Description Usage Arguments Value Author(s) References See Also Examples
View source: R/DAISIE_sumstats_rates.R
Calculates the summary statistics of per capita rates throught an ontogeny simulation
1 2 3 4 5 6 7 8 9 10 11 12 13 | DAISIE_calc_sumstats_pcrates(
pars,
ext_pars,
totaltime,
area_pars = NULL,
hyper_pars = NULL,
dist_pars = NULL,
island_ontogeny = 1,
sea_level = 0,
extcutoff = 100,
mainland_n = 1000,
resol = 100
)
|
pars |
A numeric vector:
|
ext_pars |
A numeric vector:
|
totaltime |
A numeric indicating total time of simulation. |
area_pars |
a named list containing area and sea level parameters as
created by
|
hyper_pars |
A numeric vector for hyperparameters for the rate calculations:
|
dist_pars |
A named list of a numeric distance from the mainland as
created by
|
island_ontogeny |
a numeric describing the type of island ontogeny.
Can be |
sea_level |
a numeric describing sea level. 0 corresponds to no sea level dynamics. |
extcutoff |
A numeric with the cutoff for extinction rate preventing it from being too large and slowing down simulation. Should be big. Default is 1100. |
mainland_n |
A numeric stating the number of mainland species, that is the number of species that can potentially colonize the island. If DAISIE_sim function uses a clade-specific diversity dependence, this value is set to 1. If DAISIE_sim function uses an island-wide diversity dependence, this value is set to the number of mainland species. Default is 1000 |
resol |
A numeric > 0 indicating number of decimals per unit time. |
A named list with mean and median values of specified parameters
Pedro Neves
Valente, Luis M., Rampal S. Etienne, and Albert B. Phillimore. "The effects of island ontogeny on species diversity and phylogeny." Proceedings of the Royal Society of London B: Biological Sciences 281.1784 (2014): 20133227.
Other rate calculations:
DAISIE_plot_area()
,
get_ana_rate()
,
get_immig_rate()
,
island_area_vector()
,
island_area()
,
update_max_rates()
,
update_rates()
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 | pars <- c(0.01, 1, 20, 0.01, 1)
ext_pars <- c(0.2, 10)
area_pars <- create_area_pars(
max_area = 13500,
proportional_peak_t = 0.1,
peak_sharpness = 1,
total_island_age = 15,
sea_level_amplitude = 0,
sea_level_frequency = 0,
island_gradient_angle = 0
)
hyper_pars <- NULL
dist_pars <- create_dist_pars(1)
island_ontogeny <- 1
sea_level <- 0
extcutoff <- 1100
resol <- 100
totaltime <- 10
mainland_n <- 1000
mean_med <- DAISIE_calc_sumstats_pcrates(
pars = pars,
ext_pars = ext_pars,
totaltime = totaltime,
area_pars = area_pars,
hyper_pars = hyper_pars,
dist_pars = dist_pars,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
extcutoff = extcutoff,
mainland_n = mainland_n,
resol = resol
)
|
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