Galapagos_datalist: Colonization and branching times of 8 terrestrial avifaunal...
In rsetienne/DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction
Galapagos_datalist R Documentation
Colonization and branching times of 8 terrestrial avifaunal clades in list
format, accepted by DAISIE_ML and DAISIE_loglik_all
Description
A list containing the colonization and branching times of the terrestrial
avifauna in the Galapagos where no distinction is made between types of
colonists. This list can be generated using the DAISIE_dataprep function,
which converts a user-specified data table into a data object, but the
object can of course also be entered directly. It is an R list object with
the following elements.
The first element of the list has two
components:
$island_age - the island age
$not_present - the number of mainland lineages that are not present
on the island
The following 8 elements of the list each contains
information on a single colonist lineage on the island and has 5
components:
$colonist_name - the name of the species or clade
that colonized the island
$branching_times - island age followed by stem age of the population/species
in the case of Non-endemic, Non-endemic_MaxAge species and Endemic species with no close
relatives on the island. For endemic clades with more than one species on the island
(cladogenetic clades/ radiations) these should be island age followed by the
branching times of the island cladeincluding the stem age of the clade.
$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)
$type1or2 - whether the colonist belongs to type 1 or
type 2. In this dataset all are equal to 1.
Format
A list with 9 elements the first of which contains 2 elements and
the following 8 containing 5 components.
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_dataprep, DAISIE_ML
rsetienne/DAISIE documentation built on Oct. 25, 2023, 4:32 a.m.
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| Galapagos_datalist | R Documentation |
Colonization and branching times of 8 terrestrial avifaunal clades in list format, accepted by DAISIE_ML and DAISIE_loglik_all
Description
A list containing the colonization and branching times of the terrestrial
avifauna in the Galapagos where no distinction is made between types of
colonists. This list can be generated using the DAISIE_dataprep function,
which converts a user-specified data table into a data object, but the
object can of course also be entered directly. It is an R list object with
the following elements.
The first element of the list has two
components:
$island_age - the island age
$not_present - the number of mainland lineages that are not present
on the island
The following 8 elements of the list each contains
information on a single colonist lineage on the island and has 5
components:
$colonist_name - the name of the species or clade
that colonized the island
$branching_times - island age followed by stem age of the population/species
in the case of Non-endemic, Non-endemic_MaxAge species and Endemic species with no close
relatives on the island. For endemic clades with more than one species on the island
(cladogenetic clades/ radiations) these should be island age followed by the
branching times of the island cladeincluding the stem age of the clade.
$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)
$type1or2 - whether the colonist belongs to type 1 or
type 2. In this dataset all are equal to 1.
Format
A list with 9 elements the first of which contains 2 elements and the following 8 containing 5 components.
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_dataprep, DAISIE_ML
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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