| Type: | Package |
| Title: | Extracts Phylogenetic Island Community Data from Phylogenetic Trees |
| Version: | 1.0.0 |
| Maintainer: | Joshua W. Lambert <j.w.l.lambert@rug.nl> |
| Description: | Extracts colonisation and branching times of island species to be used for analysis in the R package 'DAISIE'. It uses phylogenetic and endemicity data to extract the separate island colonists and store them. |
| URL: | https://github.com/joshwlambert/DAISIEprep, https://joshwlambert.github.io/DAISIEprep/ |
| BugReports: | https://github.com/joshwlambert/DAISIEprep/issues |
| License: | GPL (≥ 3) |
| Encoding: | UTF-8 |
| LazyData: | true |
| RoxygenNote: | 7.3.1 |
| Depends: | R (≥ 4.0) |
| Imports: | methods, ape, phylobase, ggplot2, scales, ggtree, DAISIE, castor, tibble, rlang |
| Suggests: | testthat (≥ 3.0.0), knitr, rmarkdown, covr, diversitree, corHMM, tidyr, dplyr, ggimage |
| VignetteBuilder: | knitr |
| Config/testthat/edition: | 3 |
| Collate: | 'DAISIEprep-package.R' 'add_asr_node_states.R' 'add_island_colonist.R' 'add_missing_species.R' 'add_multi_missing_species.R' 'add_outgroup.R' 'all_descendants_conspecific.R' 'any_back_colonisation.R' 'any_outgroup.R' 'any_polyphyly.R' 'as_daisie_datatable.R' 'benchmark.R' 'bind_colonist_to_tbl.R' 'check_phylo_data.R' 'count_missing_species.R' 'create_daisie_data.R' 'create_endemicity_status.R' 'create_test_phylod.R' 'data.R' 'default_params_doc.R' 'endemicity_to_sse_states.R' 'extract_asr_clade.R' 'extract_clade_name.R' 'extract_endemic_clade.R' 'extract_endemic_singleton.R' 'extract_island_species.R' 'extract_multi_tip_species.R' 'extract_nonendemic.R' 'extract_species_asr.R' 'extract_species_min.R' 'extract_stem_age.R' 'extract_stem_age_asr.R' 'extract_stem_age_genus.R' 'extract_stem_age_min.R' 'get_endemic_species.R' 'is_back_colonisation.R' 'is_duplicate_colonist.R' 'is_identical_island_tbl.R' 'is_multi_tip_species.R' 'island_colonist-class.R' 'island_colonist-accessors.R' 'island_tbl-class.R' 'island_tbl-accessors.R' 'island_tbl-methods.R' 'multi_extract_island_species.R' 'multi_island_tbl-class.R' 'multi_island_tbl-methods.R' 'plot_colonisation.R' 'plot_performance.R' 'plot_phylod.R' 'plot_sensitivity.R' 'print-methods.R' 'read_performance.R' 'read_sensitivity.R' 'rm_duplicate_island_species.R' 'rm_island_colonist.R' 'rm_multi_missing_species.R' 'rm_nonendemic_in_clade.R' 'sensitivity.R' 'translate_status.R' 'unique_island_genera.R' 'utils.R' 'write_biogeobears_input.R' |
| NeedsCompilation: | no |
| Packaged: | 2024-12-18 00:04:39 UTC; joshlambert |
| Author: | Joshua W. Lambert 
[aut, cre],
Luis Valente
[aut],
Pedro Santos Neves
[aut],
Lizzie Roeble
[aut],
Theo Pannetier
[aut] |
| Repository: | CRAN |
| Date/Publication: | 2024-12-18 00:20:02 UTC |
DAISIEprep: Extracts Phylogenetic Island Community Data from Phylogenetic Trees
Description
Extracts colonisation and branching times of island species to be used for analysis in the R package 'DAISIE'. It uses phylogenetic and endemicity data to extract the separate island colonists and store them.
Author(s)
Maintainer: Joshua W. Lambert j.w.l.lambert@rug.nl (ORCID)
Authors:
Luis Valente luis.valente@naturalis.nl (ORCID)
Pedro Santos Neves p.m.santos.neves@rug.nl (ORCID)
Lizzie Roeble lizzie.roeble@naturalis.nl (ORCID)
Theo Pannetier t.s.c.pannetier@rug.nl (ORCID)
See Also
Useful links:
Report bugs at https://github.com/joshwlambert/DAISIEprep/issues
Phylogenetic trees of the Galapagos bird lineages and sister species on the mainland.
