAJ8I&s=scG5V3F1V1aUsSumjdxEGkXJSzdFYTKIJK_9JZ4hzWU&e=> בלי
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Post by Hilmar Lapp
Hi Ayelet,
http://rmesquite.r-forge.r-project.org
<https://urldefense.proofpoint.com/v2/url?u=http-3A__rmesquite.r-2Dforge.r-2Dproject.org&d=DwMFaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y&m=XtWaA86jwYiS-E38jiKUh2-Wy8M5rAzczsBO5xyAJ8I&s=D2Hm5Yrj5iT0hEg8gG21JtHki93r-kOPIVgtUq7LA9g&e=>
Let us know if the information there doesn’t answer your question.
-hilmar

Post by Ayelet Salman
Dear r-SIG-phylo members,
I have tried to call the RMesquite package from R but got an error that

it

Post by Ayelet Salman
is not available.
Do you know how to download and install RMesquite (on windows or

server)?

Post by Ayelet Salman
Any other idea how to use Mesquite or the pairwise comparison tool
(Maddison 2000) on a large scale data?
Best,
Ayelet
[[alternative HTML version deleted]]
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Post by Ayelet Salman
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