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Randomisations - add enhanced randomisation outputs #607

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shawnlaffan opened this issue Aug 3, 2016 · 3 comments
Closed

Randomisations - add enhanced randomisation outputs #607

shawnlaffan opened this issue Aug 3, 2016 · 3 comments
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enhancement randomisations
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Release_2.0

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@shawnlaffan
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The randomisations produce rank-relative scores that can be converted into significances at varying levels of alpha, but outside of Biodiverse.

It would be useful to add it as a function within Biodiverse.
@shawnlaffan shawnlaffan added this to the Release_2.0 milestone Aug 3, 2016
@shawnlaffan shawnlaffan self-assigned this Aug 3, 2016
shawnlaffan added a commit that referenced this issue Aug 4, 2016
@shawnlaffan
calculate significance scores from rand comparisons (spatial outputs)
c6bd36e 
Only works on spatial outputs at the moment.

Need to:
1.  Relocate the convert_comparisons_to_significances sub
2.  Do the same for cluster node calculations
3.  Refactor the logic

Also not sure this is the best output format (e.g. -0.01 for sig low at alpha = 0.01).

Updates #607
shawnlaffan added a commit that referenced this issue Aug 4, 2016
@shawnlaffan
move get_significance_from_comp_results to Common.pm
cc354e9 
Updates #607
shawnlaffan added a commit that referenced this issue Aug 4, 2016
@shawnlaffan
Calculate significance levels for cluster nodes
e644a11 
Updates #607
shawnlaffan added a commit that referenced this issue Aug 4, 2016
@shawnlaffan
refactor get_significance_from_comp_results
a5ed728 
Hard code the default thresholds to avoid repeated map calls.

Only calculate the two tail scores if the relevant one tail threshold is passed.

Also test that we get at least some defined results (although this does not happen if we up the number of iterations to 99 due to the data set used).

Updates #607
@shawnlaffan
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All newly run randomisations now get this by default.

We could perhaps add the option to calculate it for existing randomisations, but can be under its on issue.

shawnlaffan added a commit to NunzioKnerr/biodiverse_pipeline that referenced this issue Aug 7, 2016
@shawnlaffan
plot CANAPE using Biodiverse significance categories
c771ed0 
Distinct functions to plot CANAPE classes using the newly introduced Biodiverse significance classification (see  shawnlaffan/biodiverse#607 and http://biodiverse-analysis-software.blogspot.com.au/2016/08/biodiverse-now-categorises-your.html )

Differs from the current system by thresholding using >, not >=, but it has little effect for phylo indices.
shawnlaffan added a commit that referenced this issue Aug 7, 2016
@shawnlaffan
check the significance categorisation lists after reintegration
a47e9aa 
These lists were added in issue #607 and need to be re-categorised, not incremented.

Updates #588
@shawnlaffan
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Re-opening. The negated threshold is confusing. Percentile rank would be cleaner.

@shawnlaffan shawnlaffan reopened this Aug 24, 2016
shawnlaffan added a commit that referenced this issue Aug 26, 2016
@shawnlaffan
add capacity to rename randomisation outputs
8cdcb81 
Updates #607
shawnlaffan added a commit that referenced this issue Aug 29, 2016
@shawnlaffan
Change threshold list subname from sig to p_rank
7f99f4a 
Also add better tests for the threshold calculations.

Updates issue #607
shawnlaffan added a commit that referenced this issue Aug 29, 2016
@shawnlaffan
separate the randomisation scores more extreme than 0.05/0.95
58dc97e 
This is a much cleaner approach and
allows for greater flexibility in later code.

Updates #607
@shawnlaffan shawnlaffan changed the title Randomisations - add option for significance thresholds Randomisations - add enhanced randomisation outputs Aug 29, 2016
@shawnlaffan
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Mark as fixed (again)

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