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• Where to place the R code for R+Sweave+LaTeX workflow

  - by claytontstanley

  I spent the last week learning 3 new tools: R, Sweave, and LaTeX. One question that came to my mind though when working through my first project: Where do I place the majority of the R code? The tutorials that I read online placed the majority of the R code in the LaTeX .Rnw file. However, I find having a bunch of R calculations in the LaTeX file distracting. What I do find extremely helpful (of course) is to call out to R code in the LaTeX file and embed the result. So the workflow I've been using is to place 99% of my R code in my .R file. I run that file first, save a bunch of calculations as objects, and output the .Rout file once finished (to save the work). Then when running Sweave, I load up that .Rout file, so that I have the majority of my calculations already completed and in the Sweave R session. Then my LaTeX callouts to R are quite simple: Just give me the XTable stored in 'res.table', or give me the result of an already-computed calculation stored in the variable 'res'. So I push towards the minimal amount of R code in the LaTex file possible, to achieve the desired result (embedding stats results in the LaTeX writeup). Does anyone have any experience with this approach? I'm just worried I might run into trouble further down the line, when I start really trying to load up and leverage this workflow.

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• OS X: What does the '@' attribute on a file mean?

  - by claytontstanley

  On a Snow Leopard machine, at the Terminal: la ~/src/rmcl/ | grep RMCL -rw-r--r--@ 1 claytonstanley staff 6766167 Nov 13 2009 RMCL What is that '@' attribute? This file is part of an older OS X program that runs under Rosetta. I'm having issues where some older programs running under Rosetta require the @ attribute when opening files. But I'm not sure what that attribute is, so I have no way to know how to add/remove it. I did try a thorough Google search on this, but I wasn't able to find the answer. I would have thought this would be an easy one to find. Maybe the Google query isn't acting properly because of the single @ special character. Any info. is much appreciated. Thanks!

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• How do I translate this Matlab bsxfun call to R?

  - by claytontstanley

  I would also (fingers crossed) like the solution to work with R Sparse Matrices in the Matrix package. >> A = [1,2,3,4,5] A = 1 2 3 4 5 >> B = [1;2;3;4;5] B = 1 2 3 4 5 >> bsxfun(@times, A, B) ans = 1 2 3 4 5 2 4 6 8 10 3 6 9 12 15 4 8 12 16 20 5 10 15 20 25 >> EDIT: I would like to do a matrix multiplication of these sparse vectors, and return a sparse array: > class(NRowSums) [1] "dsparseVector" attr(,"package") [1] "Matrix" > class(NColSums) [1] "dsparseVector" attr(,"package") [1] "Matrix" > NRowSums * NColSums (I think) w/o using a non-sparse variable to temporarily store data.

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• Removing "Using temporary; Using filesort" from this MySQL select+join+group by query

  - by claytontstanley

  I have the following query: select t.Chunk as LeftChunk, t.ChunkHash as LeftChunkHash, q.Chunk as RightChunk, q.ChunkHash as RightChunkHash, count(t.ChunkHash) as ChunkCount from chunksubset as t join chunksubset as q on t.ID = q.ID group by LeftChunkHash, RightChunkHash And the following explain table: id select_type table type possible_keys key key_len ref rows Extra 1 SIMPLE subsets ref PRIMARY,IDIndex,SubsetIndex SubsetIndex 767 const 522014 "Using where; Using temporary; Using filesort" 1 SIMPLE subsets eq_ref PRIMARY,IDIndex,SubsetIndex PRIMARY 771 sotero.subsets.Id,const 1 "Using where; Using index" 1 SIMPLE c ref IDIndex IDIndex 4 sotero.subsets.Id 12 "Using where" 1 SIMPLE c ref IDIndex IDIndex 4 sotero.subsets.Id 12 note the "using temporary; using filesort". When this query is run, I quickly run out of RAM (presumably b/c of the temp table), and then the HDD kicks in, and the query slows to a halt. I thought it might be an index issue, so I started adding a few that sort of made sense: Table Non_unique Key_name Seq_in_index Column_name Collation Cardinality Sub_part Packed Null Index_type Comment Index_comment chunks 0 PRIMARY 1 ChunkId A 17796190 NULL NULL BTREE chunks 1 ChunkHashIndex 1 ChunkHash A 243783 NULL NULL BTREE chunks 1 IDIndex 1 Id A 1483015 NULL NULL BTREE chunks 1 ChunkIndex 1 Chunk A 243783 NULL NULL BTREE chunks 1 ChunkTypeIndex 1 ChunkType A 2 NULL NULL BTREE chunks 1 chunkHashByChunkIDIndex 1 ChunkHash A 243783 NULL NULL BTREE chunks 1 chunkHashByChunkIDIndex 2 ChunkId A 17796190 NULL NULL BTREE chunks 1 chunkHashByChunkTypeIndex 1 ChunkHash A 243783 NULL NULL BTREE chunks 1 chunkHashByChunkTypeIndex 2 ChunkType A 261708 NULL NULL BTREE chunks 1 chunkHashByIDIndex 1 ChunkHash A 243783 NULL NULL BTREE chunks 1 chunkHashByIDIndex 2 Id A 17796190 NULL NULL BTREE But still using the temporary table. The db engine is MyISAM. How can I get rid of the using temporary; using filesort in this query? Just changing to InnoDB w/o explaining the underlying cause is not a particularly satisfying answer. Besides, if the solution is to just add the proper index, then that's much easier than migrating to another db engine.

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