Description
Each dataset is a phylogenetic tree used to extract the Galapagos avifaunal lineages.
Usage
coccyzus_tree
columbiformes_tree
finches_tree
mimus_tree
myiarchus_tree
progne_tree
pyrocephalus_tree
setophaga_tree
Format
A phylo object (from the ape package)
An object of class phylo of length 5.
An object of class phylo of length 4.
An object of class phylo of length 5.
An object of class phylo of length 4.
An object of class phylo of length 5.
An object of class phylo of length 5.
An object of class phylo of length 5.
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.
Defines the island_tbl class which is used when extracting information
from the phylogenetic and island data to be used for constructing a
daisie_data_tbl
Description
Defines the island_tbl class which is used when extracting information
from the phylogenetic and island data to be used for constructing a
daisie_data_tbl
Slots
clade_namecharacter.
statuscharacter.
missing_speciescharacter.
col_timenumeric.
col_max_agelogical.
branching_timesnumeric.
min_agenumeric.
speciescharacter.
clade_typenumeric.
Defines the island_tbl class which is used when extracting information
from the phylogenetic and island data to be used for constructing a
daisie_data_tbl
Description
Defines the island_tbl class which is used when extracting information
from the phylogenetic and island data to be used for constructing a
daisie_data_tbl
Slots
island_tbldata frame.
metadatalist.
Defines the Multi_island_tbl class which is multiple Island_tbls.
Description
Defines the Multi_island_tbl class which is multiple Island_tbls.
Slots
.Dataa list of
Island_tbl.
Fits a model of ancestral state reconstruction of island presence
Description
Fits a model of ancestral state reconstruction of island presence
Usage
add_asr_node_states(
phylod,
asr_method,
tie_preference = "island",
earliest_col = FALSE,
rate_model = NULL,
...
)
Arguments
phylod |
A |
asr_method |
A character string, either "parsimony" or "mk" determines
whether a maximum parsimony or continuous-time markov model reconstructs the
ancestral states at each node. See documentation in
|
tie_preference |
Character string, either "island" or "mainland" to
choose the most probable state at each node using the |
earliest_col |
A boolean to determine whether to take the colonisation time as the most probable time (FALSE) or the earliest possible colonisation time (TRUE), where the probability of a species being on the island is non-zero. Default is FALSE. |
rate_model |
Rate model to be used for fitting the transition rate matrix. Can be "ER" (all rates equal), "SYM" (transition rate i–>j is equal to transition rate j–>i), "ARD" (all rates can be different), "SUEDE" (only stepwise transitions i–>i+1 and i–>i-1 allowed, all 'up' transitions are equal, all 'down' transitions are equal) or "SRD" (only stepwise transitions i–>i+1 and i–>i-1 allowed, and each rate can be different). Can also be an index matrix that maps entries of the transition matrix to the corresponding independent rate parameter to be fitted. Diagonal entries should map to 0, since diagonal entries are not treated as independent rate parameters but are calculated from the remaining entries in the transition matrix. All other entries that map to 0 represent a transition rate of zero. The format of this index matrix is similar to the format used by the |
... |
dots Allows arguments to be passed to |
Details
The rate_model argument documentation is inherited from
castor::asr_mk_model(), therefore, the last sentence about the
transition_matrix argument does not apply to add_asr_node_states().
Value
An object of phylo4d class with tip and node data
Adds an island colonists (can be either a singleton lineage or an island clade) to the island community (island_tbl).
Description
Adds an island colonists (can be either a singleton lineage or an island clade) to the island community (island_tbl).
Usage
add_island_colonist(
island_tbl,
clade_name,
status,
missing_species,
col_time,
col_max_age,
branching_times,
min_age,
species,
clade_type
)
Arguments
island_tbl |
An instance of the |
clade_name |
Character name of the colonising clade. |
status |
Character endemicity status of the colonising clade. Either
|
missing_species |
Numeric number of missing species from the phylogeny
that belong to the colonising clade. For a clade with missing species this
is |
col_time |
Numeric with the colonisation time of the island colonist |
col_max_age |
Boolean determining whether colonisation time should be considered a precise time of colonisation or a maximum time of colonisation |
branching_times |
Numeric vector of one or more elements which are the branching times on the island. |
min_age |
Numeric minimum age (time before the present) that the species must have colonised the island by. This is known when there is a branching on the island, either in species or subspecies. |
species |
Character vector of one or more elements containing the name of the species included in the colonising clade. |
clade_type |
Numeric determining which type of clade the island colonist
is, this determines which macroevolutionary regime (parameter set) the island
colonist is in. After formatting the |
Value
An object of Island_tbl class
Examples
# create an empty island_tbl to add to
island_tbl <- island_tbl()
# add a new island colonist
island_tbl <- add_island_colonist(
island_tbl,
clade_name = "new_clade",
status = "endemic",
missing_species = 0,
col_time = 1,
col_max_age = FALSE,
branching_times = NA,
min_age = NA,
species = "new_clade",
clade_type = 1
)
Adds a specified number of missing species to an existing island_tbl at the
colonist specified by the species_to_add_to argument given. The species
given is located within the island_tbl data and missing species are
assigned. This is to be used after extract_island_species() to input
missing species.
