doc/robustness_specs.md

In xieshu95/robustness: Test the Robustness of DAISIE to Geodynamics

DAISIE Analysis pipeline specifications

This document aims to layout a standardized structure for analysis pipeline runs in future DAISIE studies. DAISIE simulation output objects currently consist of nested lists. These lists always contain the following information.

1) island_age - The island age (numeric scalar) of a simulation. 2) not_present - The number of mainland species that did not colonize the island (numeric scalar). 3) stt_all - The species-through-time table with the number of immigrant, anagenetic, cladogenetic and total species present on the island (matrix).

For clade-specific simulations, the following levels of the list are a set of the following elements per each colonizing lineage: 1) branching_times - The branching (or colonization) times of extant species on the island at present. The first element always corresponds to the island age. 2) stac - The status of the clade formed by the immigrant (numeric scalar). stac = 1 : immigrant is present but has not formed an extant clade stac = 2 : immigrant is not present but has formed an extant clade stac = 3 : immigrant is present and has formed an extant clade stac = 4 : immigrant is present but has not formed an extant clade, and it is known when it immigrated. stac = 5 : immigrant is not present and has not formed an extant clade, but only an endemic species stac = 6 : like 2, but with max colonization time stac = 7 : like 3, but with max colonization time 3) missing_species - The number of species that were not sampled for a particular clade (only applicable for endemic clades) (numeric scalar).

The final output of a pipeline run should be a list. Each top level of this list should refer to one geodynamic replicate and contain the following:

1) Simulate with Geodynamics (1000x replicates) 2) Maximum likelihood estimates obtained replicate (1000 ML estimates) 3) Simulate without geodynamics obtained using ML values from step 2 as generating parameters (1 replicate per ML, thus 1000 total replicates) 4) MLEs from simulations from step 3 (1000 ML estimates) 5) Simulate without geodynamics using ML values from step 4 as generating parameters (1 replicate per ML, thus 1000 total replicates) 6) Calculate delta nLTT of paired simulations from step 1 and step 3. 7) Calculate delta nLTT of paired simulations from step 3 and step 5.

xieshu95/robustness documentation built on April 13, 2020, 1 p.m.