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POPassing a list of files to XLConnect
 

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  1. POPassing a list of files to XLConnect
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    <p>I've written a script based on a for-loop to read in columns of multiple .xls files, combine them to a single data frame, search for negative values and write a .txt file with these values and the name of the file.<br> The script works basically, but I have several hundred files to process, and it's a bit slow. This version of the script is only a basic framework for later statistical analysis, and I want to parallelize the execution to speed it up.<br> I've tried to avoid the for-loop by applying the function via lapply and the plyr-package, but had problems passing the file list to "readWorkSheetFromFile" (Error in path.expand (filename) : invalid 'path' argument).</p> <p>Here is the working script: </p> <pre><code>require(XLConnect) setwd(choose.dir()) input = list.files(pattern = ".xls$") # creates empty data frame df = data.frame(Name=NULL, PCr=NULL, bATP=NULL, Pi=NULL) for(i in seq(along=input)){ data = data.frame(readWorksheetFromFile(input[i], sheet="Output Data", startRow=2, startCol=c(10, 13, 16), endCol=c(10, 13, 16), header=TRUE)) head(data, n = -1L) colnames(data) = c("PCr", "bATP", "Pi") data$Name = file.path(input[i]) attach(data) df = rbind(data, df) attach(df) rm(data) } # searches for negative values in df and writes to txt file neg_val = subset(df, bATP&lt;0 | Pi&lt;0 | PCr&lt;0) write.table(neg_val, file = "neg_val.txt", sep = "\t", quote=F) </code></pre> <p>Any solutions to this problem, or other suggestions to speed up execution? </p> <p>Thanks, Markus </p>
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    1. COYour speed issues are probably due to your [lack of preallocation](http://www.burns-stat.com/pages/Tutor/R_inferno.pdf), not the for loop. (The idea that for loops are inherently slow in R is a bit of a myth.)
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    2. COThanks for the link!
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