I want to carry out a symbolic regression with R. The rgp package is the most recommended package on the internet but it was removed from CRAN.
https://cran.r-project.org/web/packages/rgp/index.html
Does anybody know some other equivalent packages in R?
An alternative package is the gramEvol package (on CRAN).
I wrote a blog post about it with several examples: https://blog.ephorie.de/symbolic-regression-genetic-programming-or-if-kepler-had-r
Ok, so you can download rgp from the (unofficial) repository of CRAN at github.com
You should start trying the git tool to do it. This way, once you've installed it, you can clone the repository with:
git clone https://github.com/cran/rgp.git
In the R/ folder of the repository (the local copy that you've downloaded or in the very github website of the rgp package) you should see all functions of the package, as .R files.
Other way to use these functions would be to build (R CMD build) the package, install it (install.packages("builtrepo.tgz",repos=NULL,type="source")) and load (with require or include).
Related
I need to have the tar.gz build version of a package from git.
The git link would look like
devtools::install_github('repo/package#x.1.0')
Let's assume it is
devtools::install_github("tidyverse/lubridate") but instead of installing I need the actual file so I can install it in in an offline container at some point.
The package I need is not on CRAN, on git only, and I need a specific version of the release, not the latest.
I tried to run a different download.file arguments, no success.
I am working on a package, and it imports the development version of the DT package from github as well as several other packages. If I want to distribute my package to a computer that does not have internet access, is there a way I can zip my package with all of its imports/depends so that I don't have to distribute separate zips for each of the packages that it imports/depends, and install each of the packages separately?
It would be nice to have a single tar.gz that contains everything. Is this possible?
Kind Regards
Well, if you use an R kernel for jupyter, and Conda installation, there is a way to create and distribute R bundle
Please read "Creating your custom R bundle", link: https://www.continuum.io/blog/developer/jupyter-and-conda-r
This, question, is, asked, over, and, over, and, over,
on the R-sig-finance mailing list, but I do not think it has been asked on stackoverflow.
It goes like this:
Where can I obtain the latest version of package XYZ that is hosted on R-forge? I tried to install it with install.packages, but this is what happened:
> install.packages("XYZ",repos="http://r-forge.r-project.org")
Warning message: package ‘XYZ’ is not available (for R version 2.15.0)
Looking on the R-forge website for XYZ, I see that the package failed to build.
Therefore, there is no link to download the source. Is there any other way
to get the source code? Once I get the source code, how can I turn that into a
package that I can load with library("XYZ")?
R-Forge may fail to build a package for a few different reasons. It could be that
the documentation has not been updated to reflect recent changes in the code. Or,
it could be that some of the dependencies were not available at build time.
You can checkout the source code using svn. First, search for the project on the
R-Forge website and go to the project home page -- for example http://r-forge.r-project.org/projects/returnanalytics/
Click the SCM link to get to a page like this http://r-forge.r-project.org/scm/?group_id=579
This page will tell you the command to use to checkout the project. In this case you get
This project's SVN repository can be checked out through anonymous access with the following command(s).
svn checkout svn://svn.r-forge.r-project.org/svnroot/returnanalytics/
If you are on Windows, you probably want to download and install TortoiseSVN
Once you have installed TortoiseSVN, you can right click in a Windows Explorer window and select
"SVN checkout". In the "URL of repository:" field, enter everything except the
"svn checkout " part of the command that you found on R-Forge. In this case, you'd
enter "svn://svn.r-forge.r-project.org/svnroot/returnanalytics/".
When you click OK, the project will be downloaded into the current directory.
If you are on a UNIX-alike system (or if you installed the command line client tools
when you installed TortoiseSVN for Windows, which is not the default), you can
type the command that R-forge gave you in your terminal (System terminal, not the R terminal)
svn checkout svn://svn.r-forge.r-project.org/svnroot/returnanalytics/
That will create a new directory under the current working directory that
contains all of the files in the package. In the top level of that directory
will be a subdirectory called "pkg". This particular project (returnanalytics)
contains more than one package.
ls returnanalytics/pkg
#FactorAnalytics MPO PApages PerformanceAnalytics PortfolioAnalytics
But some R-forge projects only have a single package. e.g.
svn checkout svn://svn.r-forge.r-project.org/svnroot/random/
#Checked out revision 14.
ls random/pkg
#DESCRIPTION inst man NAMESPACE R
Now that you have a local copy all of the code, if you would like to be able to
install the package, you have to build it first.
A WORD OF CAUTION: Since R-Forge failed to build the package, there is a good chance
that there are problems with the package. Therefore, if you just build it, you may find
that some things do not work as expected. In particular, it is likely that there
is missing or incomplete documentation.
