Function reference
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adapt.prior.plot.code() - adapt.prior.plot.code- Create Prior Plot for Adaptive Model
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adapt.prior.post.plot.code() - adapt.prior.post.plot.code- Create Prior vs. Posterior Plot for Adaptive Model
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antler.data - Antler Size Dataset from Tsuboi et al. (2024), Evol. Biol.
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blouch.adapt.prep() - blouch.adapt.prep - Setup dat file to run adaptive model
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blouch.direct.adapt.prep() - blouch.direct.adapt.prep - Setup dat file to run direct effect and adpative model
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blouch.direct.prep() - blouch.direct.prep - Setup dat file to run direct effect model
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blouch.reg.adapt.mlm.prep() - blouch.reg.adapt.mlm.prep - Setup dat file to run Multilevel Multi-Optima adaptive model
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blouch.reg.adapt.prep() - blouch.reg.adapt.prep - Setup dat file to run multi-optima adaptive model
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blouch.reg.direct.adapt.mlm.prep() - blouch.reg.direct.adapt.mlm.prep - Setup dat file to run multi-optima direct effect adaptive model
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blouch.reg.direct.adapt.prep() - blouch.reg.direct.adapt.prep - Setup dat file to run multi-optima direct effect adaptive model
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blouch.reg.direct.mlm.prep() - blouch.reg.direct.mlm.prep - Setup dat file to run Multilevel Multi-Optima direct effect model
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blouch.reg.direct.prep() - blouch.reg.direct.prep - Setup dat file to run multi-optima direct effect model
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blouch.reg.mlm.prep() - blouch.reg.mlm.prep - Setup dat file to run multilevel multi-optima model
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blouch.reg.prep() - blouch.reg.prep - Setup dat file to run multi-optima model
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calc_adaptive_V() - calc_adaptive_V - Calculate adaptive variance/covariance matrix
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calc_adaptive_cov_plot() - calc_adaptive_cov_plot - Calculate covariance matrix for adaptive covariance plot
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calc_adaptive_dmX() - calc_adaptive_dmX - Calculate adaptive predictor matrix for Blouch
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calc_direct_V() - calc_direct_V - Calculate direct effect model V/CV matrix
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calc_mixed_dmX() - calc_mixed_dmX - Calculate mixed direct effect and adaptive predictor matrix for Blouch
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calc_multiadaptive_cov_plot() - calc_multiadaptive_cov_plot - Calcualte covariance matrix for mult-adaptive covariance plot
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cervidae.tree - Cervidae phylogent from Tsuboi et al. (2024), Evol. Biol.
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concat.factor() - concat.factor - For internal Blouch use Thanks to user "snaut" at stackoverflow, http://stackoverflow.com/users/1999873/snaut
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covariance.prior.adapt.plot.code() - covariance.prior.adapt.plot.code- Create Prior Covariance Plot for Adaptive Model
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covariance.prior.direct.plot.code() - covariance.prior.direct.plot.code- Create Prior Covariance Plot for Direct Effect Model
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covariance.prior.post.adapt.plot.code() - covariance.prior.post.adapt.plot.code- Create Prior vs. Posterior Covariance Plot for Adaptive Model
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covariance.prior.post.direct.plot.code() - covariance.prior.post.direct.plot.code- Create Prior vs. Posterior Covariance Plot for Direct Effect Model
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direct.adapt.prior.plot.code() - direct.adapt.prior.plot.code- Create Prior Plot for Direct Effect + Adaptive Model
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direct.adapt.prior.post.plot.code() - direct.adapt.prior.post.plot.code- Create Prior vs. Posterior Plot for Direct Effect + Adaptive Model - Simulated Data
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direct.prior.plot.code() - direct.prior.plot.code- Create Prior Plot for Direct Effect Model
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direct.prior.post.plot.code() - direct.prior.plot.code- Create Prior vs. Posterior Plot for Direct Effect Model
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hl.prior.plot.code() - hl.prior.plot.code- Create Plot for Half-life Prior Distribution
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hl.prior.post.emp.plot.code() - hl.prior.post.emp.plot.code- Create Prior vs. Posterior Plot for Half-life Prior Distribution for Empirical Dataset
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hl.prior.post.plot.code() - hl.prior.plot.code- Create Prior vs Posterior Plot for Half-life Prior Distribution for Simulated Dataset
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lineage.constructor() - lineage.constructor function - Construct a list with variables based on regime timing and placement
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lineage.nodes() - lineage.nodes - Function for internal Blouch use Given a certain node, return the list of all parent nodes back to the root of the tree
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optima.prior.plot.code() - optima.prior.plot.code- Create Prior Plot for Multi-Optima Model
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optima.prior.post.plot.code() - optima.prior.post.plot.code- Create Prior Plot for Multi-Optima Model
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parent() - parent function - Returns parent node of offspring node given node number
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reg.adapt.mlm.ve.prior.post.plot.code() - reg.adapt.mlm.ve.prior.post.plot.code- Create Prior vs. Posterior Plot for Multilevel Multi-Optima Adaptive Model - Varying Effects - Simulated Data
