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Prepare colonisation and branching time data to run in DAISIE.

Source: R/DAISIE_dataprep.R
DAISIE_dataprep.Rd

This function produces a data object that can be run in DAISIE likelihood computation/optimization functions. The function converts a user-specified table to a DAISIE-compatible format. See Galapagos_datatable.Rdata for a template of an input table.)

Usage

DAISIE_dataprep(
  datatable,
  island_age,
  M,
  number_clade_types = 1,
  list_type2_clades = NA,
  prop_type2_pool = "proportional",
  epss = 1e-05,
  verbose = TRUE
)

Arguments

datatable

Data frame (table) with user-specified data. See file Galapagos_datatable.Rdata for a template of an input table. Each row on the table represents and independent colonisation event. Table has the following four columns.

$Clade_name - name of independent colonization event
$Status - One of the following categories:
* "Non_endemic": applies to non-endemic species when an approximate colonisation time is known
* "Non_endemic_MaxAge": applies to non-endemic species for cases where colonisation time is unknown
* "Endemic": applies to endemic species or endemic clades when an approximate colonisation time is known
* "Endemic_MaxAge": applies to endemic species or endemic clades for cases where the colonisation time is unknown, or when the user wants to specify an upper bound for colonisation. This could for example apply to endemic species that have recently gone extinct because of anthropogenic causes, and which are not included in the phylogeny ("NA" should be given in the branching times column). It could also apply to insular radiations with long stem branches, for which the time of the first cladogenetic event is known, but the precise time of colonisation is not.
* "Endemic_MaxAge_MinAge": same as Endemic_MaxAge but also includes a minimum age for colonisation.
* "Non_endemic_MaxAge_MinAge": same as Non_endemic_MaxAge but also includes a minimum age for colonisation.#'
* "Endemic&Non_Endemic": when endemic clade is present and its mainland ancestor has re-colonized
$Missing_species - Number of island species that were not sampled for particular clade (only applicable for "Endemic" clades). If NA is given in branching times column, this should be equal to the number of species in the clade minus 1
$Branching_times - Stem age of the population/species in the case of "Non_endemic", "Non_endemic_MaxAge" and "Endemic" species with no extant close relatives on the island. Set "NA" if colonisation time unknown and no upper bound is known. For "Endemic" cladogenetic species these should be branching times of the radiation, including the stem age of the radiation (colonisation time estimate).

island_age

Age of island in appropriate units

M

The size of the mainland pool, i.e the number of species that can potentially colonize the island

number_clade_types

Number of clade types. Default: number_clade_types = 1 all species are considered to belong to same macroevolutionary process. If number_clade_types = 2, there are two types of clades with distinct macroevolutionary processes.

list_type2_clades

If number_clade_types = 2, list_type2_clades specifies the names of the clades that have a distinct macroevolutionary process. The names must match those in the $Clade_name column of the source data table (e.g. list_type2_clades = "Finches"). If number_clade_types = 1, then list_type2_clades = NA should be specified (default)

prop_type2_pool

Specifies the fraction of potential mainland colonists that have a distinct macroevolutionary process. Applies only if number_clade_types = 2. Default "proportional" sets the fraction to be proportional to the number of clades of distinct macroevolutionary process that have colonised the island. Alternatively, the user can specify a value between 0 and 1 (e.g. if mainland pool size is 1000 and prop_type2_pool = 0.02 then number of type2 species is 20).

epss

Default= 1E-5 should be appropriate in most cases. This value is used to set the maximum age of colonisation of "Non_endemic_MaxAge" and "Endemic_MaxAge" species to an age that is slightly younger than the island for cases when the age provided for that species is older than the island. The new maximum age is then used as an upper bound to integrate over all possible colonisation times.

verbose

Boolean. States if intermediate results should be printed to console. Defaults to TRUE.

Value

datalist

R list object containing data:
The first element of the list has two or three components:
$island_age - the island age
Then, depending on whether a distinction between species types is made, we have:
$not_present - the number of mainland lineages that are not present on the island
or:
$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
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 and stem age of the population/species in the case of "Non-endemic", "Non-endemic_MaxAge" and "Endemic" anagenetic species. For "Endemic" cladogenetic species these are 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
* Endemic_MaxAge: 5 (if only colonisation time was given)
* Endemic_MaxAge: 6 (if colonisation time and cladogenesis times were given)
$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

Details

The output is an R list containing the data formatted to be run on other DAISIE functions.

