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Indices - add species richness estimators #420

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GoogleCodeExporter opened this issue Mar 27, 2015 · 28 comments
Closed

Indices - add species richness estimators #420

GoogleCodeExporter opened this issue Mar 27, 2015 · 28 comments
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@shawnlaffan
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auto-migrated enhancement
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Release_2.0

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It would be useful to add some of the richness estimators as indices.  See the 
EstimateS software for more details.  
http://viceroy.eeb.uconn.edu/estimates/EstimateSPages/EstSUsersGuide/EstimateSUs
ersGuide.htm#Appendices

Original issue reported on code.google.com by shawnlaffan on 19 Nov 2013 at 5:18
@shawnlaffan shawnlaffan self-assigned this Apr 9, 2015
shawnlaffan added a commit that referenced this issue Apr 15, 2015
@shawnlaffan
Update issue #420. Update version numbers in branch to match master. …
63287b9 
…Maybe this will avoid some of the merge conflicts.

Signed-off-by: Shawn Laffan <shawnlaffan@gmail.com>
shawnlaffan added a commit that referenced this issue Apr 15, 2015
@shawnlaffan
Merge branch 'master' into issue_420_richness_estimators
1f06c6c 
Updates issue #420

The following conflicts were edited.  Most likely we will just cherry pick the RichnessEstimation.pm file into master when we merge it all back, rather than merge all the changes.

	bin/BiodiverseGUI.pl
	bin/run_randomisation.pl
	etc/pp/build.pl
	etc/versions.txt
	example_scripts/import_rasters_and_analyse.pl
	lib/Biodiverse/BaseData.pm
	lib/Biodiverse/BaseStruct.pm
	lib/Biodiverse/Common.pm
	lib/Biodiverse/GUI/BasedataImport.pm
	lib/Biodiverse/GUI/Callbacks.pm
	lib/Biodiverse/GUI/Help.pm
	lib/Biodiverse/GUI/MatrixGrid.pm
	lib/Biodiverse/GUI/Project.pm
	lib/Biodiverse/GUI/Tabs/Labels.pm
	lib/Biodiverse/GUI/Tabs/Tab.pm
	lib/Biodiverse/Indices.pm
	lib/Biodiverse/Indices/PhyloCom.pm
	lib/Biodiverse/Indices/Phylogenetic.pm
	lib/Biodiverse/Indices/PhylogeneticRelative.pm
	lib/Biodiverse/Randomise.pm
	lib/Biodiverse/ReadNexus.pm
	lib/Biodiverse/Statistics.pm
	lib/Biodiverse/Tree.pm
	lib/Biodiverse/TreeNode.pm
	t/13-Tree.t
	t/lib/Biodiverse/TestHelpers.pm

Signed-off-by: Shawn Laffan <shawnlaffan@gmail.com>
shawnlaffan added a commit that referenced this issue Apr 10, 2016
@shawnlaffan
Update Chao1 test values to use those generated from the SpadeR packa…
e8009b4 
…ge for R.

Updates issue #420
shawnlaffan added a commit that referenced this issue Apr 10, 2016
@shawnlaffan
Add Chao2 standard errors
386ac2d 
Updates issue #420
@shawnlaffan
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This issue is now close to completed.
Need to decide whether or not to include the ACE and ICE variance estimators. The formulae can be taken from SpadeR.

shawnlaffan added a commit that referenced this issue Apr 20, 2016
@shawnlaffan
Add initial code for ICE variance calculations.
e4a4f27 
Adapted directly from SpadeR, and completely untested at this stage.

Updates issue #420
shawnlaffan added a commit that referenced this issue Apr 25, 2016
@shawnlaffan
Add more tests for Chao2 calcs.
0e2fb57 
We check for cases (Q1==0 && Q2>0), (Q1 > 0 && Q2==0) and (Q1==0 && Q2==0).

Flush out an error in the confidence interval logic by doing so.

Updates issue #420
shawnlaffan added a commit that referenced this issue Apr 25, 2016
@shawnlaffan
Add more tests for Chao1 calcs.
d8c9731 
As with the Chao2 calcs in 0e2fb57 we now check for cases (F1==0 && F2>0), (F1 > 0 && F2==0) and (F1==0 && F2==0).

Flushes out some errors with the variance calcs in the process.

Updates issue #420
shawnlaffan added a commit that referenced this issue Apr 28, 2016
@shawnlaffan
Use a higher precision estimate of z for the confidence interval
7be885e 
Update the test expectations as appropriate.

