[0-9] or \d or [:digit:] in grep

If you want search for a number using grep, you have 4 options:
[0123456789] or [0-9] or \d or [:digit:]

Here is a comparison:
library(microbenchmark)

 microbenchmark({grep(pattern="[0123456789][0123456789][0123456789][0123456789]", "Ussiosuus8980JJDUD98")}, 
               {grep(pattern="[0-9][0-9][0-9][0-9]", "Ussiosuus8980JJDUD98")}, 
               {grep(pattern="[[:digit:]][[:digit:]][[:digit:]][[:digit:]]", "Ussiosuus8980JJDUD98")}, 
               {grep(pattern="\\d\\d\\d\\d", "Ussiosuus8980JJDUD98")}, times = 1000L)

    min      lq      mean  median      uq    max neval  cld
 21.729 22.1840 22.887585 22.3090 22.4645 64.542  1000    d
  5.219  5.3740  5.696937  5.4665  5.8495 47.618  1000 a   
  9.778 10.0425 10.482301 10.1470 10.5400 25.602  1000  b  
 10.296 10.5000 11.099359 10.6360 11.0440 39.759  1000   c 

Clearly the solution [0-9] is the best

This is the same for letters:

microbenchmark({grep(pattern="[ABCDEFGHIJKLMNOPQRSTUVWXYZ][ABCDEFGHIJKLMNOPQRSTUVWXYZ][ABCDEFGHIJKLMNOPQRSTUVWXYZ][ABCDEFGHIJKLMNOPQRSTUVWXYZ]", "Ussiosuus8980JJDUD98")}, 
               {grep(pattern="[A-Z][A-Z][A-Z][A-Z]", "Ussiosuus8980JJDUD98")}, 
               {grep(pattern="[[:upper:]][[:upper:]][[:upper:]][[:upper:]]", "Ussiosuus8980JJDUD98")}, 
               times = 1000L)

    min      lq      mean  median      uq     max neval cld
 72.475 74.2315 80.536616 79.0655 79.7905 251.430  1000   c
  5.150  6.3040  7.304987  6.8855  7.5765  96.529  1000 a  
 13.637 14.7285 16.466666 16.0080 17.1880  78.308  1000  b 

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

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

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 name] read the g
Lire la suite