If you are on a UNIX-alike system, the package can be built and installed relatively easily. For a multi-package project like returnanalytics, if you want to install, e.g. the
PortfolioAnalytics package, you can do it like this
R --vanilla CMD INSTALL --build returnanalytics/pkg/PortfolioAnalytics
"PortfolioAnalytics" is the name of the directory that contains the package that
you want to build/install. For a single-package project, you can build and install like
this
R --vanilla CMD INSTALL --build random/pkg
If you would like to build/install a package on Windows, see this question and follow the two links that #JoshuaUlrich provided
More information can be found in R Installation and Administration, the R-Forge User Manual, and the SVN manual.
If (and only if) you have the appropriate toolchain for your OS, then this may succeed:
# First download source file to your working directory
# As an example use browser to download pkg:partykit from:
# http://download.r-forge.r-project.org/src/contrib/partykit_1.1-2.tar.gz
# Move to working directory
# Or in the case of returnanalytics (which is a bundle of packages):
# http://r-forge.r-project.org/R/?group_id=579 and download the tar.gz (source)
# Then in R:
install.packages( "partykit_1.1-2.tar.gz", repo=NULL, type="source")
# for the first of the ReturnAnalytics packages:
install.packages( "Dowd_0.11.tar.gz", repo=NULL, type="source")
These direction should be "cross-platform". I'm not sure the directions in the accepted answer are applicable to Macs (OSX). (I later confirmed that they do "work" on a Mac but found the process more involved that what I suggested above. They do result in a directory that do contain the packages in a form that should succeed with R --vanilla CMD INSTALL --build pathToEachPackageSeparately)
It is also possible that the current version of the package you are trying to install requires a newer version of R, for example, you may see error like:
"ERROR: this R is version 2.15.0, package 'PerformanceAnalytics' requires R >= 3.0.0"
then you can try to update your R
or, if you are facing the same situation with me, which is trying to use pqR (currently using R version 2.15), you can find the out-of-date achieved package here:
http://cran.at.r-project.org/src/contrib/Archive/PerformanceAnalytics/
You can get here from R-Forge packages page -> "Stable Release: Get PerformanceAnalytics 1.4.3541 from CRAN" -> Old sources: PerformanceAnalytics archive
for example, you will find package PerformanceAnalytics version 1.1.0 just requires R >= 2.14
Good luck
Alternatively, you can install the particular package from GitHub, if it has a repo at GitHub.
I ran install.packages('ggfortify'), and got
Warning message: “package ‘ggfortify’ is not available (for R version
3.3.2)”
ggfortify was the GitHub repo for the same package.
The devtools library allows you to install a package from GitHub directly with install_github('username/repo').
library(devtools)
install_github('sinhrks/ggfortify')
I need to install R packages in several nodes (10+) in AWS.
I wont be able to open R shell in each and do install.packages("foo")
This will be done using a configuration management tool like Puppet and it'll be easier if i can do an apt-get installation of R packages automatically.
I found a list of R debian packages here:
http://cran.cnr.berkeley.edu/bin/linux/ubuntu/lucid/
But it does not contain all the packages that i need.
Is there a way to convert any R package and it's internal dependencies to a Debian package similar to the approach used in creating r-cran-*.deb?
Have you looked at http://debian-r.debian.net/ ?
All CRAN (and many other) packages already packaged
You can install packages without starting the R console. You can download the tar.gz packages from the cran website. For example here is the tar.gz for the randomForest package: http://cran.r-project.org/src/contrib/randomForest_4.6-7.tar.gz
R CMD INSTALL ${package}.tar.gz
The cran2deb project claims to do exactly this, turning an R package into a Debian package and noting the correct dependencies.
I haven't used it myself yet.
This, question, is, asked, over, and, over, and, over,
on the R-sig-finance mailing list, but I do not think it has been asked on stackoverflow.
It goes like this:
Where can I obtain the latest version of package XYZ that is hosted on R-forge? I tried to install it with install.packages, but this is what happened:
> install.packages("XYZ",repos="http://r-forge.r-project.org")
Warning message: package ‘XYZ’ is not available (for R version 2.15.0)
Looking on the R-forge website for XYZ, I see that the package failed to build.
Therefore, there is no link to download the source. Is there any other way
to get the source code? Once I get the source code, how can I turn that into a
package that I can load with library("XYZ")?
R-Forge may fail to build a package for a few different reasons. It could be that
the documentation has not been updated to reflect recent changes in the code. Or,
it could be that some of the dependencies were not available at build time.