Description
Adds a specified number of missing species to an existing island_tbl at the
colonist specified by the species_to_add_to argument given. The species
given is located within the island_tbl data and missing species are
assigned. This is to be used after extract_island_species() to input
missing species.
Usage
add_missing_species(island_tbl, num_missing_species, species_to_add_to)
Arguments
island_tbl |
An instance of the |
num_missing_species |
Numeric for the number of missing species in the clade. |
species_to_add_to |
Character string with the name of the species to identify which clade to assign missing species to. |
Value
Object of Island_tbl class
Examples
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
phylo <- ape::rcoal(5)
phylo$tip.label <- c("bird_a", "bird_b", "bird_c", "bird_d", "bird_e")
phylo <- phylobase::phylo4(phylo)
endemicity_status <- c(
"not_present", "not_present", "endemic", "not_present", "not_present"
)
phylod <- phylobase::phylo4d(phylo, as.data.frame(endemicity_status))
island_tbl <- extract_island_species(phylod, extraction_method = "min")
island_tbl <- add_missing_species(
island_tbl = island_tbl,
num_missing_species = 1,
species_to_add_to = "bird_c"
)
Calculates the number of missing species to be assigned to each island clade in the island_tbl object and assigns the missing species to them. In the case that multiple genera are in an island clade and each have missing species the number of missing species is summed. Currently the missing species are assigned to the genus that first matches with the missing species table, however a more biologically or stochastic assignment is in development.
Description
Calculates the number of missing species to be assigned to each island clade in the island_tbl object and assigns the missing species to them. In the case that multiple genera are in an island clade and each have missing species the number of missing species is summed. Currently the missing species are assigned to the genus that first matches with the missing species table, however a more biologically or stochastic assignment is in development.
Usage
add_multi_missing_species(missing_species, missing_genus, island_tbl)
Arguments
missing_species |
Numeric number of missing species from the phylogeny
that belong to the colonising clade. For a clade with missing species this
is |
missing_genus |
A list of character vectors containing the genera in each island clade |
island_tbl |
An instance of the |
Value
Object of Island_tbl class
Examples
phylod <- create_test_phylod(test_scenario = 6)
island_tbl <- suppressWarnings(extract_island_species(
phylod = phylod,
extraction_method = "asr",
))
phylod <- create_test_phylod(test_scenario = 7)
island_tbl <- suppressWarnings(extract_island_species(
phylod = phylod,
extraction_method = "asr",
island_tbl = island_tbl
))
missing_species <- data.frame(
clade_name = "bird",
missing_species = 1,
endemicity_status = "endemic"
)
missing_genus <- list("bird", character(0))
island_tbl <- add_multi_missing_species(
missing_species = missing_species,
missing_genus = missing_genus,
island_tbl = island_tbl
)
Add an outgroup species to a given phylogeny.
Description
Add an outgroup species to a given phylogeny.
Usage
add_outgroup(phylo)
Arguments
phylo |
A phylogeny either as a |
Value
A phylo object
Examples
phylo <- ape::rcoal(10)
phylo_with_outgroup <- add_outgroup(phylo)
Checks whether all species given in the descendants vector are the same species.
Description
Checks whether all species given in the descendants vector are the same species.
Usage
all_descendants_conspecific(descendants)
Arguments
descendants |
A vector character strings with the names of species to determine whether they are the same species. |
Value
Boolean
Examples
# Example where species are not conspecific
descendants <- c("bird_a", "bird_b", "bird_c")
all_descendants_conspecific(descendants = descendants)
# Example where species are conspecific
descendants <- c("bird_a_1", "bird_a_2", "bird_a_3")
all_descendants_conspecific(descendants = descendants)
All possible endemicity statuses
Description
All possible endemicity statuses
Usage
all_endemicity_status()
Value
A vector of character strings with all the endemicity status options
Detects any cases where a non-endemic species or species not present on the
island has likely been on the island given its ancestral state reconstruction
indicating ancestral presence on the island and so is likely a back
colonisation from the island to the mainland (or potentially different
island). This function is useful if using extraction_method = "min" in
DAISIEprep::extract_island_species() as it may brake up a single colonist
into multiple colonists because of back-colonisation.
