Plotting ancestral states | Using CLA secsse

Introduction | Set-up | Fitting the model | Comparing with reconstructed trees | References

Secsse introduction | Secsse input files | Note on assigning ambiguity to taxon trait states | Setting up an analysis | ETD | Lambda matrices | Mu vector | Transition matrix | Maximum Likelihood | CTD | CR | Model comparisong using AIC | Further help | References

DAISIE – Dynamic Assembly of Island biotas through Speciation, Immigration and Extinction | Loading data table | Formatting table to run in DAISIE | Optimizing parameters using maximum likelihood | Example 1: Optimizing all parameters, with diversity-dependence in speciation and colonisation | Example 2: Optimizing model without diversity-dependence | Example 3: Optimizing model with no diversity-dependence and no anagenesis | Example 4: Optimizing all parameters, but allowing Darwin’s finches to have a separate rate of cladogenesis. | Example 5: Optimizing a model with no diversity-dependence, but allowing Darwin’s finches to have a separate rate of cladogenesis and extinction. | Example 6: Optimizing a model with no diversity-dependence, using the DAISIE-DE approach.

Prep work | Creating parameter structure | Simulating | Conditioning

Key for the different values of stac that can be used in DAISIE objects, and how they can be specified in the function DAISIE_dataprep.

DAISIE – Dynamic Assembly of Island biotas through Speciation, Immigration and Extinction | Loading | Simulating islands | Example 5.1 – Simulating r n_replicates islands with no diversity-dependence, all species sharing the same parameters, and plotting the results | Example 5.2 – Simulating r n_replicates islands with diversity-dependence (K’=10), all species sharing the same parameters, and plotting the results | Example 5.3 – Simulating r n_replicates islands allowing Darwin’s finches to have a higher rate of cladogenesis:

1. Load, prepare and visualize data | The table contains the following 4 columns (column headers need to be written exactly like this): | 1.1. Create DAISIE datalist from the input table | 1.2. View DAISIE datalist | 1.3. Visualise the data | Plot age versus diversity | 2. Fit DAISIE models | 2.1 Fit DI model | 2.2 Fit CS model | 2.3 Fit CS_no_ana model | 2.4 Fit IW model | 2.5 Fit IW_no_ana model | 3. Simulate islands under given DAISIE models | 3.1 Simulate islands with the parameters estimated from the best model for the Hispaniolan Eleutherodacytlus data | 3.2 Plot the species-through-time plots resulting from the simulations.

SADISA introduction | SADISA usage