DAISIE_dataprep: Prepare colonisation and branching time data to run in...

In xieshu95/DAISIE_new: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

Description

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 for cases where both island and non-island populations of the species have been sampled) * "Non_endemic_MaxAge": applies to non-endemic species for cases where island individuals of the species have not been sampled and only the age of the species is available) * "Endemic": applies to endemic species and is applicable for both cladogenetic and anagenetic species * "Endemic_MaxAge": applies to endemic species for cases where island individuals of the species have not been sampled and only the age of the species is available. This could apply to endemic species that have recently gone extinct because of antropogenic causes that are (evidently) not modelled, and for which no DNA data is available. * "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) $Branching_times - Stem age of the population/species in the case of "Non-endemic", "Non-endemic_MaxAge" and "Endemic" anagenetic species. For "Endemic" cladogenetic species these should be branching times of the radiation including the stem age of the radiation.
island_age	Age of island in appropriate units. In DAISIE_plot_age_diversity and DAISIE_plot_island if island input is in table format, the age of the island must be specified. If island input is in DAISIE list format, this option will override the island age specified in the island list.
M	Numeric defining the size of 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	Fraction of mainland species that belongs to the second subset of species (type 2). Applies only when two types of species are simulated (length(pars) = 10). For DAISIE_dataprep applies only if number_clade_types = 2. In DAISIE_dataprep the default "proportional" sets the fraction to be proportional to the number of clades of distinct macroevolutionary process that have colonised the island.
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.
verbose	In simulation and dataprep functions a logical, Default = TRUE gives intermediate output should be printed. For ML functions a numeric determining if intermediate output should be printed, Default = 0 does not print, verbose = 1 prints intermediate output of the parameters and loglikelihood, verbose = 2 means also intermediate progress during loglikelihood computation is shown.

Details

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

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 $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

Author(s)

Luis M Valente

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.

Examples

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

utils::data(Galapagos_datatable)
DAISIE_dataprep(
   datatable = Galapagos_datatable,
   island_age = 4,
   M = 1000
   )

### 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)
DAISIE_dataprep(
   datatable = Galapagos_datatable,
   island_age = 4,
   M = 1000,
   number_clade_types = 2,
   list_type2_clades = "Finches"
   )

### 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)
DAISIE_dataprep(
   datatable = Galapagos_datatable,
   island_age = 4,
   M = 1000,
   number_clade_types = 2,
   list_type2_clades = "Finches",
   prop_type2_pool = 0.163
   )

xieshu95/DAISIE_new documentation built on March 20, 2020, 5:31 a.m.