lineprof | Visualise line profiling results in R | Performance Testing library
kandi X-RAY | lineprof Summary
kandi X-RAY | lineprof Summary
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QUESTION
I am trying to find triangles in a distance matrix where a direct path is longer than going via another point. The goal is to reduce the number of edges in a fully connected graph. The function works well for low values of n but is slow for larger values. I am trying to find out how to speed up this process.
I had hoped that by keeping the data as a matrix and manipulating it like that the process would be vectorised and very fast, however, this is not what has happened.
I have tried to use lineprof
and click through to lower functions, but I don't understand what it is telling me. I don't know if there is some function in igraph
that would help?
ANSWER
Answered 2018-Sep-29 at 17:26As the matrix is symmetrical the process can be sped up by only calculating the lower triangular matrix. By doing this we can reduce the number of calculations from $n^3$ to
$\frac{n}{6}(2n^2+3n+1)$ which gives a ratio of $\frac{(2n+1)(n+1)}{6n^2}$ which results in approx 2/3 reduction in the total number of calculations when n is large.
The adjusted function is below.
This function starts slowly and speeds up as more rows are calculated. At small values of n it is slower than the original function due to the additional overhead, but becomes faster when n is greater than a couple of hundred.
QUESTION
I have a set of functions that run within a wrapper:
...ANSWER
Answered 2018-Aug-14 at 06:34You can use Rprof
to profile your R code and find the performance bottlenecks; here's a short example
QUESTION
How do I make multiple plots of the same data but colored differently by different factors (columns) while recycling data? Is this what gridExtra
does differently than cowplot
?
Objective: My objective is to visually compare different results of clustering the same data efficiently. I currently believe the easiest way to compare 2-4 clustering algorithms visually is to have them plotted next to each other.
Thus, how do I plot the same data side by side colored differently?
Challenge/Specifications: Performance is very important. I have roughly 30,000 graphs to make, each with 450 - 480 points. It is critical that the data is "recycled."
I am able to plot them side by side using packages cowplot
and gridExtra
. I just started using gridExtra
today but it seems to recycle data and is better than cowplot for my purposes. Update: u/eipi10 demonstrated facet_wrap
could work if I gathered the columns before plotting.
Set up
...ANSWER
Answered 2018-May-04 at 19:13Faceting will work here if you convert your data to long format. Here's an example:
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