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Replace Biodiverse::Statistics with Statistics::Descriptive::PDL #798

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shawnlaffan opened this issue Sep 5, 2021 · 1 comment
Closed
4 tasks done

Replace Biodiverse::Statistics with Statistics::Descriptive::PDL #798

shawnlaffan opened this issue Sep 5, 2021 · 1 comment
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enhancement
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Release_4.0

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shawnlaffan commented Sep 5, 2021 •
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Statistics::Descriptive::PDL has just been released to CPAN.

It is faster than Statistics::Descriptive, upon which Biodiverse::Statistics is based, and also supports weighted variants.

The weighting will help with many of the element properties calculations as we currently have to duplicate the values to achieve weighting.

The main issue is that the median and percentiles are calculated differently, so the tests and metadata will need to be updated.
@shawnlaffan shawnlaffan added this to the Release_4.0 milestone Sep 5, 2021
@shawnlaffan shawnlaffan self-assigned this Sep 5, 2021
@shawnlaffan shawnlaffan mentioned this issue Sep 13, 2021
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shawnlaffan added a commit that referenced this issue Sep 14, 2021
@shawnlaffan
LabelProperties.pm: Simplify some code
49d161a 
Updates #798
shawnlaffan added a commit that referenced this issue Sep 14, 2021
@shawnlaffan
replace while-each idiom with foreach-key and map
4967d09 
Iterating over a hash using each is best avoided

Updates #798
shawnlaffan added a commit that referenced this issue Sep 14, 2021
@shawnlaffan
_get_gistar_score: exit early if sum of weights is undefined
5a2dbfe 
Related to #798
shawnlaffan added a commit that referenced this issue Sep 14, 2021
@shawnlaffan
cpanfile: bump required version of Statistics::Descriptive::PDL to 0.10
55a26e8 
updates #798
shawnlaffan added a commit that referenced this issue Sep 14, 2021
@shawnlaffan
BaseStruct::get_element_properties_summary_stats now uses PDL
5104414 
Updates #798
shawnlaffan added a commit that referenced this issue Sep 14, 2021
@shawnlaffan
BaseStruct all stats use Stats::Descr::PDL
d6cfcfa 
weighted and unweighted

Updates #798
shawnlaffan added a commit that referenced this issue Sep 14, 2021
@shawnlaffan
Indices: use weighted stats in GroupProperties.pm
22fb81f 
Updates #798
shawnlaffan added a commit that referenced this issue Sep 14, 2021
@shawnlaffan
cpanfile: Bump min version of Stats::Desc::PDL to 0.12
c0ddb92 
Updates #798
shawnlaffan added a commit that referenced this issue Sep 14, 2021
@shawnlaffan
Label properties tests: update expected percentiles
c76194b 
Stats::Desc::PDL uses interpolation

Updates #798
shawnlaffan added a commit that referenced this issue Sep 14, 2021
@shawnlaffan
LabelProperties: use package lexical to flag if weighted stats
8d3430a 
Updates #798
shawnlaffan added a commit that referenced this issue Sep 14, 2021
@shawnlaffan
LabelProperties: switch to sample weighted stats
3d6e2b9 
Allows for re-use with calc_abc3 and similar

Updates #798
shawnlaffan added a commit that referenced this issue Sep 14, 2021
@shawnlaffan
Update expected percentiles for range weighted label props
51e9962 
Interpolated values in Stats::Desc::PDL differ from Biodiverse::Stats

Updates #798
shawnlaffan added a commit that referenced this issue Sep 14, 2021
@shawnlaffan
Code cleanup
0e701a2 
Updates #798
shawnlaffan added a commit that referenced this issue Sep 14, 2021
@shawnlaffan
Cleanup redundant package lexicals for stats
1f3a047 
These were never used in the packages.

Updates #798
shawnlaffan added a commit that referenced this issue Sep 21, 2021
@shawnlaffan
Clean up some metadata
82feadb 
Updates #798
shawnlaffan added a commit that referenced this issue Sep 21, 2021
@shawnlaffan
Clean up some metadata
6e6fa2b 
Updates #798
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Tasks are done, closing

shawnlaffan added a commit that referenced this issue Apr 24, 2022
@shawnlaffan
Indices: numeric labels now use Statistics::Descriptive::PDL
e6b83f5 
A late update to #798
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