Databases
StackOverflow2013
Postsdbo
PO
 

Note that there are some explanatory texts on larger screens.

plurals
  1. PO
    primarykey
    data
    text
    <p>First look at these general suggestions on speeding up code: <a href="https://stackoverflow.com/a/8474941/636656">https://stackoverflow.com/a/8474941/636656</a></p> <p>The first thing that jumps out at me is that I'd create only one results matrix. That way you're not duplicating the <code>sampleIDs begin finish</code> columns, and you can avoid any overhead that comes with running the matching algorithm twice.</p> <p>Doing that, you can avoid selecting more than once (although it's trivial in terms of speed as long as you store your selection vector rather than re-calculate).</p> <p>Here's a solution using <code>apply</code>:</p> <pre><code>myMatrix1 &lt;- data.frame(sampleIDs=c(19990224,20000224),begin=c(4,5),finish=c(5,6)) myMatrix2 &lt;- data.frame(begin=c(0,11),finish=c(10,367),sed=c(1.002,2.01),boreWidth=c(.014,.056)) glommer &lt;- function(x,myMatrix2) { x[4:5] &lt;- as.numeric(myMatrix2[ myMatrix2$begin &lt;= x["begin"] &amp; myMatrix2$finish &gt;= x["finish"], c("sed","boreWidth") ]) names(x)[4:5] &lt;- c("sed","boreWidth") return( x ) } &gt; t(apply( myMatrix1, 1, glommer, myMatrix2=myMatrix2)) sampleIDs begin finish sed boreWidth [1,] 19990224 4 5 1.002 0.014 [2,] 20000224 5 6 1.002 0.014 </code></pre> <p>I used <code>apply</code> and stored everything as numeric. Other approaches would be to return a data.frame and have the sampleIDs and begin, finish be ints. That might avoid some problems with floating point error.</p> <p>This solution assumes there are no boundary cases (e.g. the begin, finish times of myMatrix1 are entirely contained within the begin, finish times of the other). If your data is more complicated, just change the glommer() function. How you want to handle that is a substantive question.</p>
    singulars
    1. This table or related slice is empty.
    1. POMake Dataframe loop code run faster
      singulars
      1. PTQuestion
    1. PTAnswer
    1. USCommunity
    1. USAri B. Friedman
    plurals
    1. This table or related slice is empty.
    1. PL
      singulars
      1. LTLinked
    1. POMake Dataframe loop code run faster
      singulars
      1. PTQuestion
    1. This table or related slice is empty.
    1. VO
      singulars
      1. PO
      1. This table or related slice is empty.
      1. VTUpMod
    2. VO
      singulars
      1. PO
      1. This table or related slice is empty.
      1. VTUpMod
    3. VO
      singulars
      1. PO
      1. This table or related slice is empty.
      1. VTUpMod
    1. COI can't move the first line in the loop outside the loop because I need to capture those rows of `myMatrix1$begin` that have a value that is both greater than the value in the ith row of `myMatrix2$begin` and less than the value in the ith row of `myMatrix2$end`. I'll try to update with a brief summary of my data. Btw, since I'm new to R and have had to dive straight in, I do not know what you mean by vectorization. From what I understand, I should vectorize instead of loop if there is no dependency on a previous iteration. However, there is with my data: hence I'm using `cbind`
      singulars
      1. PO
      1. USKaleb
    2. COAh, I missed the `i` in that line. Vectorization would let you avoid the loop. Whether or not it would make it faster depends how its implemented. Perhaps you could describe what you're going for and what your data looks like a little bit? It would be easy to just copy your code and make little snippets faster, while missing the bigger picture of what you're trying to accomplish (potentially only in a line or two) if we don't know what you're aiming for.
      singulars
      1. PO
      1. USAri B. Friedman
    3. COOk. I'll post an update.
      singulars
      1. PO
      1. USKaleb
 

Querying!

 
Guidance
A row detail

Detail views are divided into sections. All the information in the data section comes from columns in the selected row. The other sections display data from other, related rows.

Related data can be related in a to-one or a to-many fashion. Captions of data related in a to-many fashion link to a list view showing a filtered view of the table.

Try moving around until you find a non-empty to-many entry and click on the label to get to one. You can move back to the root by clicking on the database name in the header.

SQuiL has stopped working due to an internal error.

If you are curious you may find further information in the browser console, which is accessible through the devtools (F12).

Reload