Organized EcoSim functions into modules

[ngotelli]

Hi Ted -

Here is a catalog of all the functions that are currently in EcoSimR, and how they should be organized into distinct modules. For co-occurrence, the Sim9 and Sim9.Fast modules do not work inside of the original Null.Model.Engine because the replicate matrices are not independent of one another, but are built consecutively. Also, some of the algorithms contain special inputs, such as site or species weights (e.g., Sim10)..

Let me know if you have any questions.

Best,

Nick

General Functions

• Get.Params
• Data.Read
• Set.The.Seed
• Null.Model.Engine
• Null.Model.Summary
• Output.Results

  Co-occurrence Module

  Metrics

• Species.Combo
• Checker
• C.Score [DEFAULT]
• C.Score.var
• C.Score.skew
• V.Ratio

  Algorithms

• Sim9
• (Sim9.Single) [Single replicate of Sim9.Fast]
• Sim9.Fast [DEFAULT]
• (VectorSample) [used by other functions]
• Sim1
• Sim2
• Sim3
• Sim4
• Sim5
• Sim6
• Sim7
• Sim8
• Sim10

  Graphics

• Null.Model.Plot [DEFAULT]
• CoOccurrence.Plot [DEFAULT]
• Burn.In.Plot [Useful for adjusting burn-in parameter for Sim9.Fast]

  Sample Data

• West Indies Finches.csv [DEFAULT]

  Niche Overlap Module

  Metrics

• Pianka [DEFAULT]
• Czekanowski
• Pianka.var
• Czekanowski.var
• Pianka.skew
• Czekanowski.skew

  Algorithms

• RA1
• RA2
• RA3 [DEFAULT]
• RA4

  Graphics

• Null.Model.Plot [DEFAULT]
• Niche.Overlap.Plot [DEFAULT]

  Sample Data

• MacArthur Warblers.csv [DEFAULT]

  Size Ratio Module

  Metrics

• Min.Diff
• Min.Ratio
• Var.Diff
• Var.Ratio [DEFAULT]

  Algorithms

• Uniform.Size [DEFAULT]
• Uniform.Size.User
• Source.Pool.Draw
• Gamma.Size

  Graphics

• Null.Model.Plot [DEFAULT]
• Size.Ratio.Plot [DEFAULT]

  Sample Data

• Desert Rodents.csv [DEFAULT]

[emhart]

All of this is implemented.