Dynamical Assembly of Islands by Speciation, Immigration and Extinction
Add a column to a data frame
Determines if object rates are rates
Calculates the area at a point in time from a beta function
Calculates when the next timestep will be, and if a shift has occured.
Calculates when the next timestep will be.
Calculates the peak of ontogeny curve (beta function)
Count the number of species
Create named list of area parameters
Creates the list object for CS_version argument in DAISIE_ML_CS
Unsampled CS full STT
Create list of hyperparameters
Create vector of model parameters
Create named list of trait state parameters
Create named list of trait state parameters
Cumulative Gamma distribution parameterised with mean and standard dev...
Sets or retrieves the factor to calculate the step-size used by the od...
Converts the joint distribution of endemics and non-endemics under the...
Count number of species in DAISIE datalist or simulated data.
Converts simulation output into island output
CS iteration control
Prepare colonisation and branching time data to run in DAISIE.
The expected number of endemics and non-endemics under the DAISIE mode...
The expected number of endemics and non-endemics under the DAISIE mode...
Extract the STT median from the output of DAISIE_sim functions
Formats clade-specific simulation output into standard DAISIE list out...
Formats clade-specific simulation output into standard DAISIE list out...
Wrapper function around for the DAISIE_format_CS_full_stt and DAISIE_f...
Formats guild-wide simulation output into standard DAISIE list output
Formats clade-specific simulation output into standard DAISIE list out...
Formats island-wide simulation output into standard DAISIE list output
Calculates information criterion from DAISIE ML estimates?
IW concurrency control
Computes the loglikelihood of the DAISIE model with clade-specific div...
Integrand to be integrated to calculate the log likelihood for the rel...
Integrates the loglikelihood of a single clade across a parameter weig...
Computes the loglikelihood of the DAISIE model with island-wide divers...
function to calculate the log likelihood for the relaxed rate model.
Computes the log probability of no species present under the DAISIE mo...
Does some things
Does something
The marginal distribution of endemics and non-endemics under the DAISI...
The probability distribution of the number of endemics and non-endemic...
Maximization of the loglikelihood under the DAISIE model with island-w...
Maximization of the loglikelihood under the DAISIE model with clade-sp...
Computes MLE for single type species under a clade specific scenario
Computes MLE for multiple islands under a clade specific scenario
Computes MLE for single type species under a clade specific scenario w...
Maximization of the loglikelihood under the DAISIE model with clade-sp...
The expectation and marginal distribution of the number of colonizatio...
Driver for the boost::odeint solver for the CS model
Driver for the boost::odeint solver for the IW model
Convert intermediate output to final simulation output
Plot clade age against clade diversity.
Plots island area function through time
Plot cladogenesis rate through time
Plots extinction rate function through time
Plot immigration rate through time
DAISIE tree plot
Plot colonisation and branching time of species found on an island dat...
Plot per capita STT and per-capita rate change thourgh simulation
Plot island species-through-time (STT) plots
Create the Species-Through-Time plot. This is used to visualize the ou...
The joint distribution of endemics and non-endemics under the DAISIE m...
Samples what event to happen next
Samples what event to happen next
Samples what event to happen next
Internal function of the DAISIE simulation
Internal function of the DAISIE simulation
Internal function of the DAISIE simulation
Internal function of the DAISIE simulation
Simulates island replicates with an clade-specific (CS) diversity-depe...
Simulates island replicates with an guild-wide (GW) diversity-dependen...
Simulates island replicates with an island-wide (IW) diversity-depende...
Simulate (non-)oceanic islands with given parameters under a rate-shif...
Internal function of the DAISIE simulation
Simulate multiple islands based on hyperparameters that describe relat...
Simulate (non-)oceanic islands with given parameters under a relaxed-r...
Simulates island replicates with an clade-specific (CS) diversity-depe...
Simulates island replicates with an guild-wide (GW) diversity-dependen...
Simulates island replicates with an island-wide (IW) diversity-depende...
Simulate (non-)oceanic islands with given parameters under a time-depe...
Simulate islands with given trait-dependent parameters.
Simulate islands with given trait-dependent parameters.
Updates state of island given sampled event for a constant rate case.
Updates state of island given sampled event
Updates state of island given sampled event with two trait states.
Simulate (non-)oceanic islands with given parameters under time-consta...
Computes the loglikelihood of the DAISIE model with clade-specific div...
Maximization of the loglikelihood under the DAISIE model with clade-sp...
DEPRECATED - Algorithm component of DAISIE_SR_sim.
DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and E...
Default parameter documentation
Calculate anagenesis rate
Calculate cladogenesis rate
Calculate extinction rate
Calculate immigration rate
Calculate transition rate
Computes integral of a very peaked function, modified from the SADISA ...
Computes island_area, but takes vector as argument (needed by )
Function to describe changes in area through time.
Remove superfluous lines in empty simulations
Gamma distribution density parameterised with mean and standard deviat...
Samples from distribution when parameter is relaxed
Transforms mean and standard deviation to shape and scale gamma parame...
Calculates the maximum rates for a Gillespie simulation
Calculates algorithm rates
Simulates and computes the (maximum) likelihood of a dynamical model of island biota assembly through speciation, immigration and extinction. See Valente et al. (2015) <doi:10.1111/ele.12461>.
Useful links