R CMD Check example times

[Namita Gupta]

Examples with CPU or elapsed time > 5s
                           user system elapsed
rescaleMutability        37.507  0.076  37.570
createTargetingMatrix    37.580  0.000  37.567
calcTargetingDistance    37.364  0.067  37.418
createTargetingModel     36.949  0.001  36.933
extendMutabilityMatrix   36.691  0.001  36.675
createMutabilityMatrix   35.616  0.005  35.604
plotBaselineDensity      12.264  0.129  12.380
plotBaselineSummary      11.714  0.145  11.844
groupBaseline            10.629  0.113  10.729
summarizeBaseline        10.129  0.090  10.208
calcBaseline              9.465  0.062   9.520
getBaselineStats          9.373  0.085   9.449
calcDBExpectedMutations   6.376  0.036   6.409
extendSubstitutionMatrix  5.450  0.000   5.447
plotMutability            5.215  0.011   5.225

[Jason Vander Heiden]

We should start by searching for rbind and unlist calls. Those bastards are slooooow. I know there are still some hiding in the code.

[Namita Gupta]

This is now:

Examples with CPU or elapsed time > 5s
                           user system elapsed
rescaleMutability        36.457  0.355  36.798
createTargetingModel     36.359  0.004  36.347
createTargetingMatrix    35.594  0.001  35.579
extendMutabilityMatrix   35.287  0.003  35.275
calcTargetingDistance    33.936  0.012  33.933
createMutabilityMatrix   33.231  0.013  33.229
plotMutability           11.257  0.067  11.320
extendSubstitutionMatrix  5.553  0.001   5.551

[Namita Gupta]

Now:

Examples with CPU or elapsed time > 5s
                           user system elapsed
createTargetingMatrix    25.247  0.018  25.255
calcTargetingDistance    24.888  0.007  24.885
rescaleMutability        24.509  0.004  24.502
extendMutabilityMatrix   24.408  0.000  24.397
createTargetingModel     24.406  0.000  24.396
createMutabilityMatrix   22.925  0.009  22.924
plotMutability           11.133  0.001  11.128
extendSubstitutionMatrix  5.500  0.002   5.500

[Namita Gupta]

Examples with CPU or elapsed time > 5s
                         user system elapsed
createTargetingMatrix  22.359  0.006  22.356
calcTargetingDistance  21.469  0.006  21.466
createTargetingModel   21.402  0.004  21.396
extendMutabilityMatrix 20.472  0.001  20.466
createMutabilityMatrix 20.196  0.005  20.192
plotMutability          5.324  0.005   5.327

[Namita Gupta]

Examples with CPU or elapsed time > 5s
                        user system elapsed
createTargetingModel   9.326  0.001   9.322
createTargetingMatrix  9.324  0.000   9.320
extendMutabilityMatrix 8.749  0.000   8.745
createMutabilityMatrix 8.134  0.008   8.139
plotMutability         5.347  0.008   5.353

[Jason Vander Heiden]

Examples with CPU or elapsed time > 5s
                        user system elapsed
createTargetingMatrix  7.170  0.003   7.175
createTargetingModel   7.104  0.012   7.119
extendMutabilityMatrix 6.274  0.004   6.280
createMutabilityMatrix 5.778  0.022   5.802
plotMutability         5.493  0.004   5.499

So close! I'm not sure what else we can do to fix createMutabilityMatrix() without a complete redesign. Maybe there is still something.

[Jason Vander Heiden]

Examples with CPU or elapsed time > 5s
               user system elapsed
plotMutability  5.5  0.007   5.511

With 57 sequences in the examples. Which is awful. Maybe we can add some longer dontrun examples.

[Jason Vander Heiden]

plotMutability() speed does not appear fixable. There are faster ways with both geom_tile and geom_raster, but they either don't work at all with polar coordinates or render poorly.

[Jason Vander Heiden]

I spoke too soon. All better.