refactor: adapt to cut.prob's new handling of NULL in the C core (sim…

[maelle]

…pler default for the R interface)

Fix #1570

Work needed in the tests.

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[maelle]

mmh this does not work at all currently.

[maelle]

@szhorvat actually, I think things are fine. What do you think of the tests

rigraph/tests/testthat/test-motifs.R

Line 1 in 30518c2

test_that("motif finding works", {

?

They're failing for small differences. Furthermore they do not make any sense to me, why are we testing for the value of the divisions?

── Failure ('test-motifs.R:11:3'): motif finding works ─────────────────────────
c(mno0/mno, mno1/mno, mno2/mno) (`actual`) not equal to c(0.654821903845065, 0.666289144345659, 0.668393831285275) (`expected`).

  `actual`: 0.67454 0.66614 0.66597
`expected`: 0.65482 0.66629 0.66839

[szhorvat]

I'm really tired today ... could you please help me by showing me a specific before/after example that changes output? Passing c(0,0,0) vs NULL should NOT change anything.

But as I'm writing this, I think I'm starting to remember what's going on:

I think passing NULL instead of c(0,0,0) vs will cause some (unnecessary) RNG calls to be omitted. This means that later calls that use different values than c(0,0,0), and therefore return stochastic results, should indeed be affected. And yes, this is not a bug, don't worry.

It'll be cleanest for each test to use its own random seed.

[szhorvat]

Yes, this is certainly what's going on. If you pass NULL or c(0,0,0,...), the result will be the exactly same. But the RNG state will be mutated differently, which means that any subsequent uses of the RNG are affected.

The results are approximately the same and everything is fine.

Adding a tolerance won't work very well here because the noise in the results is still quite high and will continue to be high unless we use large enough graphs and small enough cut probabilities that the computation time becomes too long for a test.

[szhorvat]

Furthermore they do not make any sense to me, why are we testing for the value of the divisions?

The interface is not very nice, unfortunately, but improvements are for a later version and for the C core.

If we give cut probabilities $p_1, p_2, \dots$, then only a fraction of the motifs will be sampled. This fraction is $\prod_i (1-p_i)$. This is the value you should see in the ratio of the counts obtained with a non-zero cut probability and the full counts (with no cuts). Since some motifs are rare, some entries in the result vector will fluctuate wildly.

So, if you give c(1/3, 0, 0), then the ratios should all be about $1-1/3 \approx 0.66$.

[szhorvat]

When you resolve conflicts, be sure that you don't accidentally re-add as.numeric to sample.

[maelle]

I'll make a new PR, thank you!!

[maelle]

@szhorvat would you mind re-reviewing? thank you!

[maelle]

Errors in tests

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-motifs.R:11:3'): motif finding works ─────────────────────────
c(mno0/mno, mno1/mno, mno2/mno) (`actual`) not equal to c(0.654821903845065, 0.666289144345659, 0.668393831285275) (`expected`).

  `actual`: 0.67454 0.66614 0.66597
`expected`: 0.65482 0.66629 0.66839
── Failure ('test-motifs.R:19:3'): motif finding works ─────────────────────────
c(mno3/mno, mno4/mno, mno5/mno) (`actual`) not equal to c(0.443959957465819, 0.441952797125797, 0.446004870037941) (`expected`).

  `actual`: 0.4417 0.4456 0.4405
`expected`: 0.4440 0.4420 0.4460
── Failure ('test-motifs.R:34:3'): motif finding works ─────────────────────────
m0/m (`actual`) not equal to c(...) (`expected`).