References

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.

Author

Luis M Valente

Examples





### Create Galapagos data object where all taxa have the same macroevolutionary process

utils::data(Galapagos_datatable, package = "DAISIE")
DAISIE_dataprep(
   datatable = Galapagos_datatable,
   island_age = 4,
   M = 1000
   )
#> Colonisation time of 7.456 for Coccyzus is older than island age
#> Colonisation time of 10.285 for Pyrocephalus is older than island age
#> [[1]]
#> [[1]]$island_age
#> [1] 4
#> 
#> [[1]]$not_present
#> [1] 992
#> 
#> 
#> [[2]]
#> [[2]]$colonist_name
#> [1] "Coccyzus"
#> 
#> [[2]]$branching_times
#> [1] 4.00000 3.99999
#> 
#> [[2]]$stac
#> [1] 1
#> 
#> [[2]]$missing_species
#> [1] 0
#> 
#> [[2]]$type1or2
#> [1] 1
#> 
#> 
#> [[3]]
#> [[3]]$colonist_name
#> [1] "Dendroica"
#> 
#> [[3]]$branching_times
#> [1] 4.00 0.34
#> 
#> [[3]]$stac
#> [1] 4
#> 
#> [[3]]$missing_species
#> [1] 0
#> 
#> [[3]]$type1or2
#> [1] 1
#> 
#> 
#> [[4]]
#> [[4]]$colonist_name
#> [1] "Finches"
#> 
#> [[4]]$branching_times
#>  [1] 4.0000 3.0282 1.3227 0.8223 0.4286 0.3462 0.2450 0.1180 0.0808 0.0756
#> [11] 0.0527 0.0525 0.0327 0.0322 0.0221 0.0118
#> 
#> [[4]]$stac
#> [1] 2
#> 
#> [[4]]$missing_species
#> [1] 0
#> 
#> [[4]]$type1or2
#> [1] 1
#> 
#> 
#> [[5]]
#> [[5]]$colonist_name
#> [1] "Mimus"
#> 
#> [[5]]$branching_times
#> [1] 4.000 3.958 3.422 2.884 0.459
#> 
#> [[5]]$stac
#> [1] 2
#> 
#> [[5]]$missing_species
#> [1] 0
#> 
#> [[5]]$type1or2
#> [1] 1
#> 
#> 
#> [[6]]
#> [[6]]$colonist_name
#> [1] "Myiarchus"
#> 
#> [[6]]$branching_times
#> [1] 4.000 0.855
#> 
#> [[6]]$stac
#> [1] 2
#> 
#> [[6]]$missing_species
#> [1] 0
#> 
#> [[6]]$type1or2
#> [1] 1
#> 
#> 
#> [[7]]
#> [[7]]$colonist_name
#> [1] "Progne"
#> 
#> [[7]]$branching_times
#> [1] 4.000 0.086
#> 
#> [[7]]$stac
#> [1] 2
#> 
#> [[7]]$missing_species
#> [1] 0
#> 
#> [[7]]$type1or2
#> [1] 1
#> 
#> 
#> [[8]]
#> [[8]]$colonist_name
#> [1] "Pyrocephalus"
#> 
#> [[8]]$branching_times
#> [1] 4.00000 3.99999
#> 
#> [[8]]$stac
#> [1] 1
#> 
#> [[8]]$missing_species
#> [1] 0
#> 
#> [[8]]$type1or2
#> [1] 1
#> 
#> 
#> [[9]]
#> [[9]]$colonist_name
#> [1] "Zenaida"
#> 
#> [[9]]$branching_times
#> [1] 4.00 3.51
#> 
#> [[9]]$stac
#> [1] 2
#> 
#> [[9]]$missing_species
#> [1] 0
#> 
#> [[9]]$type1or2
#> [1] 1
#> 
#> 

