Comments (2)
I've fixed a plethora of small bugs and issues with the diploid version of bitwise.IA. It now produces values fairly close to the existing win.ia code. Unfortunately the output is still not exactly the same, and occasionally spikes upwards of 20% relative error (although it averages much better than that). It seems something is wrong with the accumulation of distance at each locus (M[] and M2[]). Everything else is matching up to win.IA exactly.
Right now I can generate the following output from both functions while running ia_comparison. Each time the values shown are computed they are written to a file. This is the diff between (the first few differences in) those two output files ( > represents bitwise.IA output, < represents snpia):
2,5c2,5
< Sd*Sd/np:1543.372929
< Sd2:3384
< vars:0.371844
<
---
> Sd*Sd/np:1722.505051
> Sd2:3664
> vars:0.392221
>
9,21c9,21
<
< Sd*Sd/np:986.686869
< Sd2:2210
< vars:0.247134
<
< Sd*Sd/np:2673.746263
< Sd2:4982
< vars:0.466314
<
< Sd*Sd/np:1355.171717
< Sd2:3110
< vars:0.354511
<
---
>
> Sd*Sd/np:1138.560808
> Sd2:2504
> vars:0.275846
>
> Sd*Sd/np:2872.816364
> Sd2:5211
> vars:0.472360
>
> Sd*Sd/np:1527.777778
> Sd2:3400
> vars:0.378227
>
29,37c29,37
<
< Sd*Sd/np:1813.336566
< Sd2:4004
< vars:0.442558
<
< Sd*Sd/np:1961.506263
< Sd2:4480
< vars:0.508787
<
---
>
> Sd*Sd/np:2004.545455
> Sd2:4284
> vars:0.460496
>
> Sd*Sd/np:2560.323232
> Sd2:5296
> vars:0.552662
>
41,45c41,45
<
< Sd*Sd/np:1397.353535
< Sd2:3250
< vars:0.374272
<
---
>
> Sd*Sd/np:1931.406869
> Sd2:4084
> vars:0.434867
>
49,53c49,53
<
< Sd*Sd/np:983.118384
< Sd2:2342
< vars:0.274522
<
---
>
> Sd*Sd/np:1136.643232
> Sd2:2644
> vars:0.304517
>
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Commit c4059d2 resolves the issues and completes this functionality. bitwise.IA should now correctly support diploids.
from poppr.
Related Issues (20)
- Fix inefficient implementation of boot.bruvo HOT 3
- Interpretation of negative values in AMOVA HOT 3
- Error with reverse dependency checks for phangorn HOT 12
- genind2genalex() produces all zero genotypes with some SNP data. HOT 1
- bitwise.ia() degraded performance on windows HOT 1
- Clade rooting abnormally with updated HOT 4
- Error in bruvo.boot HOT 4
- CRAN test failure in R-devel on Debian
- Cannot re-level strata of a snpclone object HOT 1
- DUE 2021-09-21: Packages including omp.h after Rincludes.h
- Feature request: separation/removal of sf package requirement HOT 5
- Optional disabling of statistics in poppr table HOT 6
- threads not being respected and defaulting to 1 HOT 1
- PAIRWISE FST Calculation HOT 1
- Find All Duplicate MLGs HOT 4
- [read.genalex()]: Detect semicolon-separated files and throw error with correct command
- IS there a way to make a table indicated the multilocus genotypes for each isolate? where is that info stored? HOT 1
- Error Message from R using read.genalex HOT 1
- CRAN Errors to fix by 2023-03-22 HOT 2
- Preserve state of random number generator in .onAttach() HOT 6
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