# DAISIE_calc_sumstats_pcrates: Calculate summary statistics of per capita rates In DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

 DAISIE_calc_sumstats_pcrates R Documentation

## Calculate summary statistics of per capita rates

### Description

Calculates the summary statistics of per capita rates throught an ontogeny simulation

### Usage

```DAISIE_calc_sumstats_pcrates(
pars,
total_time,
area_pars,
hyper_pars,
island_ontogeny = 1,
sea_level = 0,
extcutoff = 100,
mainland_n = 1000,
resol = 100
)
```

### Arguments

 `pars` A numeric vector containing the model parameters: `pars[1]`: lambda^c (cladogenesis rate) `pars[2]`: mu (extinction rate) `pars[3]`: K (carrying capacity), set K=Inf for diversity independence. `pars[4]`: gamma (immigration rate) `pars[5]`: lambda^a (anagenesis rate) `pars[6]`: lambda^c (cladogenesis rate) for either type 2 species or rate set 2 in rate shift model `pars[7]`: mu (extinction rate) for either type 2 species or rate set 2 in rate shift model `pars[8]`: K (carrying capacity) for either type 2 species or rate set 2 in rate shift model, set K=Inf for diversity independence. `pars[9]`: gamma (immigration rate) for either type 2 species or rate set 2 in rate shift model `pars[10]`: lambda^a (anagenesis rate) for either type 2 species or rate set 2 in rate shift model Elements 6:10 are required only when type 2 species are included or in the rate shift model. For `DAISIE_sim_relaxed_rate()` `pars[6]` is the standard deviation of the gamma distribution for the relaxed parameter and the parameter chosen by the `relaxed_par` argument is the mean of the gamma distribution for the relaxed parameter. `total_time` Numeric defining the length of the simulation in time units. `area_pars` A named list containing area and sea level parameters as created by `create_area_pars()`: [1]: maximum area [2]: current area [3]: value from 0 to 1 indicating where in the island's history the peak area is achieved [4]: total island age [5]: amplitude of area fluctuation from sea level [6]: frequency of sine wave of area change from sea level [7]: angle of the slope of the island `hyper_pars` A named list of numeric hyperparameters for the rate calculations as returned by `create_hyper_pars()`: [1]: is d the scaling parameter for exponent for calculating cladogenesis rate [2]: is x the exponent for calculating extinction rate `island_ontogeny` In `DAISIE_sim_time_dep()`, `DAISIE_ML_CS` and plotting a string describing the type of island ontogeny. Can be `"const"`, `"beta"` for a beta function describing area through time. String checked by `is_island_ontogeny_input()`. In all other functions a numeric describing the type of island ontogeny. Can be `0` for constant, `1` for a beta function describing area through time. In ML functions `island_ontogeny = NA` assumes constant ontogeny. Time dependent estimation is not yet available as development is still ongoing. Will return an error if called in that case. `sea_level` In `DAISIE_sim_time_dep()` and plotting a string describing the type of sea level. Can be `"const"` or `"sine"` for a sine function describing area through time. String checked by `is_sea_level_input()`. In all other functions a numeric describing the type of sea level. Can be `0` for constant, `1` for a sine function describing area through time. `extcutoff` A numeric with the cutoff for the the maximum extinction rate preventing it from being too large and slowing down simulation. `mainland_n` A numeric stating the number of mainland species, that is the number of species that can potentially colonize the island. If using a clade-specific diversity dependence, this value is set to 1. If using an island-wide diversity dependence, this value is set to the number of mainland species. `resol` numeric for resolution of summary stats calculation. Should be > 1.

### Value

A named list with mean and median values of specified parameters

Pedro Neves

### Examples

```pars <- c(0.01, 1, 20, 0.01, 1)
area_pars <- create_area_pars(
max_area = 13500,
current_area = 3500,
proportional_peak_t = 0.1,
total_island_age = 15,
sea_level_amplitude = 0,
sea_level_frequency = 0,
)
hyper_pars <- create_hyper_pars(d = 0.2, x = 0.1)
island_ontogeny <- 1
sea_level <- 0
extcutoff <- 1100
resol <- 100
total_time <- 10
mainland_n <- 1000

mean_med <- DAISIE:::DAISIE_calc_sumstats_pcrates(
pars = pars,
total_time = total_time,
area_pars = area_pars,
hyper_pars = hyper_pars,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
extcutoff = extcutoff,
mainland_n = mainland_n,
resol = resol
)
```

DAISIE documentation built on June 2, 2022, 5:07 p.m.