  `actual[1:15]`: NA NA 0.672 NA 0.675 0.633 0.676 0.699 NaN 0.785 and 5 more...
`expected[1:15]`: NA NA 0.654 NA 0.654 0.612 0.658 0.630 NaN 0.538           ...
── Failure ('test-motifs.R:35:3'): motif finding works ─────────────────────────
m1/m (`actual`) not equal to c(...) (`expected`).

     actual | expected               
 [1] NA     | NA       [1]           
 [2] NA     | NA       [2]           
 [3] 0.6665 - 0.6696   [3]           
 [4] NA     | NA       [4]           
 [5] 0.6663 - 0.6681   [5]           
 [6] 0.6327 - 0.7347   [6]           
 [7] 0.6685 - 0.6708   [7]           
 [8] 0.6712 - 0.6575   [8]           
 [9] NaN    | NaN      [9]           
[10] 0.6000 - 0.7692   [10]          
 ... ...      ...      and 5 more ...
── Failure ('test-motifs.R:36:3'): motif finding works ─────────────────────────
m2/m (`actual`) not equal to c(...) (`expected`).

     actual  | expected               
 [1] NA      | NA       [1]           
 [2] NA      | NA       [2]           
 [3] 0.66327 - 0.66645  [3]           
 [4] NA      | NA       [4]           
 [5] 0.66744 - 0.66529  [5]           
 [6] 0.65306 - 0.59184  [6]           
 [7] 0.66628 - 0.66668  [7]           
 [8] 0.65753 - 0.67123  [8]           
 [9] NaN     | NaN      [9]           
[10] 0.66154 - 0.75385  [10]          
 ... ...       ...      and 5 more ...
── Failure ('test-motifs.R:41:3'): motif finding works ─────────────────────────
m3/m (`actual`) not equal to c(...) (`expected`).

     actual  | expected               
 [1] NA      | NA       [1]           
 [2] NA      | NA       [2]           
 [3] 0.43906 - 0.44561  [3]           
 [4] NA      | NA       [4]           
 [5] 0.44174 - 0.44279  [5]           
 [6] 0.40816 - 0.44898  [6]           
 [7] 0.44432 - 0.44470  [7]           
 [8] 0.43836 - 0.42466  [8]           
 [9] NaN     | NaN      [9]           
[10] 0.41538 - 0.36923  [10]          
 ... ...       ...      and 5 more ...
── Failure ('test-motifs.R:43:3'): motif finding works ─────────────────────────
m4/m (`actual`) not equal to c(...) (`expected`).

     actual  | expected               
 [1] NA      | NA       [1]           
 [2] NA      | NA       [2]           
 [3] 0.43977 - 0.43925  [3]           
 [4] NA      | NA       [4]           
 [5] 0.44104 - 0.43928  [5]           
 [6] 0.22449 - 0.73469  [6]           
 [7] 0.43875 - 0.44509  [7]           
 [8] 0.53425 - 0.46575  [8]           
 [9] NaN     | NaN      [9]           
[10] 0.43077 - 0.63077  [10]          
 ... ...       ...      and 5 more ...
── Failure ('test-motifs.R:45:3'): motif finding works ─────────────────────────
m5/m (`actual`) not equal to c(...) (`expected`).

     actual      | expected                  
 [1] NA          | NA          [1]           
 [2] NA          | NA          [2]           
 [3] 0.444436015 - 0.439985333 [3]           
 [4] NA          | NA          [4]           
 [5] 0.445736750 - 0.440288167 [5]           
 [6] 0.489795918 - 0.346938776 [6]           
 [7] 0.445353602 - 0.441597531 [7]           
 [8] 0.575342466 - 0.452054795 [8]           
 [9] NaN         | NaN         [9]           
[10] 0.415384615 - 0.323076923 [10]          
 ... ...           ...         and 3 more ...
── Error ('test-motifs.R:54:3'): sample_motifs works ───────────────────────────
Error in `sample_motifs(g)`: At vendor/cigraph/src/misc/motifs.c:604 : The number of vertices to use as a sample for motif count estimation must be at least one, got 0. Invalid value
Backtrace:
    ▆
 1. └─igraph::sample_motifs(g) at test-motifs.R:54:3

[ FAIL 9 | WARN 0 | SKIP 5 | PASS 5059 ]
Error: Test failures
Execution halted

[maelle]

there's a second PR which I had forgotten

[szhorvat]

@szhorvat would you mind re-reviewing? thank you!

there's a second PR which I had forgotten

I assume you don't need a re-review on the 2nd PR. If you still need one, please ping me there.