You can checkout the source code using svn. First, search for the project on the
R-Forge website and go to the project home page -- for example http://r-forge.r-project.org/projects/returnanalytics/
Click the SCM link to get to a page like this http://r-forge.r-project.org/scm/?group_id=579
This page will tell you the command to use to checkout the project. In this case you get
This project's SVN repository can be checked out through anonymous access with the following command(s).
svn checkout svn://svn.r-forge.r-project.org/svnroot/returnanalytics/
If you are on Windows, you probably want to download and install TortoiseSVN
Once you have installed TortoiseSVN, you can right click in a Windows Explorer window and select
"SVN checkout". In the "URL of repository:" field, enter everything except the
"svn checkout " part of the command that you found on R-Forge. In this case, you'd
enter "svn://svn.r-forge.r-project.org/svnroot/returnanalytics/".
When you click OK, the project will be downloaded into the current directory.
If you are on a UNIX-alike system (or if you installed the command line client tools
when you installed TortoiseSVN for Windows, which is not the default), you can
type the command that R-forge gave you in your terminal (System terminal, not the R terminal)
svn checkout svn://svn.r-forge.r-project.org/svnroot/returnanalytics/
That will create a new directory under the current working directory that
contains all of the files in the package. In the top level of that directory
will be a subdirectory called "pkg". This particular project (returnanalytics)
contains more than one package.
ls returnanalytics/pkg
#FactorAnalytics MPO PApages PerformanceAnalytics PortfolioAnalytics
But some R-forge projects only have a single package. e.g.
svn checkout svn://svn.r-forge.r-project.org/svnroot/random/
#Checked out revision 14.
ls random/pkg
#DESCRIPTION inst man NAMESPACE R
Now that you have a local copy all of the code, if you would like to be able to
install the package, you have to build it first.
A WORD OF CAUTION: Since R-Forge failed to build the package, there is a good chance
that there are problems with the package. Therefore, if you just build it, you may find
that some things do not work as expected. In particular, it is likely that there
is missing or incomplete documentation.
If you are on a UNIX-alike system, the package can be built and installed relatively easily. For a multi-package project like returnanalytics, if you want to install, e.g. the
PortfolioAnalytics package, you can do it like this
R --vanilla CMD INSTALL --build returnanalytics/pkg/PortfolioAnalytics
"PortfolioAnalytics" is the name of the directory that contains the package that
you want to build/install. For a single-package project, you can build and install like
this
R --vanilla CMD INSTALL --build random/pkg
If you would like to build/install a package on Windows, see this question and follow the two links that #JoshuaUlrich provided
More information can be found in R Installation and Administration, the R-Forge User Manual, and the SVN manual.
If (and only if) you have the appropriate toolchain for your OS, then this may succeed:
# First download source file to your working directory
# As an example use browser to download pkg:partykit from:
# http://download.r-forge.r-project.org/src/contrib/partykit_1.1-2.tar.gz
# Move to working directory
# Or in the case of returnanalytics (which is a bundle of packages):
# http://r-forge.r-project.org/R/?group_id=579 and download the tar.gz (source)
# Then in R:
install.packages( "partykit_1.1-2.tar.gz", repo=NULL, type="source")
# for the first of the ReturnAnalytics packages:
install.packages( "Dowd_0.11.tar.gz", repo=NULL, type="source")
These direction should be "cross-platform". I'm not sure the directions in the accepted answer are applicable to Macs (OSX). (I later confirmed that they do "work" on a Mac but found the process more involved that what I suggested above. They do result in a directory that do contain the packages in a form that should succeed with R --vanilla CMD INSTALL --build pathToEachPackageSeparately)
It is also possible that the current version of the package you are trying to install requires a newer version of R, for example, you may see error like:
"ERROR: this R is version 2.15.0, package 'PerformanceAnalytics' requires R >= 3.0.0"
then you can try to update your R
or, if you are facing the same situation with me, which is trying to use pqR (currently using R version 2.15), you can find the out-of-date achieved package here:
http://cran.at.r-project.org/src/contrib/Archive/PerformanceAnalytics/
You can get here from R-Forge packages page -> "Stable Release: Get PerformanceAnalytics 1.4.3541 from CRAN" -> Old sources: PerformanceAnalytics archive
for example, you will find package PerformanceAnalytics version 1.1.0 just requires R >= 2.14
Good luck
Alternatively, you can install the particular package from GitHub, if it has a repo at GitHub.
I ran install.packages('ggfortify'), and got
Warning message: “package ‘ggfortify’ is not available (for R version
3.3.2)”
ggfortify was the GitHub repo for the same package.
The devtools library allows you to install a package from GitHub directly with install_github('username/repo').
library(devtools)
install_github('sinhrks/ggfortify')