DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

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Simulates and computes the (maximum) likelihood of a dynamical model of island biota assembly through speciation, immigration and extinction. See Valente et al. 2015. Ecology Letters 18: 844-852, <DOI:10.1111/ele.12461>.

Author
Rampal S. Etienne, Luis M. Valente, Albert B. Phillimore & Bart Haegeman
Date of publication
2016-11-14 11:32:39
Maintainer
Rampal S. Etienne <r.s.etienne@rug.nl>
License
GPL-2
Version
1.2

View on CRAN

Man pages

DAISIE_convertprobdist
Converts the joint distribution of endemics and non-endemics...
DAISIE_dataprep
Prepare colonisation and branching time data to run in...
DAISIE_ExpEIN
The expected number of endemics and non-endemics under the...
DAISIE_format_sim
Converting simulation output from RAW to DAISIE format
DAISIE-internal
Internal DAISIE Functions
DAISIE_loglik_all
Computes the loglikelihood of the DAISIE model given data and...
DAISIE_margprobdist
The marginal distribution of endemics and non-endemics under...
DAISIE_ML
Maximization of the loglikelihood under the DAISIE model
DAISIE_numcol
The expectation and marginal distribution of the number of...
DAISIE-package
Dynamical Assembly of Islands by Speciation, Immigration and...
DAISIE_plot_sims
Plot island species-through-time (STT) plots
DAISIE_probdist
The joint distribution of endemics and non-endemics under the...
DAISIE_sim
Simulate islands with given parameters.
DAISIE_tutorial
Opens DAISIE tutorial
Galapagos_datalist
Colonization and branching times of 8 terrestrial avifaunal...
Galapagos_datalist_2types
Colonization and branching times of 8 terrestrial avifaunal...
Galapagos_datatable
Colonization and branching times of 8 terrestrial avifaunal...
islands_10reps_RAW
1000 islands in RAW format simulated with the ML parameters...
islands_1type_1000reps
1000 islands in DAISIE format simulated with the ML...
islands_2types_1000reps
1000 islands in DAISIE format simulated with the ML...

Files in this package

DAISIE
DAISIE/inst
DAISIE/inst/DAISIE_tutorial.pdf
DAISIE/NAMESPACE
DAISIE/data
DAISIE/data/islands_10reps_RAW.RData
DAISIE/data/Galapagos_datatable.RData
DAISIE/data/islands_2types_1000reps.RData
DAISIE/data/islands_1type_1000reps.RData
DAISIE/data/Galapagos_datalist_2types.RData
DAISIE/data/Galapagos_datalist.RData
DAISIE/R
DAISIE/R/DAISIE_IC.R
DAISIE/R/DAISIE_PEI.R
DAISIE/R/DAISIE_ExpEIN.R
DAISIE/R/DAISIE_utils.R
DAISIE/R/DAISIE_sim_core.R
DAISIE/R/DAISIE_loglik_all.R
DAISIE/R/DAISIE_sim.R
DAISIE/R/DAISIE_loglik_high_lambda.R
DAISIE/R/DAISIE_ML.R
DAISIE/R/DAISIE_dataprep.R
DAISIE/R/DAISIE_sim_min_type2.R
DAISIE/R/DAISIE_format_sim.R
DAISIE/R/DAISIE_plot_sims.R
DAISIE/R/DAISIE_tutorial.R
DAISIE/MD5
DAISIE/DESCRIPTION
DAISIE/man
DAISIE/man/islands_1type_1000reps.Rd
DAISIE/man/DAISIE_ML.Rd
DAISIE/man/DAISIE-package.Rd
DAISIE/man/DAISIE_tutorial.Rd
DAISIE/man/DAISIE_probdist.Rd
DAISIE/man/Galapagos_datatable.Rd
DAISIE/man/DAISIE_sim.Rd
DAISIE/man/DAISIE_plot_sims.Rd
DAISIE/man/islands_10reps_RAW.Rd
DAISIE/man/DAISIE_numcol.Rd
DAISIE/man/islands_2types_1000reps.Rd
DAISIE/man/DAISIE_margprobdist.Rd
DAISIE/man/DAISIE_ExpEIN.Rd
DAISIE/man/DAISIE_loglik_all.Rd
DAISIE/man/Galapagos_datalist_2types.Rd
DAISIE/man/DAISIE_format_sim.Rd
DAISIE/man/DAISIE_dataprep.Rd
DAISIE/man/DAISIE-internal.Rd
DAISIE/man/DAISIE_convertprobdist.Rd
DAISIE/man/Galapagos_datalist.Rd