### Create Galapagos data object with a distinct macroevolutionary processes
# for the Darwin's finches. One process applies to type 1 species (all species
# except for Darwin's finches) and the other applies only to type 2 species
# (Darwin's finches). Set fraction of potential colonists of type 2 to be
# proportional to the number of type2 clades present on the island.

utils::data(Galapagos_datatable, package = "DAISIE")
DAISIE_dataprep(
   datatable = Galapagos_datatable,
   island_age = 4,
   M = 1000,
   number_clade_types = 2,
   list_type2_clades = "Finches"
   )
#> Colonisation time of 7.456 for Coccyzus is older than island age
#> Colonisation time of 10.285 for Pyrocephalus is older than island age
#> [[1]]
#> [[1]]$island_age
#> [1] 4
#> 
#> [[1]]$not_present_type1
#> [1] 868
#> 
#> [[1]]$not_present_type2
#> [1] 124
#> 
#> 
#> [[2]]
#> [[2]]$colonist_name
#> [1] "Coccyzus"
#> 
#> [[2]]$branching_times
#> [1] 4.00000 3.99999
#> 
#> [[2]]$stac
#> [1] 1
#> 
#> [[2]]$missing_species
#> [1] 0
#> 
#> [[2]]$type1or2
#> [1] 1
#> 
#> 
#> [[3]]
#> [[3]]$colonist_name
#> [1] "Dendroica"
#> 
#> [[3]]$branching_times
#> [1] 4.00 0.34
#> 
#> [[3]]$stac
#> [1] 4
#> 
#> [[3]]$missing_species
#> [1] 0
#> 
#> [[3]]$type1or2
#> [1] 1
#> 
#> 
#> [[4]]
#> [[4]]$colonist_name
#> [1] "Finches"
#> 
#> [[4]]$branching_times
#>  [1] 4.0000 3.0282 1.3227 0.8223 0.4286 0.3462 0.2450 0.1180 0.0808 0.0756
#> [11] 0.0527 0.0525 0.0327 0.0322 0.0221 0.0118
#> 
#> [[4]]$stac
#> [1] 2
#> 
#> [[4]]$missing_species
#> [1] 0
#> 
#> [[4]]$type1or2
#> [1] 2
#> 
#> 
#> [[5]]
#> [[5]]$colonist_name
#> [1] "Mimus"
#> 
#> [[5]]$branching_times
#> [1] 4.000 3.958 3.422 2.884 0.459
#> 
#> [[5]]$stac
#> [1] 2
#> 
#> [[5]]$missing_species
#> [1] 0
#> 
#> [[5]]$type1or2
#> [1] 1
#> 
#> 
#> [[6]]
#> [[6]]$colonist_name
#> [1] "Myiarchus"
#> 
#> [[6]]$branching_times
#> [1] 4.000 0.855
#> 
#> [[6]]$stac
#> [1] 2
#> 
#> [[6]]$missing_species
#> [1] 0
#> 
#> [[6]]$type1or2
#> [1] 1
#> 
#> 
#> [[7]]
#> [[7]]$colonist_name
#> [1] "Progne"
#> 
#> [[7]]$branching_times
#> [1] 4.000 0.086
#> 
#> [[7]]$stac
#> [1] 2
#> 
#> [[7]]$missing_species
#> [1] 0
#> 
#> [[7]]$type1or2
#> [1] 1
#> 
#> 
#> [[8]]
#> [[8]]$colonist_name
#> [1] "Pyrocephalus"
#> 
#> [[8]]$branching_times
#> [1] 4.00000 3.99999
#> 
#> [[8]]$stac
#> [1] 1
#> 
#> [[8]]$missing_species
#> [1] 0
#> 
#> [[8]]$type1or2
#> [1] 1
#> 
#> 
#> [[9]]
#> [[9]]$colonist_name
#> [1] "Zenaida"
#> 
#> [[9]]$branching_times
#> [1] 4.00 3.51
#> 
#> [[9]]$stac
#> [1] 2
#> 
#> [[9]]$missing_species
#> [1] 0
#> 
#> [[9]]$type1or2
#> [1] 1
#> 
#> 

