Configure Rstudio server

 sudo vi /etc/rstudio/rserver.conf


# Server Configuration File

# 

www-port=8080

rsession-which-r=usr/bin/R

auth-timeout-minutes=0

auth-stay-signed-in-days=3000


Note that the option

session-timeout-minutes=0

Does not work. Perhaps it is only for the pro version

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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...
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Multivariable analysis and correlation of iconography

Image
Introduction Correlation iconography is a not very well known method to study multivariate data. It was developed long-time ago by Michel Lesty: Lesty M (1999) Une nouvelle approche dans le choix des régresseurs de la régression multiple en présence d'intéractions et de colinearités. La revue de Modulad 22:41-77 It is also well described in a French Wikipedia page: https://fr.wikipedia.org/wiki/Iconographie_des_corrélations After checking the possibilities of this method, I think that it deserves more attention. Let take the example of the wikipedia page: dta <- read.table(text=gsub(",", ".", "Élève Poids Âge Assiduité Note e1 52 12 12 5 e2 59 12,5 9 5 e3 55 13 15 9 e4 58 14,5 5 5 e5 66 15,5 11 13,5 e6 62 16 15 18 e7 63 17 12 18 e8 69 18 9 18"), header=TRUE) > dta   Élève Poids  Âge Assiduité Note 1    e1    52 12.0        12  5.0 2    e...
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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...
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