Description
Detects any cases where a non-endemic species or species not present on the
island has likely been on the island given its ancestral state reconstruction
indicating ancestral presence on the island and so is likely a back
colonisation from the island to the mainland (or potentially different
island). This function is useful if using extraction_method = "min" in
DAISIEprep::extract_island_species() as it may brake up a single colonist
into multiple colonists because of back-colonisation.
Usage
any_back_colonisation(phylod, only_tips = FALSE)
Arguments
phylod |
A |
only_tips |
A boolean determing whether only the tips (i.e. terminal branches) are searched for back colonisation events. |
Value
A single or vector of character strings. Character string is in the format ancestral_node -> focal_node, where the ancestral node is not on mainland but the focal node is. In the case of no back colonisations a different message string is returned.
Examples
# Example with no back colonisation
phylod <- create_test_phylod(test_scenario = 15)
any_back_colonisation(phylod)
# Example with back colonisation
set.seed(
3,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
phylo <- ape::rcoal(5)
phylo$tip.label <- c("bird_a", "bird_b", "bird_c", "bird_d", "bird_e")
phylo <- phylobase::phylo4(phylo)
endemicity_status <- c("endemic", "endemic", "not_present",
"endemic", "not_present")
phylod <- phylobase::phylo4d(phylo, as.data.frame(endemicity_status))
phylod <- add_asr_node_states(phylod = phylod, asr_method = "parsimony")
# aritificially modify data to produce back-colonisation
phylobase::tdata(phylod)$island_status[8] <- "endemic"
any_back_colonisation(phylod = phylod)
Checks whether the phylogeny has an outgroup that is not present on the island. This is critical when extracting data from the phylogeny so the stem age (colonisation time) is correct.
Description
Checks whether the phylogeny has an outgroup that is not present on the island. This is critical when extracting data from the phylogeny so the stem age (colonisation time) is correct.
Usage
any_outgroup(phylod)
Arguments
phylod |
A |
Value
Boolean
Examples
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
phylo <- ape::rcoal(10)
phylo$tip.label <- c("bird_a", "bird_b", "bird_c", "bird_d", "bird_e",
"bird_f", "bird_g", "bird_h", "bird_i", "bird_j")
phylo <- phylobase::phylo4(phylo)
endemicity_status <- sample(c("not_present", "endemic", "nonendemic"),
size = length(phylobase::tipLabels(phylo)),
replace = TRUE)
phylod <- phylobase::phylo4d(phylo, as.data.frame(endemicity_status))
any_outgroup(phylod)
Checks whether there are any species in the phylogeny that have multiple tips (i.e. multiple subspecies per species) and whether any of those tips are paraphyletic (i.e. are their subspecies more distantly related to each other than to other subspecies or species).
Description
Checks whether there are any species in the phylogeny that have multiple tips (i.e. multiple subspecies per species) and whether any of those tips are paraphyletic (i.e. are their subspecies more distantly related to each other than to other subspecies or species).
Usage
any_polyphyly(phylod)
Arguments
phylod |
A |
Value
Boolean
Examples
phylod <- create_test_phylod(test_scenario = 1)
any_polyphyly(phylod)
Converts the Island_tbl class to a data frame in the format of a DAISIE
data table (see DAISIE R package for details). This can then be input into
DAISIEprep::create_daisie_data() function which creates the list input into
the DAISIE ML models.
Description
Converts the Island_tbl class to a data frame in the format of a DAISIE
data table (see DAISIE R package for details). This can then be input into
DAISIEprep::create_daisie_data() function which creates the list input into
the DAISIE ML models.
