islands_2types_1000reps: 1000 islands in DAISIE format simulated with the ML...
In DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction
islands_2types_1000reps R Documentation
1000 islands in DAISIE format simulated with the ML parameters of the
CR_lamc_mu_K model for the Galapagos data (2 types of species)
Description
Each simulated dataset is an element of the list, which can be called using
e.g. islands_2types_1000reps[[1]] Each of the island replicates is a list in
itself. The first (e.g. islands_2types_1000reps[[x]][[1]]) element of that
list has the following components:
$island_age - the island age
$not_present_type1 - the number of mainland lineages of type 1
that are not present on the island
$not_present_type2 - the
number of mainland lineages of type 2 that are not present on the island
$stt_all - STT table for all species on the island (nI - number of
non-endemic species; nA - number of anagenetic species, nC - number of
cladogenetic species, present - number of independent colonisations present
)
$stt_stt_type1 - STT table for type 1 species on the island (nI
- number of non-endemic species; nA - number of anagenetic species, nC -
number of cladogenetic species, present - number of independent
colonisations present )
$stt_stt_type2 - STT table for type 2
species on the island (nI - number of non-endemic species; nA - number of
anagenetic species, nC - number of cladogenetic species, present - number of
independent colonisations present )
The subsequent elements of the list each contain information on a single
colonist lineage on the island and has 4 components:
$branching_times - island age and stem age of the population/species
in the case of Non-endemic, Non-endemic_MaxAge and Endemic anagenetic
species. For cladogenetic species these should be island age and branching
times of the radiation including the stem age of the radiation.
$stac - the status of the colonist
* Non_endemic_MaxAge: 1
* Endemic: 2
* Endemic&Non_Endemic: 3
* Non_endemic: 4
$missing_species - number of island species that were not sampled for
particular clade (only applicable for endemic clades)
$type_1or2 - whether the colonist belongs to type 1 or type 2
Format
A list with 1000 items.
Source
Valente, L.M., A.B. Phillimore and R.S. Etienne (2015). Equilibrium
and non-equilibrium dynamics simultaneously operate in the Galapagos
islands. Ecology Letters 18: 844-852.
See Also
DAISIE_sim_cr(), DAISIE_plot_sims
DAISIE documentation built on Oct. 22, 2023, 1:06 a.m.
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| islands_2types_1000reps | R Documentation |
1000 islands in DAISIE format simulated with the ML parameters of the CR_lamc_mu_K model for the Galapagos data (2 types of species)
Description
Each simulated dataset is an element of the list, which can be called using
e.g. islands_2types_1000reps[[1]] Each of the island replicates is a list in
itself. The first (e.g. islands_2types_1000reps[[x]][[1]]) element of that
list has the following components:
$island_age - the island age
$not_present_type1 - the number of mainland lineages of type 1
that are not present on the island
$not_present_type2 - the
number of mainland lineages of type 2 that are not present on the island
$stt_all - STT table for all species on the island (nI - number of
non-endemic species; nA - number of anagenetic species, nC - number of
cladogenetic species, present - number of independent colonisations present
)
$stt_stt_type1 - STT table for type 1 species on the island (nI
- number of non-endemic species; nA - number of anagenetic species, nC -
number of cladogenetic species, present - number of independent
colonisations present )
$stt_stt_type2 - STT table for type 2
species on the island (nI - number of non-endemic species; nA - number of
anagenetic species, nC - number of cladogenetic species, present - number of
independent colonisations present )
The subsequent elements of the list each contain information on a single
colonist lineage on the island and has 4 components:
$branching_times - island age and stem age of the population/species
in the case of Non-endemic, Non-endemic_MaxAge and Endemic anagenetic
species. For cladogenetic species these should be island age and branching
times of the radiation including the stem age of the radiation.
$stac - the status of the colonist
* Non_endemic_MaxAge: 1
* Endemic: 2
* Endemic&Non_Endemic: 3
* Non_endemic: 4
$missing_species - number of island species that were not sampled for
particular clade (only applicable for endemic clades)
$type_1or2 - whether the colonist belongs to type 1 or type 2
Format
A list with 1000 items.
Source
Valente, L.M., A.B. Phillimore and R.S. Etienne (2015). Equilibrium and non-equilibrium dynamics simultaneously operate in the Galapagos islands. Ecology Letters 18: 844-852.
See Also
DAISIE_sim_cr(), DAISIE_plot_sims
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