Biwa_datalist: Colonization and branching times of 68 fish clades.
In DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction
Biwa_datalist R Documentation
Colonization and branching times of 68 fish clades.
Description
A list containing the colonization and branching times of the fishes of
Lake Biwa (Japan). Main dataset used in Hauffe et al (2020). 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 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 clade including 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
* Endemic_MaxAge: 5 or 6
$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 69 elements, the first of which contains 2 elements and
the following 68 containing 5 components.
Source
Hauffe, T., D. Delicado, R.S. Etienne and L. Valente. Lake expansion
elevates equilibrium diversity via increasing colonisation. (2020) Journal of Biogeography
See Also
DAISIE_dataprep, DAISIE_ML, DAISIE_SR_ML
DAISIE documentation built on Oct. 22, 2023, 1:06 a.m.
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| Biwa_datalist | R Documentation |
Colonization and branching times of 68 fish clades.
Description
A list containing the colonization and branching times of the fishes of
Lake Biwa (Japan). Main dataset used in Hauffe et al (2020). 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 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 clade including 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
* Endemic_MaxAge: 5 or 6
$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 69 elements, the first of which contains 2 elements and the following 68 containing 5 components.
Source
Hauffe, T., D. Delicado, R.S. Etienne and L. Valente. Lake expansion
elevates equilibrium diversity via increasing colonisation. (2020) Journal of Biogeography
See Also
DAISIE_dataprep, DAISIE_ML, DAISIE_SR_ML
R Package Documentation
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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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