Usage
as_daisie_datatable(island_tbl, island_age, precise_col_time = TRUE)
Arguments
island_tbl |
An instance of the |
island_age |
Age of the island in appropriate units. |
precise_col_time |
Boolean, TRUE uses the precise times of colonisation, FALSE makes every colonist a max age colonistion and uses minimum age of colonisation if available. |
Value
A data frame in the format of a DAISIE data table
Author(s)
Joshua W. Lambert, Pedro Neves
Examples
phylod <- create_test_phylod(10)
island_tbl <- extract_island_species(
phylod = phylod,
extraction_method = "asr"
)
# Example where precise colonisation times are known
daisie_datatable <- as_daisie_datatable(
island_tbl = island_tbl,
island_age = 0.2,
precise_col_time = TRUE
)
# Example where colonisation times are uncertain and set to max ages
daisie_datatable <- as_daisie_datatable(
island_tbl = island_tbl,
island_age = 0.2,
precise_col_time = FALSE
)
Performance analysis of the extract_island_species() function Uses system.time() for timing for reasons explained here: https://radfordneal.wordpress.com/2014/02/02/inaccurate-results-from-microbenchmark/ # nolint
Description
Performance analysis of the extract_island_species() function Uses system.time() for timing for reasons explained here: https://radfordneal.wordpress.com/2014/02/02/inaccurate-results-from-microbenchmark/ # nolint
Usage
benchmark(
phylod,
tree_size_range,
num_points,
prob_on_island,
prob_endemic,
replicates,
extraction_method,
asr_method,
tie_preference,
log_scale = TRUE,
parameter_index = NULL,
verbose = FALSE
)
Arguments
phylod |
A |
tree_size_range |
Numeric vector of two elements, the first is the smallest tree size (number of tips) and the second is the largest tree size |
num_points |
Numeric determining how many points in the sequence of smallest tree size to largest tree size |
prob_on_island |
Numeric vector of each probability on island to use in the parameter space |
prob_endemic |
Numeric vector of each probability of an island species being endemic to use in the parameter space |
replicates |
Numeric determining the number of replicates to use to account for the stochasticity in sampling the species on the island and endemic species |
extraction_method |
A character string specifying whether the
colonisation time extracted is the minimum time ( |
asr_method |
A character string, either "parsimony" or "mk" determines
whether a maximum parsimony or continuous-time markov model reconstructs the
ancestral states at each node. See documentation in
|
tie_preference |
Character string, either "island" or "mainland" to
choose the most probable state at each node using the |
log_scale |
A boolean determining whether the sequence of tree sizes are on a linear (FALSE) or log (TRUE) scale |
parameter_index |
Numeric determining which parameter set to use (i.e which row in the parameter space data frame), if this is NULL all parameter sets will be looped over |
verbose |
Boolean. States if intermediate results should be printed to console. Defaults to FALSE |
Value
Data frame
Takes an existing instance of an Island_tbl class and bind the information
from the instance of an Island_colonist class to it
Description
Takes an existing instance of an Island_tbl class and bind the information
from the instance of an Island_colonist class to it
Usage
bind_colonist_to_tbl(island_colonist, island_tbl)
Arguments
island_colonist |
An instance of the |
island_tbl |
An instance of the |
Value
An object of Island_tbl class
Examples
island_colonist <- DAISIEprep::island_colonist(
clade_name = "bird",
status = "endemic",
missing_species = 0,
col_time = 1,
col_max_age = FALSE,
branching_times = 0.5,
species = "bird_a",
clade_type = 1
)
island_tbl <- island_tbl()
bind_colonist_to_tbl(
island_colonist = island_colonist,
island_tbl = island_tbl
)
Checks the validity of the Island_colonist class
Description
Checks the validity of the Island_colonist class
Usage
check_island_colonist(object)
Arguments
object |
Instance of the island_colonist class |
Value
Boolean or errors
Examples
island_colonist <- island_colonist()
check_island_colonist(island_colonist)
Checks the validity of the Island_tbl class
Description
Checks the validity of the Island_tbl class
Usage
check_island_tbl(object)
Arguments
object |
Instance of the Island_tbl class |
Value
Boolean or errors
Examples
island_tbl <- island_tbl()
check_island_tbl(island_tbl)
Checks the validity of the Multi_island_tbl class
Description
Checks the validity of the Multi_island_tbl class
Usage
check_multi_island_tbl(object)
Arguments
object |
Instance of the Multi_island_tbl class |
Value
Boolean or errors
Examples
multi_island_tbl <- multi_island_tbl()
check_multi_island_tbl(multi_island_tbl)
Checks whether \linkS4class{phylo4d} object conforms
to the requirements of the DAISIEprep package. If the function does not
return anything the data is ready to be used, if an error is returned the
data requires some pre-processing before DAISIEprep can be used
Description
Checks whether \linkS4class{phylo4d} object conforms
to the requirements of the DAISIEprep package. If the function does not
return anything the data is ready to be used, if an error is returned the
data requires some pre-processing before DAISIEprep can be used
Usage
check_phylo_data(phylod)
Arguments
phylod |
A |
Value
Nothing or error message
Examples
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
phylo <- ape::rcoal(10)
phylo$tip.label <- c("bird_a", "bird_b", "bird_c", "bird_d", "bird_e",
"bird_f", "bird_g", "bird_h", "bird_i", "bird_j")
phylo <- phylobase::phylo4(phylo)
endemicity_status <- sample(
c("not_present", "endemic", "nonendemic"),
size = length(phylobase::tipLabels(phylo)),
replace = TRUE,
prob = c(0.6, 0.2, 0.2)
)
phylod <- phylobase::phylo4d(phylo, as.data.frame(endemicity_status))
check_phylo_data(phylod)
A phylogenetic tree of coccyzus species with endemicity status as tip states.
