My Research Notes

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[[Build An R Package]]

===Bioconductor===
<code>
source("http://www.bioconductor.org/biocLite.R") 
biocLite([package name])
</code>

===Venn Diagram===
<code>
library(VennDiagram)
venn.diagram(x=list(A=which(c3[,1]==1),B=which(c3[,2]==1),C=which(c3[,3]==1)),filename="file_dir",height=4,width=4,units="in",category.names=[vector of the name of the classes],cex=2,cat.cex=[category text size]])
</code>

===Dynamic Scoping===

Environments in R:

http://adv-r.had.co.nz/Environments.html


Summary:

  - Binding environment: how to find the function, where(), package environment.
  - Enclosing environment: how the function finds values, environment(), namespace environment.
  - Execution environment: environment to host execution.
  - Calling environment: where the function is called, parent.frame().

Applications:

<code>
MomentEstimate <- function() {
    ## inherit variables from the calling environment
    for(v in c("m1", "m2", "Mu", "Sigma", "family", "s")) {
        assign(v, parent.frame()[[v]])
    }
    ## ... codes here ...
    ## push the updated values to the calling environment
    assign("Mu", Mu, envir = parent.frame())
    assign("Sigma", Sigma, envir = parent.frame())
}
</code>

===Commandline input===

In the file:

  commandlineArgs(TRUE)
  val <- args[[1]]
  var2 <- as.character(args[[2]])

In the commandline: 

  R CMD BATCH "--args 0.05 test" file.R file.Rout

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