Description Usage Arguments Value Author(s) References
View source: R/calc_diversity.R
This function calculates the total island species richness (Equation 12 in Appendix 2 of Borregaard et al. 2016)
1 2 3 | 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)
|
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 |
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 |
Torsten Hauffe
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
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