Description
A phylogenetic tree of coccyzus species with endemicity status as tip states.
Usage
coccyzus_phylod
Format
coccyzus_phylod
A phylo4d object (from the phylobase package) with
20 tips and
19 internal
nodes.
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.
A phylogenetic tree of columbiformes species with endemicity status as tip states.
Description
A phylogenetic tree of columbiformes species with endemicity status as tip states.
Usage
columbiformes_phylod
Format
columbiformes_phylod
A phylo4d object (from the phylobase package) with
242 tips and
241 internal
nodes.
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.
Reads in the checklist of all species on an island, including those that are not in the phylogeny (represented by NA) and counts the number of species missing from the phylogeny each genus
Description
Reads in the checklist of all species on an island, including those that are not in the phylogeny (represented by NA) and counts the number of species missing from the phylogeny each genus
Usage
count_missing_species(
checklist,
phylo_name_col,
genus_name_col,
in_phylo_col,
endemicity_status_col,
rm_species_col = NULL
)
Arguments
checklist |
data frame with information on species on the island |
phylo_name_col |
A character string specifying the column name where the names in the phylogeny are in the checklist |
genus_name_col |
A character string specifying the column name where the genus names are in the checklist |
in_phylo_col |
A character string specifying the column name where the status of whether a species is in the phylogeny is in the checklist |
endemicity_status_col |
A character string specifying the column name where the endemicity status of the species are in the checklist |
rm_species_col |
A character string specifying the column name where the information on whether to remove species from the checklist before counting the number of missing species is in the checklist. This can be NULL if no species are to be removed from the checklist. This is useful when species are in the checklist because they are on the island but need to be removed as they are not in the group of interest, e.g. a migratory bird amongst terrestrial birds |
Value
Data frame
Examples
mock_checklist <- data.frame(
genus = c("bird", "bird", "bird", "bird", "bird", "bird", "bird",
"bird", "bird", "bird"),
species = c("a", "b", "c", "d", "e", "f", "g", "h", "i", "j"),
species_names = c("bird_a", "bird_b", "bird_c", "bird_d", "bird_e",
"bird_f","bird_g", "bird_h", "bird_i", "bird_j"),
sampled = c(TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, FALSE, TRUE, FALSE),
endemicity_status = c("endemic", "endemic", "endemic", "nonendemic",
"endemic", "nonendemic", "endemic", "endemic",
"endemic", "endemic"),
remove_species = (rep(FALSE, 10))
)
missing_species <- count_missing_species(
checklist = mock_checklist,
phylo_name_col = "species_names",
genus_name_col = "genus",
in_phylo_col = "sampled",
endemicity_status_col = "endemicity_status",
rm_species_col = NULL
)
This is a wrapper function for DAISIE::DAISIE_dataprep(). It allows the final DAISIE data structure to be produced from within DAISIEprep. For detailed documentation see the help documentation in the DAISIE package (?DAISIE::DAISIE_dataprep).
Description
This is a wrapper function for DAISIE::DAISIE_dataprep(). It allows the final DAISIE data structure to be produced from within DAISIEprep. For detailed documentation see the help documentation in the DAISIE package (?DAISIE::DAISIE_dataprep).
