I am trying to schematic plot of txt data but when I write schematic.plot there is no package in Rstudio. I am searching for the package but it is not downloading.
In order to install a package in Rstudio you would want to run the command to in the console as follows:
install.packages("BiocManager")
To install ELMER as this package contains the schematic.plot function I believe you are looking for we actually install it using bioconductors installer as follows:
install.packages("BiocManager")
BiocManager::install("ELMER")
Please let me know if this isn't what you're looking for and I'll try to improve the answer.
You probably need to do:
install.packages("ELMER")
library(ELMER)
to get the package in there.
Related
I'm trying to use these packages to niche analysis but both seems to be removed from CRAN and packages which should replace them are not working. There is a new source for these packages or any way to carry out this analysis using another package?
Thank you!
Here you can download the archived file:
https://cran.r-project.org/src/contrib/Archive/EcoSimR/
Save the EcoSimR_0.1.0.tar to your folder.
Got to Packages in RStudio and press install
Install from archive
Please, how can I get "GraphClusterAnalysis" package installed? I am trying to use the "Highly connected sub graphs" (HCS) clustering algorithm for my data. I have tried to use install.packages() for the installation but I keep getting: package ‘GraphClusterAnalysis’ is not available (for R version 3.0.3).
I was able to use a method called "highlyConnSG()" for the HCS clustering algorithm which I retrieved after installing "RGBL" and "graph" packages from source "https://biconductor.org/bioLite.R". So to install those packages, type in the R environment command line:
source("https://biconductor.org/biocLite.R")
biocLite("RBGL")
biocLite("graph")
As far as I can see, this is a library, written by the authors of the book ( https://www.csc2.ncsu.edu/faculty/nfsamato/practical-graph-mining-with-R/PracticalGraphMiningWithR.html ).
Also on this page is provided the link to the archive with this library itself (here is the link: https://www.csc2.ncsu.edu/faculty/nfsamato/practical-graph-mining-with-R/R-code/GraphClusterAnalysis.zip ).
So you can load this library and after that you can try to install the library from source. Here is the stackoverflow question about how to do it:
How do I install an R package from source?
Nevertheless, as for me I wasn't successful in installing it from source.
Suppose I have an R package on GitHub. Is there any way, I can have an RStudio user of my package avoid first running:
install.packages("devtools")
library(devtools)
and just directly use:
install_github("My-Github-username/My-package-name")
library(My-package-name)
Can I for example make any changes to my R package such that my package automatically does install.packages("devtools") and library(devtools) for the user?
You somehow need to get your user to install and build the package locally to use it. The package can't install itself. Think of the package as a collection of code. You somehow need to get the code from GitHub to your user's computer.
If using devtools is not an option, you could have them do this manually (by, say, downloading the .tar.gz from GitHub) and then build the package themselves, using R CMD build and R CMD install such. There are some nice explanations out there on how to go about doing this. Using devtools::install_github() is a convenient, easy function that takes care of all of those steps for you.
(The exception to my statement "The package can't install itself" is that you can use devtools to install devtools.)
I'm trying to install this cnv-seq package on my R library to help copying number variation analysis. However, when I type in
install.packages("cnv-seq")
in R command, an error code pops out saying it is not available for 3.1.1 version. So I tried the old versions as well. All says not available. And I double check with the menu, Packages-> Install packages->. No cnv-seq
Ok. Then I tried to install it from a local source which is the "cnv-seq.tar.gz"
when i type in
install.packages("C:/cnv-seq.tar.gz", repos=NULL, type="source")
it still returns an error that says cannot extract package from this file.
Installation of package had non-zero exit status.
Anything went wrong or is there another I can install this package manually to my PC? After take a look at a similar question here couple years ago,
How do I install an R package from source?
I still could not fix this problem.
This is a case of RTFM ;)
You can do the whole process from within R. Below, we download the archive to the temporary directory, then extract it and finally install it.
download.file('http://tiger.dbs.nus.edu.sg/cnv-seq/cnv-seq.tar.gz',
f <- tempfile())
untar(f, exdir=tempdir())
install.packages(file.path(tempdir(), 'cnv-seq', 'cnv'), type='source', repos=NULL)
I believe you first must untar the file. I believe 7zip has this capability if you do not have access to a linux machine. The linux command would be:
tar -xvf /path/to/file/cnv-seq.tar.gz
After you do this you should be able to import the package into R.
I am not able to upload arules package
Below is the following command I am using
library(arules)
I have downloaded the file from http://cran.r-project.org/web/packages/arules/index.html still it is not able to upload it.
Can anyone help me out
install.packages("arules")
pls. find below GUI - Screen for Rcmdr Package
Open RStudio.
Go to the “Packages” tab and click on “Install Packages”. The first time you’ll do this you’ll be prompted to choose a CRAN mirror. R will download all necessary files from the server you select here. Choose the location closest to you (probably “USA CA 1” or “USA CA 2”, which are housed at UC Berkeley and UCLA, respectively).
Install packages in Windows
Start typing “Rcmdr” until you see it appear in a list. Select the first option (or finish typing Rcmdr), ensure that “Install dependencies” is checked, and click “Install”.
Install Rcmdr in Windows
Wait while all the parts of the R Commander package are installed.
I had a similar problem. I solve it using
#install and load devtools to install directly from github
install("devtools")
library("devtools")
install_github("mhahsler/arules")
If you want to install "arules" package, you may not be able to install it just using the code below.
<< install.packages("arules") >>
follow the steps in order to solve problem:
go to the package's address and download it manually.you will find it in the link below:
https://cran.r-project.org/web/packages/arules/index.html
If you are using R-Studio just install that package you have got, by "tools" menu in your IDE (R-studio)
Tools->Install packages->...
brows the file in your computer and install it.
go to the command line and using library(arules) function test the package. If there is still an error it could belong to incompatibility of the package with the version of R (Not R-Studio or any other IDE that you are using), just upgrade R and try installation period again.
I had a related problem where I could not install arules after being able to successfully install many libraries. I finally learned that I needed to update to 3.4 for arules. In order to do that, I followed duckmayr's answer HERE. Then, I was able to install arules with no issues, and it worked.