Claddis: a new R package for automating disparity analyses based on cladistic datasets
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Claddis: a new R package for automating disparity analyses based on cladistic datasets
- 1. Claddis: a new R package for automating disparity analyses based on cladistic datasets Graeme T. Lloyd
- 3. Extinction Random Marginal Asymmetric Korn et al. in press Intensity
- 5. Center of gravity Hughes et al. 2013
- 6. Caveat emptor Anderson and Friedman 2012
- 10. Claddis Safe taxonomic reduction #NEXUS TNT Step matrices Continuous characters Other features Current limitations
- 11. Data Choiniere et al. in press
- 12. Data Choiniere et al. in press 114 taxa | 555 characters
- 13. Distance Taxon_i 001011 Taxon_j 101101 Taxon_i 001011 Taxon_j 101101 Wills et al. 1994
- 15. Missing data Taxon_A 0000000000 Taxon_B 00000111?? Taxon_C 11???????? Taxon_D 00110????? Taxon_E ?????01100 A B A C 1.73 1.41 Euclidean 8 2 N 2.83 1.41 Max
- 16. Rescaled distances Distance / N = Gower Dissimilarity Distance / Max = MOD Dissimilarity A B A C 0.22 0.71 Gower 0.61 1.00 MOD
- 18. Gower vs. MOD PC2(16.0%) PC1 (34.1%) Gower
- 20. Gower vs. MOD PC2(9.5%) PC1 (14.1%) MOD
- 21. Missing data Taxon_A 0000000000 Taxon_B 00000111?? Taxon_C 11???????? Taxon_D 00110????? Taxon_E ?????01100 D E ? Euclidean 0 N 0 Max
- 22. Prune Taxon_A 0000000000 Taxon_B 00000111?? Taxon_C 11???????? Taxon_D 00110????? Taxon_E ?????01100
- 23. Fill gaps Butler et al. 2011 Average values: (Wills 1997) Phylogenetic prediction: (Brusatte et al. 2011; Butler et al. 2011)
- 24. Phylogenetic prediction Estimateallstates Estimate tips No Yes NoYes ? ? = = = = = ? ?
- 25. Phylogenetic prediction Estimateallstates Estimate tips No Yes NoYes = ? ? = = = = = ? ? = ? ? = = = = ? ? ? ?
- 26. = ? ? = = = = ? ? ? ? Phylogenetic prediction Estimateallstates Estimate tips No Yes NoYes = = = = = ? ? = = = = = ? ?
- 27. Phylogenetic prediction Estimateallstates Estimate tips No Yes NoYes = = = = = ? ? = = = = = ? ? = ? ? = = = = ? ? ? ? = = = = =
- 28. Phylogenetic signal Estimateallstates Estimate tips No Yes NoYes 0.63 0.66 0.530.52
- 32. Ordination with ancestors PC1 PC2 N Y N Y Tips States
- 33. Ordination with ancestors N Y N Y Tips States PC1 PC2
- 34. Ordination with ancestors N Y N Y Tips States PC1 PC2
- 35. Ordination with ancestors N Y N Y Tips States PC1 PC2
- 36. Ordination with ancestors Phylogenetic distances PC1 PC2
- 37. Disparity time series Cladistic matrix Distance matrix Ordination ‘Morphospace’ Time series
- 38. Disparity time series Cladistic matrix Distance matrix Ordination ‘Morphospace’ Time series Time series Benson and Druckenmiller in press
- 39. Disparity time series Tips only All nodes
- 40. Phylogenetic distance time series Tips only All nodes
- 41. Model residual time series Tips only Significantly +ve Significantly -ve
- 42. Model residual time series All nodes Significantly +ve