Usage
create_daisie_data(
data,
island_age,
num_mainland_species,
num_clade_types = 1,
list_type2_clades = NA,
prop_type2_pool = "proportional",
epss = 1e-05,
verbose = FALSE,
precise_col_time = TRUE
)
Arguments
data |
Either an object of class |
island_age |
Age of the island in appropriate units. |
num_mainland_species |
The size of the mainland pool, i.e. the number of species that can potentially colonise the island. |
num_clade_types |
Number of clade types. Default num_clade_types = 1 all species are considered to belong to the same macroevolutionary process. If num_clade_types = 2, there are two types of clades with distinct macroevolutionary processes. |
list_type2_clades |
If num_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. If num_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 the mainland pool size is 1000 and prop_type2_pool = 0.02 then the number of type 2 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 FALSE |
precise_col_time |
Boolean, TRUE uses the precise times of colonisation, FALSE makes every colonist a max age colonistion and uses minimum age of colonisation if available. |
Value
DAISIE data list
Examples
phylod <- create_test_phylod(3)
island_tbl <- extract_island_species(
phylod = phylod,
extraction_method = "min"
)
daisie_datatable <- as_daisie_datatable(island_tbl, island_age = 10)
daisie_data_list <- create_daisie_data(
data = daisie_datatable,
island_age = 10,
num_mainland_species = 1000,
num_clade_types = 1,
list_type2_clades = NA,
prop_type2_pool = NA,
epss = 1e-5,
verbose = FALSE
)
Creates a data frame with the endemicity status (either 'endemic', 'nonendemic', 'not_present') of every species in the phylogeny using a phylogeny and a data frame of the island species and their endemicity (either 'endemic' or 'nonendemic') provided.
Description
Creates a data frame with the endemicity status (either 'endemic', 'nonendemic', 'not_present') of every species in the phylogeny using a phylogeny and a data frame of the island species and their endemicity (either 'endemic' or 'nonendemic') provided.
Usage
create_endemicity_status(phylo, island_species)
Arguments
phylo |
A phylogeny either as a |
island_species |
Data frame with two columns. The first is a character string of the tip_labels with the tip names of the species on the island. The second column a character string of the endemicity status of the species, either endemic or nonendemic. |
Details
Species included in the island_species data frame but not included in the
phylo will not be included in the output and warning will print all of the
species that are in the island_species that are not found in the phylo.
Value
Data frame with single column of character strings and row names
Examples
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
phylo <- ape::rcoal(4)
phylo$tip.label <- c("species_a", "species_b", "species_c", "species_d")
phylo <- methods::as(phylo, "phylo4")
island_species <- data.frame(
tip_labels = c("species_a", "species_b", "species_c", "species_d"),
tip_endemicity_status = c("endemic", "endemic", "endemic", "nonendemic")
)
endemicity_status <- create_endemicity_status(
phylo = phylo,
island_species = island_species
)
Creates phylod objects.
Description
A helper function that is useful in tests and examples to
easily create phylod objects (i.e. phylogenetic trees with data).
Usage
create_test_phylod(test_scenario)
Arguments
test_scenario |
Integer specifying which test phylod object to create. |
Value
A phylo4d object
Examples
create_test_phylod(test_scenario = 1)
Documentation for function in the DAISIEprep package
Description
Documentation for function in the DAISIEprep package
Usage
default_params_doc(
island_colonist,
island_tbl,
phylod,
extraction_method,
species_label,
species_endemicity,
x,
value,
clade_name,
status,
missing_species,
col_time,
col_max_age,
branching_times,
min_age,
species,
clade_type,
endemic_clade,
phylo,
island_species,
descendants,
clade,
asr_method,
tie_preference,
earliest_col,
include_not_present,
nested_asr_species,
num_missing_species,
species_to_add_to,
node_pies,
test_scenario,
data,
island_age,
num_mainland_species,
num_clade_types,
list_type2_clades,
prop_type2_pool,
epss,
verbose,
precise_col_time,
n,
digits,
include_crown_age,
only_tips,
node_label,
multi_phylod,
island_tbl_1,
island_tbl_2,
unique_clade_name,
genus_name,
stem,
genus_in_tree,
missing_genus,
checklist,
phylo_name_col,
genus_name_col,
in_phylo_col,
endemicity_status_col,
rm_species_col,
tree_size_range,
num_points,
prob_on_island,
prob_endemic,
replicates,
log_scale,
parameter_index,
sse_model,
force_nonendemic_singleton,
...