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reg.adapt.prior.plot.code() - reg.adapt.prior.plot.code- Create Prior Plot for Multi-Optima Adaptive Model - Simulated Data
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reg.adapt.prior.post.plot.code() - reg.adapt.prior.post.plot.code- Create Prior vs. Posterior Plot for Multi-Optima Adaptive Model - Simulated Data
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reg.adapt.ve.prior.post.plot.code() - reg.adapt.ve.prior.post.plot.code- Create Prior vs. Posterior Plot for Multi-Optima Adaptive Model - Varying Effects - Simulated Data
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reg.direct.adapt.prior.plot.code() - reg.direct.adapt.prior.plot.code- Create Prior Plot for Multi-Optima Direct Effect + Adaptive Model
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reg.direct.adapt.prior.post.plot.code() - reg.direct.adapt.prior.post.plot.code- Create Prior vs. Posterior Plot for Multi-Optima Direct Effect + Adaptive Model - Simulated Data
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reg.direct.adapt.ve.prior.post.plot.code() - reg.direct.adapt.ve.prior.post.plot.code- Create Prior vs. Posterior Plot for Multi-Optima Direct Effect + Adaptive Model - Varying Effects - Simulated Data
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reg.direct.mlm.ve.prior.post.plot.code() - reg.direct.mlm.ve.prior.post.plot.code- Create Prior vs. Posterior Plot for Multilevel Multi-Optima Direct Effect Model - Varying Effects - Simulated Data
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reg.direct.prior.plot.code() - reg.direct.prior.plot.code- Create Prior Plot for Multi-Optima Direct Effect Model - Simulated Data
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reg.direct.prior.post.emp.plot.code() - reg.direct.prior.post.emp.plot.code- Create Prior vs. Posterior Plot for Multi-Optima Direct Effect Model
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reg.direct.prior.post.plot.code() - reg.direct.prior.post.plot.code- Create Prior vs. Posterior Plot for Multi-Optima Direct Effect Model - Simulated Data
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reg.direct.ve.prior.post.emp.plot.code() - reg.direct.ve.prior.post.emp.plot.code- Create Prior vs. Posterior Plot for Multi-Optima Direct Effect Model - Varying Effects
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reg.direct.ve.prior.post.plot.code() - reg.direct.ve.prior.post.plot.code- Create Prior vs. Posterior Plot for Multi-Optima Direct Effect Model - Varying Effects - Simulated Data
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set.converge.regimes() - set.converge.regimes - function to assign regimes on a phylogeny
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sig.prior.plot.code() - sigma.prior.plot.code- Create Prior vs. Posterior Plot for Sigma
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sig.prior.post.plot.code() - sigma.prior.post.plot.code- Create Prior vs. Posterior Plot for Sigma
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sim.adaptive.data() - sim.adaptive.data- Simulate Adaptive Data
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sim.adaptive.multi.data() - sim.adaptive.multi.data- Simulate Adaptive Data with Multiple X Traits
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sim.direct.adaptive.data() - sim.adaptive.multi.data- Simulate Direct Effect + Adaptive Data with Multiple X Traits
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sim.direct.data() - sim.direct.data- Simulate Direct Effect Model Data
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sim.direct.multi.data() - sim.direct.multi.data- Simulate Direct Effect Model Data with Multiple X Traits
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sim.reg.adapt.data() - sim.reg.adapt.data- Simulate Multi-Optima Adaptive Model Data
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sim.reg.adapt.mlm.ve.data() - sim.reg.adapt.mlm.ve.data- Simulate Multilevel Multi-Optima Adaptive Model Data - Varying Effects
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sim.reg.adapt.ve.data() - sim.reg.adapt.ve.data- Simulate Multi-Optima Adaptive Model Data - Varying Effects
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sim.reg.data() - sim.reg.data- Simulate Multi-Optima Data
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sim.reg.direct.adapt.data() - sim.reg.direct.adapt.data- Simulate Multi-Optima Direct EFfect + Adaptive Model Data
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sim.reg.direct.adapt.ve.data() - sim.reg.direct.adapt.data- Simulate Multi-Optima Direct EFfect + Adaptive Model Data - Varying Effects
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sim.reg.direct.data() - sim.reg.direct.data- Simulate Multi-Optima Direct Effect Model Data
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sim.reg.direct.mlm.ve.data() - sim.reg.direct.mlm.ve.data- Simulate Multilevel Multi-Optima Direct Effect Data - Varying Effects
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sim.reg.direct.ve.data() - sim.reg.direct.ve.data- Simulate Multi-Optima Direct Effect Model Data - Varying Effects
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tree.10K - Primate tree with 301 tip species This is the primate phylogeny for Version 3 of 10K trees
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ts_fxn() - ts_fxn function - Internal Blouch function to return tree data
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vy.prior.plot.code() - vy.prior.plot.code- Create plot for Vy Prior Distribution
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vy.prior.post.emp.plot.code() - vy.prior.post.emp.plot.code- Create Prior vs. Posterior Plot for Vy for Empirical Dataset
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vy.prior.post.plot.code() - vy.prior.post.plot.code- Create Prior vs. Posterior Plot for Vy
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weight.matrix() - weight.matrix - For internal Blouch use - wrapper to apply weights_regimes to each lineage
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weights_regimes() - weights_regimes - For internal Blouch use For individual lineage, sum up the segments in each regimes
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weights_segments() - weights_segments - For internal Blouch use For individual lineage, determine the weighting of each segment
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ysim.ppc.plot.code() - ysim.ppc.plot.code - Create plot for Prior and Poserior Predictive Checks