DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction
Version 1.4

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, .

Browse man pages Browse package API and functions Browse package files

AuthorRampal S. Etienne, Luis M. Valente, Albert B. Phillimore & Bart Haegeman
Date of publication2017-04-13 17:50:28 UTC
MaintainerRampal S. Etienne <r.s.etienne@rug.nl>
LicenseGPL-2
Version1.4
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("DAISIE")

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-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_age_diversity: Plot clade age against clade diversity.
DAISIE_plot_island: Plot colonisation and branching time of species found on an...
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...
Macaronesia_datalist: Colonization and branching times of terrestrial avifaunal...

Functions

Add_brt_table Man page Source code
DAISIE Man page
DAISIE-package Man page
DAISIE_ExpEIN Man page Source code
DAISIE_IC Man page Source code
DAISIE_KLdist Man page Source code
DAISIE_ML Man page Source code
DAISIE_ML1 Man page Source code
DAISIE_ML2 Man page Source code
DAISIE_ONEcolonist Man page Source code
DAISIE_convertprobdist Man page Source code
DAISIE_dataprep Man page Source code
DAISIE_eq Man page Source code
DAISIE_format_CS Man page Source code
DAISIE_format_IW Man page Source code
DAISIE_loglik Man page Source code
DAISIE_loglik_CS Man page
DAISIE_loglik_all Man page
DAISIE_loglik_all_choosepar Man page Source code
DAISIE_loglik_all_choosepar2 Man page Source code
DAISIE_loglik_high_lambda Man page Source code
DAISIE_loglik_rhs Man page Source code
DAISIE_loglik_rhs2 Man page Source code
DAISIE_margprobdist Man page Source code
DAISIE_numcol Man page Source code
DAISIE_numcol_dist Man page Source code
DAISIE_plot_age_diversity Man page Source code
DAISIE_plot_island Man page Source code
DAISIE_plot_sims Man page Source code
DAISIE_probdist Man page Source code
DAISIE_probdist_rhs Man page Source code
DAISIE_sim Man page Source code
DAISIE_sim_core Man page Source code
DAISIE_sim_min_type2 Man page Source code
DAISIE_simplex Man page
DAISIE_test Man page Source code
DAISIE_tutorial Man page Source code
Galapagos_datalist Man page
Galapagos_datalist_2types Man page
Galapagos_datatable Man page
Macaronesia_datalist Man page
antidiagSums Man page Source code
calcMN Man page Source code
checkprobs Man page Source code
checkprobs2 Man page Source code
countimmi Man page Source code
countspecies Man page Source code
countspeciestype1 Man page Source code
counttype1 Man page Source code
divdepvec Man page Source code
fconstr13 Man page Source code
fconstr15 Man page Source code
islands_10reps_RAW Man page
islands_1type_1000reps Man page
islands_2types_1000reps Man page
quantiles Man page Source code
roundn Man page

Files

inst
inst/DAISIE_tutorial.pdf
tests
tests/testthat
tests/testthat/test_DAISIE.R
NAMESPACE
data
data/islands_10reps_RAW.RData
data/Macaronesia_datalist.RData
data/Galapagos_datatable.RData
data/islands_2types_1000reps.RData
data/islands_1type_1000reps.RData
data/Galapagos_datalist_2types.RData
data/Galapagos_datalist.RData
R
R/DAISIE_IC.R
R/DAISIE_PEI.R
R/DAISIE_ExpEIN.R
R/DAISIE_format_CS.R
R/DAISIE_utils.R
R/DAISIE_sim_core.R
R/DAISIE_loglik_all.R
R/DAISIE_sim.R
R/DAISIE_plot_age_diversity.R
R/DAISIE_loglik_high_lambda.R
R/DAISIE_ML.R
R/DAISIE_dataprep.R
R/DAISIE_test.R
R/DAISIE_ML2.R
R/DAISIE_ML1.R
R/DAISIE_sim_min_type2.R
R/DAISIE_plot_island.R
R/DAISIE_plot_sims.R
R/DAISIE_format_IW.R
R/DAISIE_tutorial.R
MD5
DESCRIPTION
man
man/DAISIE_plot_island.Rd
man/islands_1type_1000reps.Rd
man/DAISIE_ML.Rd
man/DAISIE-package.Rd
man/DAISIE_tutorial.Rd
man/DAISIE_probdist.Rd
man/Galapagos_datatable.Rd
man/DAISIE_sim.Rd
man/DAISIE_plot_sims.Rd
man/islands_10reps_RAW.Rd
man/DAISIE_numcol.Rd
man/islands_2types_1000reps.Rd
man/DAISIE_margprobdist.Rd
man/DAISIE_ExpEIN.Rd
man/DAISIE_loglik_all.Rd
man/Galapagos_datalist_2types.Rd
man/Macaronesia_datalist.Rd
man/DAISIE_plot_age_diversity.Rd
man/DAISIE_dataprep.Rd
man/DAISIE-internal.Rd
man/DAISIE_convertprobdist.Rd
man/Galapagos_datalist.Rd
DAISIE documentation built on May 19, 2017, 8:05 a.m.