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POreshape alternating columns in less time and using less memory
 

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    <p>How can I do this reshape faster and so that it takes up less memory? My aim is to reshape a dataframe that is 500,000 rows by 500 columns with 4 Gb RAM. </p> <p>Here's a function that will make some reproducible data:</p> <pre><code>make_example &lt;- function(ndoc, ntop){ # doc numbers V1 = seq(1:ndoc) # filenames V2 &lt;- list("vector", size = ndoc) for (i in 1:ndoc){ V2[i] &lt;- paste(sample(c(rep(0:9,each=5),LETTERS,letters),5,replace=TRUE),collapse='') } # topic proportions tvals &lt;- data.frame(matrix(runif(1:(ndoc*ntop)), ncol = ntop)) # topic number tnumvals &lt;- data.frame(matrix(sample(1:ntop, size = ndoc*ntop, replace = TRUE), ncol = ntop)) # now make topic props and topic numbers alternating columns (rather slow!) alternating &lt;- data.frame(c(matrix(c(tnumvals, tvals), 2, byrow = T)) ) # make colnames for topic number and topic props ntopx &lt;- sapply(1:ntop, function(j) paste0("ntop_",j)) ptopx &lt;- sapply(1:ntop, function(j) paste0("ptop_",j)) tops &lt;- c(rbind(ntopx,ptopx)) # make data frame dat &lt;- data.frame(V1 = V1, V2 = unlist(V2), alternating) names(dat) &lt;- c("docnum", "filename", tops) # give df as result return(dat) } </code></pre> <p>Make some reproducible data:</p> <pre><code>set.seed(007) dat &lt;- make_example(500000, 500) </code></pre> <p>Here's my current method (thanks to <a href="https://stackoverflow.com/a/8058714/1036500">https://stackoverflow.com/a/8058714/1036500</a>): </p> <pre><code>library(reshape2) NTOPICS = (ncol(dat) - 2 )/2 nam &lt;- c('num', 'text', paste(c('topic', 'proportion'), rep(1:NTOPICS, each = 2), sep = "")) system.time( dat_l2 &lt;- reshape(setNames(dat, nam), varying = 3:length(nam), direction = 'long', sep = "")) system.time( dat.final2 &lt;- dcast(dat_l2, dat_l2[,2] ~ dat_l2[,3], value.var = "proportion" ) ) </code></pre> <p>Some timings, just for the <code>reshape</code> since that's the slowest step:</p> <p><code>make_example(5000,100)</code> = 82 sec</p> <p><code>make_example(50000,200)</code> = 2855 sec (crashed on attempting the second step)</p> <p><code>make_example(500000,500)</code> = not yet possible...</p> <p>What other methods are there that are faster and less memory intensive for this reshape (<code>data.table</code>, <a href="https://stackoverflow.com/a/9344168/1036500">this</a>)?</p>
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