### Create Galapagos data object with a distinct macroevolutionary processes
# for the Darwin's finches. One process applies to type 1 species (all species
# except for Darwin's finches) and the other applies only to type 2 species
# (Darwin's finches). Set fraction of potential colonists of type 2 to be 0.163.

utils::data(Galapagos_datatable, package = "DAISIE")
DAISIE_dataprep(
   datatable = Galapagos_datatable,
   island_age = 4,
   M = 1000,
   number_clade_types = 2,
   list_type2_clades = "Finches",
   prop_type2_pool = 0.163
   )
#> Colonisation time of 7.456 for Coccyzus is older than island age
#> Colonisation time of 10.285 for Pyrocephalus is older than island age
#> [[1]]
#> [[1]]$island_age
#> [1] 4
#> 
#> [[1]]$not_present_type1
#> [1] 830
#> 
#> [[1]]$not_present_type2
#> [1] 162
#> 
#> 
#> [[2]]
#> [[2]]$colonist_name
#> [1] "Coccyzus"
#> 
#> [[2]]$branching_times
#> [1] 4.00000 3.99999
#> 
#> [[2]]$stac
#> [1] 1
#> 
#> [[2]]$missing_species
#> [1] 0
#> 
#> [[2]]$type1or2
#> [1] 1
#> 
#> 
#> [[3]]
#> [[3]]$colonist_name
#> [1] "Dendroica"
#> 
#> [[3]]$branching_times
#> [1] 4.00 0.34
#> 
#> [[3]]$stac
#> [1] 4
#> 
#> [[3]]$missing_species
#> [1] 0
#> 
#> [[3]]$type1or2
#> [1] 1
#> 
#> 
#> [[4]]
#> [[4]]$colonist_name
#> [1] "Finches"
#> 
#> [[4]]$branching_times
#>  [1] 4.0000 3.0282 1.3227 0.8223 0.4286 0.3462 0.2450 0.1180 0.0808 0.0756
#> [11] 0.0527 0.0525 0.0327 0.0322 0.0221 0.0118
#> 
#> [[4]]$stac
#> [1] 2
#> 
#> [[4]]$missing_species
#> [1] 0
#> 
#> [[4]]$type1or2
#> [1] 2
#> 
#> 
#> [[5]]
#> [[5]]$colonist_name
#> [1] "Mimus"
#> 
#> [[5]]$branching_times
#> [1] 4.000 3.958 3.422 2.884 0.459
#> 
#> [[5]]$stac
#> [1] 2
#> 
#> [[5]]$missing_species
#> [1] 0
#> 
#> [[5]]$type1or2
#> [1] 1
#> 
#> 
#> [[6]]
#> [[6]]$colonist_name
#> [1] "Myiarchus"
#> 
#> [[6]]$branching_times
#> [1] 4.000 0.855
#> 
#> [[6]]$stac
#> [1] 2
#> 
#> [[6]]$missing_species
#> [1] 0
#> 
#> [[6]]$type1or2
#> [1] 1
#> 
#> 
#> [[7]]
#> [[7]]$colonist_name
#> [1] "Progne"
#> 
#> [[7]]$branching_times
#> [1] 4.000 0.086
#> 
#> [[7]]$stac
#> [1] 2
#> 
#> [[7]]$missing_species
#> [1] 0
#> 
#> [[7]]$type1or2
#> [1] 1
#> 
#> 
#> [[8]]
#> [[8]]$colonist_name
#> [1] "Pyrocephalus"
#> 
#> [[8]]$branching_times
#> [1] 4.00000 3.99999
#> 
#> [[8]]$stac
#> [1] 1
#> 
#> [[8]]$missing_species
#> [1] 0
#> 
#> [[8]]$type1or2
#> [1] 1
#> 
#> 
#> [[9]]
#> [[9]]$colonist_name
#> [1] "Zenaida"
#> 
#> [[9]]$branching_times
#> [1] 4.00 3.51
#> 
#> [[9]]$stac
#> [1] 2
#> 
#> [[9]]$missing_species
#> [1] 0
#> 
#> [[9]]$type1or2
#> [1] 1
#> 
#>