Install Ubuntu 20.04 lts and R 4.0.1 and Rstudio 1.3

# Install Ubuntu 20.04 lts
# 2 hours

sudo apt install update-manager-core
sudo apt update
sudo apt upgrade
sudo apt dist-upgrade
sudo apt autoremove
sudo reboot

sudo do-release-upgrade -d

# Remove old R installation

# If you want install again your packages, follow this trick
# https://biostatsr.blogspot.com/2019/05/reinstall-packages-after-updating-r.html

sudo vi /etc/apt/sources.list

# Remove all lines with CRAN or r-project
# In vi, use / to search

# Remove files shown using:
ls /etc/apt/sources.list.d

# For example:
sudo rm /etc/apt/sources.list.d/marutter-ubuntu-rrutter3_5-xenial.list
sudo rm /etc/apt/sources.list.d/marutter-ubuntu-rrutter3_5-xenial.list.distUpgrade
sudo rm /etc/apt/sources.list.d/marutter-ubuntu-rrutter3_5-xenial.list.save

# I am not sure that reboot is necessary, but better to do!
sudo reboot

sudo apt-get purge r-base* r-recommended r-cran-*
sudo apt autoremove
sudo apt update

# Packages are located in .libPaths() read from R
# Example
# > .libPaths()
# [1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library"    
# [3] "/usr/lib/R/library"

sudo rm -rf /usr/local/lib/R/
sudo rm -rf /usr/lib/R

# Install new R version

sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/'
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
sudo apt update

sudo apt install r-base r-base-core r-recommended r-base-dev

sudo add-apt-repository ppa:c2d4u.team/c2d4u4.0+
sudo apt update

# Take a look at https://launchpad.net/~c2d4u.team/+archive/ubuntu/c2d4u4.0+?field.series_filter=focal

sudo apt install r-cran-rgl r-cran-rjags r-cran-snow r-cran-ggplot2 r-cran-igraph r-cran-lme4 r-cran-rjava r-cran-devtools r-cran-roxygen2 r-cran-rjava

sudo apt install libgdal-dev libproj-dev libgeos-dev libudunits2-dev libnode-dev libcairo2-dev libnetcdf-dev

# Install Rstudio 1.3

rstudio-server stop

sudo apt-get install gdebi-core
wget https://download2.rstudio.org/server/bionic/amd64/rstudio-server-1.3.959-amd64.deb
sudo gdebi rstudio-server-1.3.959-amd64.deb
rm rstudio-server-1.3.959-amd64.deb

# To allow a user to use /usr/local/lib/R/site-library

sudo usermod -a -G staff $USER

Commentaires

Enregistrer un commentaire

Posts les plus consultés de ce blog

Standard error from Hessian Matrix... what can be done when problem occurs

An Hessian matrix is a square matrix of partial second order derivative. From the square-root of the inverse of the diagonal, it is possible to estimate the standard error of parameters. Let take an example: val=rnorm(100, mean=20, sd=5) # Return -ln L of values in val in Gaussian distribution with mean and sd in par fitnorm<-function(par, val) {   -sum(dnorm(val, par["mean"], par["sd"], log = TRUE)) } # Initial values for search p<-c(mean=20, sd=5) # fit the model result <- optim(par=p, fn=fitnorm, val=val, method="BFGS", hessian=TRUE) # Inverse the hessian matrix to get SE for each parameters mathessian <- result$hessian inversemathessian <- solve(mathessian) res <- sqrt(diag(inversemathessian)) # results data.frame(Mean=result$par, SE=res)   library(MASS) (r<-fitdistr(val, "normal")) It works well. However, the inverse of the matrix cannot be calculated if the second order derivative for some paramete...
Lire la suite

Install treemix in ubuntu 20.04

Informations are available here  https://bitbucket.org/nygcresearch/treemix/downloads/ In terminal, enter for  Ubuntu 20.04: wget https://bitbucket.org/nygcresearch/treemix/downloads/treemix-1.13.tar.gz tar -xvf treemix-1.13.tar.gz sudo apt-get install libgsl-dev sudo apt install libboost-dev sudo apt install libboost-all-dev cd treemix-1.13/ ./configure make sudo make install And it works: $ treemix TreeMix v. 1.13 $Revision: 231 $ Options: -h display this help -i [file name] input file -o [stem] output stem (will be [stem].treeout.gz, [stem].cov.gz, [stem].modelcov.gz) -k [int] number of SNPs per block for estimation of covariance matrix (1) -global Do a round of global rearrangements after adding all populations -tf [file name] Read the tree topology from a file, rather than estimating it -m [int] number of migration edges to add (0) -root [string] comma-delimited list of populations to set on one side of the root (for migration) -g [vertices file name] [edges file na...
Lire la suite

stepAIC from package MASS with AICc

Due to a bug in dropterm() and addterm() in package MASS, it is impossible to use AICc with stepAIC() . Here is a solution. Enter these commands and now you can use: stepAIC(g0, criteria="AICc") or stepAIC(g0, criteria="BIC") For example: datax <- data.frame(y=rnorm(100), x1=rnorm(100),                     x2=rnorm(100), x3=rnorm(100), x4=rnorm(100)) g0 <- glm(y ~ x1+x2+x3+x4, data=datax) gx_AICc <- stepAIC(g0, criteria="AICc") gx_AIC <- stepAIC(g0, criteria="AIC") gx_AIC <- stepAIC(g0, criteria="BIC")
Lire la suite