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Current function name
Current collection
Function or workflow?What does it do?Does it work?
Is it worth keeping?
Target collection (* = dataset specific)
Notes
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aceArborArborFunction Function for ancestral state reconstructionyesyesphylogenies
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aceArborVariableFontArborFunction
Ancestral state reconstruction with a few extra options
nono
redundant with aceArbor and outdated
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aceWorkflowArborWorkflowWorkflow for ancestral state reconstruction
no - at least not unless you know the opaque required arguments
no
not useful yet but we could have something like this. has mutate filter and select with ancestral state reconstruction
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Add columnsArborFunctionadds columns to a matrixyesyesbase
adds new column that is the sum of two other continuous columns; needs to work better when given strange input
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adonis UABArborFunctionruns "adonis" on a distance matrixno?nocommunities
not general but we need something that can do this
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BC-TestArborFunction
creates bray-curtis dissimilarity matrix from community data
nono
redundant with Bray-Curtis Dissimilarity
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BestFittingTraitModelArborWorkflow
Workflow to compare the fit of three different models in phylolm
yesyes
exampleWorkflows
crashes when there is a space in a column name; also needs way better output
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Bob2testArborWorkflow
Applies "decostand" and "summarizeDiversity" to community data
nono
cannot "set up and run"
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boxplotArborFucntionMakes a boxplotyesyesbase
needs to be made more general - panelcol should be optional
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Bray-Curtis DissimilarityArborFunction
creates bray-curtis dissimilarity matrix from community data
nono
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Bray-Curtis dissimilarity for hclust (adds rownames)
ArborFunction
creates bray-curtis dissimilarity matrix from community data
nono
very similar to Bray-Curtis Dissimilarity, BC-test
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BrayCurtisTestArborFunction
creates bray-curtis dissimilarity matrix from community data
yesyescommunities
this one is the one that works I think!
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coleAnalysisArborWorkflowsomething complicatedeasson*
I do not know if these work or not but
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coleDataPrepArborWorkflowsomething complicatedeasson*
they are specific to cole - they should be maintained in their
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coleDataPrepV2ArborWorkflowsomething complicatedeasson*own location!
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coleFullAnalysisArborWorkflowsomething complicatedeasson*
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coleFullAnalysis2ArborWorkflowsomething complicatedeasson*
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coleVisualizationArborWorkflowsomething complicatedeasson*
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CongruifyArborFunctioncongruificationunclearyesphylogenies
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Continuous to discreteArborFunction
changes continuous to discrete character using threshold
yesyesbase
would be nice to have control of new column name
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Convert Tree to Hierarchy Table
ArborFunctionconverts tree to "taxonomic" hierarchy tablepartiallyyesphylogenies
output is not usable for anolis tree - also spits out garbage to console
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Cophenetic Distance Matrix from Tree
ArborFunction
creates cophenetic distance matrix from a tree
noyesphylogenies
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cophenTestArborWorkflow
rescale tree then make cophenetic distance matrix
nono
this could be in "example workflows" but I don't know if it is actually a good example of something common
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Cross correlationArborFunctioncross-correlation analysis of matrix columnsyesyesbase
works but needs rownames and maybe some options
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Curt Reconstruction Debugging Wflow
ArborWorkflowsomething to do with open treenono
i am not sure what inputs this needs but i can't make it work
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Debug Return the OpenTree subtree from a node list
ArborFunctionget open tree from ottIDsno?yesopentree
need sample input
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decostandArborFunctionruns "decostand" analysisyesyescommunities
some funny business with names
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demoArbornothingnothingnono
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demo2ArborWorkflowmatches names and runs fitContinuousnoyes
exampleWorkflows
this would be a nice clean example - broken now i think
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EassonScratchArborFunctiondoes a bunch of stuff but actually nothingnono
both these can be put in *easson
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EassonScratchWflowArborWorkflowmatches two tablesnono
this looks like an experiment
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Estimate ancestral statesArborFunction
Ancestral state reconstruction for discrete states under ER
nonooutdated
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Filter by attributeArborFunction
Filter rows by some attribute: e.g. select all anoles with awesomeness > 1
yesyesbase
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find.mleArborFunctionFind maximum of functionnono
would be good to have tools like this someday
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find.mle (1)ArborWorkflowthis looks like a table matchernono
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Fit continuousArborFunctiongeiger fitcontinuousyesyesphylogenies
output leaves something to be desired
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Fit discreteArborFunctiongeiger fitDiscretenoyesphylogenies
some R error that needs to be fixed
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fitTraitModelsArborWorkflowfits three models from fitContinuousyesyes
exampleWorkflows
this is a nice example but the output is crap
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Geiger treedataArborFunctionruns geiger treedatayesno
outdated, we should use aRbor stuff
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Geiger TreeDataArborFunctionruns geiger treedatanono
outdated, we should use aRbor stuff
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getOpenTreeTaxonomyIDsArborFunctionfetch OTTIDsnoyesopentree
we need something like this but i don't know which one and i can't get this one to work
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GetOTLtreeFromTableWithIDsArborFunctionfetch tree from OTT Idsnoyesopentreelikewise
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getTipNamesArborFunctionreturn tip names from phylogenetic treenoyesphylogenies
i am not sure we need something this basic but what the hell
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getVectorArborFunctionpulls vector from trait matrixnoyesbase
not synched with new aRbor - also I am not sure why this needs a tree. maybe just redo
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hclustDendrogramArborFunctionplots a dendogram from a distance matrixyes?yesphylogenies
Plot does not show up in visualization window
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kembelBiodiversitySummArborWorkflowDoes a few community phylogenetics thingsyesyes
exampleWorkflows
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kembelDataPrepArborWorkflowprep data for downstream analyses?noeasson
this seems specific to some data somewhere but i am not sure which data
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kembelKcalcArborFunctionk-calc across rows of data tablenoyesphylogenies
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kembelMultivariateCommAnalysis
ArborWorkflowmakes some sort of dendogramnonoeasson
might be ok to put this and kembelDataPrep in the Easson folder
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kembelsummarizeDiversityArborFunctiondoes a ton of thingsnonoeassonlikewise
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kembleFaithsPDArborFunctioncalculate Faith's PDnoyescommunities
some notes there on how to make it work
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LifeMapper occurrences from Experiment Number
ArborFunctionfetches data from lifemapper APInoyeslifemapper
maybe i just don't know a good "Experiment number"
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LookupOpenTreeNamesArborFunctionfetch names and OTT IDs from opentreeenoyesopentree
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Make Fake Branch LengthsArborFunctionuses compute.brlenyesyesphylogenies
should be made into some more general thing
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make_mk2_ARD_tArborFunctionmakes a diversitree functionnono
this seems experimental and i don't think we can handle it yet!
