calc_diversity: Total island species richness

In thauffe/simGDM: simGDM

Description

This function calculates the total island species richness (Equation 12 in Appendix 2 of Borregaard et al. 2016)

Usage

calc_diversity(Elevation_t, Topography_t, Area_t, Nat_tm1, End_tm1,
  Clado_tm1, Ana_tm1, Vs, S0, E0, Ms, Iso_t, Imm, C0, Ana, Emi, Z, Ma, Msa,
  DivDep = TRUE, TargetEffect = FALSE, EnvirFilt = FALSE)

Arguments

Elevation_t	Island elevation at one moment in time
Topography_t	Island topography at one moment in time
Area_t	Island area at one moment in time
Nat_tm1	Native richness of the previous time step
End_tm1	Endemic richness of the previous time step
Clado_tm1	Cladogenetic richness of the previous time step
Ana_tm1	Anagenetic richness of the previous time step
Vs	Probability of a vicariance event when topography equals 1
S0	The per species probability of adaptive speciation at maximum empty niche space
E0	The per-species probability of extinction when richness equals Kmax
Ms	Species richness of the mainland source pool
Iso_t	A descriptor of island isolation in arbitrary units
Imm	The probability of one species arriving from the mainland per time step
C0	The per-species probability of successful colonization at full empty niche space
Ana	The per-species probability of anagenesis per time step
Emi	Probability of recolonization of the source area per time step
Z	The exponent of the species-area relationship between the island and the source area
Ma	The realized size of the source area that provides new species
Msa	Power exponent controlling the abundance distribution of the source
DivDep	TRUE (default) Diversity dependence acting on immigration, extinction and in-situ speciation
TargetEffect	FALSE (default) No effect of island area on the immigration probability
EnvirFilt	FALSE (default) No effect of island elevation as proxy for habitat diversity on the immigration probability

Value

The output is a dataframe containing diversity and rates per time step.

Richness	Native species richness
NonEndemics	Non-endemic species richness
Endemics	Endemic species richness
Kmax	Carrying capacity
EndemicsClado	Endemic species evolved via in-situ cladogenesis
EndemicsAna	Endemic species evolved via in-situ anagenesis
Immigrants	Species immigrating at that time step to the island
NewViaClado	Species evolved via in-situ cladogenesis at that time step
NewViaNonadaptClado	Species evolved via non-adaptive in-situ cladogenesis at that time step
NewViaAdaptClado	Species evolved via adaptive in-situ cladogenesis at that time step
NewViaAna	Species evolved via in-situ anagenesis at that time step
Extinctions	Species going extinct at that time step
Emigrants	Species emigrating from the island to the mainland

Author(s)

Torsten Hauffe

References

Borregaard, M. K., T. J. Matthews and R. J. Whittaker (2016). The general dynamic model: towards a unified theory of island biogeography? Global Ecology and Biogeography, 25(7), 805-816.

Hauffe, T., D. Delicado, R.S. Etienne and L. Valente (submitted). Lake expansion increases equilibrium diversity via the target effect of island biogeography

thauffe/simGDM documentation built on Feb. 19, 2020, 5:10 p.m.