Updates issue #420
shawnlaffan added a commit that referenced this issue Apr 28, 2016
@shawnlaffan
Factor out some common variables.
ccaf111 
Updates issue #420
shawnlaffan added a commit that referenced this issue Apr 28, 2016
@shawnlaffan
Initial work on the ACE variance and CI calculations
34bdfd2 
Not yet functional.

Updates issue #420
shawnlaffan added a commit that referenced this issue Apr 28, 2016
@shawnlaffan
Add confidence intervals for ACE
54370fc 
Needs more testing to shake out the various permutations.

Updates issue #420
shawnlaffan added a commit that referenced this issue Apr 28, 2016
@shawnlaffan
Make calc_ace use Chao1 if there are no rares or no singletons.
091c64d 
Updates issue #420

Still need to update the ICE code and conditions for the same cases.
shawnlaffan added a commit that referenced this issue Apr 30, 2016
@shawnlaffan
Rename CHAO1, CHAO2, ICE_SCORE and ACE_SCORE indices to use _ESTIMATE…
f7c6e7f 
… suffix for consistency

This enables some code simplification.

Updates issue #420
shawnlaffan added a commit that referenced this issue Apr 30, 2016
@shawnlaffan
calc_ice passes tests for simplest case.
97b1215 
Next is to test for Q1==0 an Q2==0.

Updates issue #420
shawnlaffan added a commit that referenced this issue Apr 30, 2016
@shawnlaffan
Handle more edge cases for ICE and ACE
a26c5ca 
Cases include all singletons, not singletons, single cells.

Still need to add a test for richness = 0

Updates issue #420
shawnlaffan added a commit that referenced this issue Apr 30, 2016
@shawnlaffan
calc_ice now uses non-empty groups
c68f533 
This entailed adding a new method to calculate the number of non-empty groups, and associated tests.

updates issue #420
shawnlaffan added a commit that referenced this issue Apr 30, 2016
@shawnlaffan
Merge remote-tracking branch 'remotes/origin/issue_420_richness_estim…
086cae6 
…ators'

Updates issue #420

# Conflicts were:
#	lib/Biodiverse/GUI/BasedataImport.pm
#	lib/Biodiverse/GUI/Exclusions.pm
#	lib/Biodiverse/GUI/Export.pm
#	lib/Biodiverse/GUI/GUIManager.pm
#	lib/Biodiverse/GUI/MatrixImport.pm
#	lib/Biodiverse/GUI/Overlays.pm
#	lib/Biodiverse/GUI/ParametersTable.pm
#	lib/Biodiverse/GUI/PhylogenyImport.pm
#	lib/Biodiverse/GUI/Popup.pm
#	lib/Biodiverse/GUI/ProgressDialog.pm
#	lib/Biodiverse/GUI/Tabs/Clustering.pm
#	lib/Biodiverse/GUI/Tabs/Labels.pm
#	lib/Biodiverse/GUI/Tabs/Outputs.pm
#	lib/Biodiverse/GUI/Tabs/Randomise.pm
#	lib/Biodiverse/GUI/Tabs/Spatial.pm
#	lib/Biodiverse/GUI/Tabs/SpatialMatrix.pm
#	lib/Biodiverse/GUI/YesNoCancel.pm
#	lib/Biodiverse/Indices.pm
#	lib/Biodiverse/Metadata/Indices.pm
#	lib/Biodiverse/SpatialConditions.pm
#	t/lib/Biodiverse/TestHelpers.pm
shawnlaffan added a commit that referenced this issue Apr 30, 2016
@shawnlaffan
ACE and ICE flag when they fell back to Chao estimators
3f0269f 
Updates issue #420
@shawnlaffan
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Now we really are close to completion.

SpadeR also gives coverage estimates and frequencies of rare species, so we could also add those if needed.

There are also the iChao estimators, but those could be added under their own issue.
http://onlinelibrary.wiley.com/doi/10.1111/biom.12200/abstract

@shawnlaffan shawnlaffan reopened this Apr 30, 2016
@shawnlaffan shawnlaffan added this to the Release_2.0 milestone Apr 30, 2016
@shawnlaffan
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Mark as closed.

The additional points in the last comment can be dealt with under new issues.

@shawnlaffan shawnlaffan mentioned this issue May 1, 2016
Open
shawnlaffan added a commit that referenced this issue May 1, 2016
@shawnlaffan
Avoid some divide by zero errors.
5575f87 
This also make sthe code consistent with EstimateS in terms of when it switches from ACE/ICE to Chao1/2.

Updates issue #420 (even though it is closed now)
shawnlaffan added a commit that referenced this issue May 3, 2016
@shawnlaffan
Add ACE test where all rares are singletons
20a06b5 
Updates issue #420
@shawnlaffan shawnlaffan mentioned this issue May 10, 2016
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