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make.mk2ArborFunctionmakes a diversitree functionnono
failed experiment?
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make.treedataArborFunctionsome tree-matching stuffnono
I don't see the point of this and I don't think it synchs with new aRbor
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Mantel TestArborFunctionmantel test?yescommunities
but may be redundant
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Marginal ASRArborFunctiona long r script with no inputsyesnodelete!
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matchPhyloCommArborFunctionruns this picante function?yescommunities
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matchTablesArborFunctionreorder one matrix to match another?yesbase
I suppose this is ok but not essential
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Mean Nearest Taxon Distance
ArborFunctionpicante mntdyescommunities
a pain to run as it takes a matrix not a tree - but easy to fix
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Merge Occurrences Into TreeArborFunction
merge locality occurences with tree - from Curt
yesyesphylomap
all of these should be documented like this function!
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MergeTreeOccurrenceMorphArborFunction
merge locality occurences with tree - from Curt
yesyesphylomap
not sure how this differs from Merge Occurences into Tree
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multi2diArborFunctionrandomly resolve all polytomies in treenoyesphylogenies
i have no idea why this doesn't work!
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openTreeAceArborWorkflowuses open tree tree for ACEnoyes
exampleWorkflows
something very strange is happening here
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openTreeAceSetupArborWorkflowuses open tree tree for ACEnoyes
exampleWorkflows
likewise, pathological
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OpenTreeCongruifyWorkflowArborWorkflowunfinishednono
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Partial Mantel TestArborFunctionthree-way mantel test?yescommunities
merge with other mantel things
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PGLSArborFunctionPGLSyesyesphylogenies
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Phylogenetic signalArborFunctionphylogenetic signal testyesyesphylogenies
new version on my github branch that works with new easy mode page
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PhylolmArborFunctionphylogenetic linear modelyesyesphylogenies
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PlotTraitsArborFunctionplots PICs with regression lineyesyesphylogenies
merge with pic function
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PlotTreeWithAPEArborFunctionPlots tree and makes a static imagenoyesphylogenies
Kind of silly to make it be a static image to begin with, but either way I don't know where it's going (being saved to)
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predictMissingDiscreteArborFunctionPredict missing discrete datanoyesphylogenies
For some reason new aRbor function needed is not available.
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Reconstruct Ancestral States with OpenTree
ArborWorkflowOpen tree ACE examplenoyes
examples or opentree
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rescalePhyloArborFunctionrescale tree branch lengthsyesyesphylogenies
but image does not show up in vis tab (known bug)
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ResolvePolytomyArborFunctionmulti2diyesyesphylogenies
redundant with multi2di above
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ScientificNamesFromCharacterMatrix
ArborFunctionpulls names from matrixnoyesbaseinteresting
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scratch-testingArborFunctionsome stuffnono
I think this was someone just messing around - delete?
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sesmpdArborFunction
Calculates standardized effect sizes of phylogenetic community structure
noyescommunities
There is currently no way to change options on this function. There are at least three parameters are user would and should tweak
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simpleAceWorkflowArborWorkflowACE workflowyesyes
workflow Examples
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summarizeDiversityArborFunctionCole analysisyesyesEasson
too detailed and a huge block - but a good guide
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summarizeDiversityTestceArborFunctionCole analysisyesyesEasson
similar to summarizeDiversity
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TableRandomRowSelectArborFunction nothingnonoempty
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TableSelectRandomRowsArborFunctionrandomly select table rowsyesyesbase
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TableUnderscoreToSpaceArborFunctionreplace underscore with spaceyesyesbase
might be nice to have more generic grep-like function
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testrownamesArborFunctionrelated to decostand experimentsyesyescommunities
reconcile with other decostand things
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testWorkflowArborWorkflowfitcontinuous workflownoyes
workflow examples
other duplicates exist though
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TestworkflowArborWorkflowpartial ace workflownono
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timeCalibrateOpenTreeArborWorkflowincomplete thingnono
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treeplyrFilterArbornothingnonodeleted?
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treeplyrMutateArbornothingnonodeleted?
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treeplyrSelectArbornothingnonodeleted?
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treeplyrSummaryArbornothingnonodeleted?
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treeplyrTreeDplyArbornothingnonodeleted?
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validateASRArbornothingnonodeleted?
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validateASRWorkflowArbornothingnonodeleted?
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WorkflowArbornothingnonoempty
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