)
Arguments
island_colonist |
An instance of the |
island_tbl |
An instance of the |
phylod |
A |
extraction_method |
A character string specifying whether the
colonisation time extracted is the minimum time ( |
species_label |
The tip label of the species of interest. |
species_endemicity |
A character string with the endemicity, either "endemic" or "nonendemic" of an island species, or "not_present" if not on the island. |
x |
An object whose class is determined by the signature. |
value |
A value which can take several forms to be assigned to an object of a class. |
clade_name |
Character name of the colonising clade. |
status |
Character endemicity status of the colonising clade. Either
|
missing_species |
Numeric number of missing species from the phylogeny
that belong to the colonising clade. For a clade with missing species this
is |
col_time |
Numeric with the colonisation time of the island colonist |
col_max_age |
Boolean determining whether colonisation time should be considered a precise time of colonisation or a maximum time of colonisation |
branching_times |
Numeric vector of one or more elements which are the branching times on the island. |
min_age |
Numeric minimum age (time before the present) that the species must have colonised the island by. This is known when there is a branching on the island, either in species or subspecies. |
species |
Character vector of one or more elements containing the name of the species included in the colonising clade. |
clade_type |
Numeric determining which type of clade the island colonist
is, this determines which macroevolutionary regime (parameter set) the island
colonist is in. After formatting the |
endemic_clade |
Named vector with all the species from a clade. |
phylo |
A phylogeny either as a |
island_species |
Data frame with two columns. The first is a character string of the tip_labels with the tip names of the species on the island. The second column a character string of the endemicity status of the species, either endemic or nonendemic. |
descendants |
A vector character strings with the names of species to determine whether they are the same species. |
clade |
A numeric vector which the indices of the species which are in the island clade. |
asr_method |
A character string, either "parsimony" or "mk" determines
whether a maximum parsimony or continuous-time markov model reconstructs the
ancestral states at each node. See documentation in
|
tie_preference |
Character string, either "island" or "mainland" to
choose the most probable state at each node using the |
earliest_col |
A boolean to determine whether to take the colonisation time as the most probable time (FALSE) or the earliest possible colonisation time (TRUE), where the probability of a species being on the island is non-zero. Default is FALSE. |
include_not_present |
A boolean determining whether species not present on the island should be included in island colonist when embedded within an island clade. Default is FALSE. |
nested_asr_species |
A |
num_missing_species |
Numeric for the number of missing species in the clade. |
species_to_add_to |
Character string with the name of the species to identify which clade to assign missing species to. |
node_pies |
Boolean determining if pie charts of the probabilities of a species being present on the island. If TRUE the correct data is required in the phylod object. |
test_scenario |
Integer specifying which test phylod object to create. |
data |
Either an object of class |
island_age |
Age of the island in appropriate units. |
num_mainland_species |
The size of the mainland pool, i.e. the number of species that can potentially colonise the island. |
num_clade_types |
Number of clade types. Default num_clade_types = 1 all species are considered to belong to the same macroevolutionary process. If num_clade_types = 2, there are two types of clades with distinct macroevolutionary processes. |
list_type2_clades |
If num_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. If num_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 the mainland pool size is 1000 and prop_type2_pool = 0.02 then the number of type 2 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 FALSE |
precise_col_time |
Boolean, TRUE uses the precise times of colonisation, FALSE makes every colonist a max age colonistion and uses minimum age of colonisation if available. |
n |
A numeric to be rounded. |
digits |
A numeric specifying which decimal places to round to |
include_crown_age |
A boolean determining whether the crown age gets plotted with the stem age. |
only_tips |
A boolean determing whether only the tips (i.e. terminal branches) are searched for back colonisation events. |
node_label |
A numeric label for a node within a phylogeny. |
multi_phylod |
A list of phylod objects. |
island_tbl_1 |
An object of |
island_tbl_2 |
An object of |
unique_clade_name |
Boolean determining whether a unique species identifier is used as the clade name in the Island_tbl object or a genus name which may not be unique if that genus has several independent island colonisations |
genus_name |
Character string of genus name to be matched with a genus name from the tip labels in the phylogeny |
stem |
Character string, either "genus" or "island_presence". The former will extract the stem age of the genussbased on the genus name provided, the latter will extract the stem age based on the ancestral presence on the island either based on the "min" or "asr" extraction algorithms. |
genus_in_tree |
A numeric vector that indicates which species in the genus are in the tree |
missing_genus |
A list of character vectors containing the genera in each island clade |
checklist |
data frame with information on species on the island |
phylo_name_col |
A character string specifying the column name where the names in the phylogeny are in the checklist |
genus_name_col |
A character string specifying the column name where the genus names are in the checklist |
in_phylo_col |
A character string specifying the column name where the status of whether a species is in the phylogeny is in the checklist |
endemicity_status_col |
A character string specifying the column name where the endemicity status of the species are in the checklist |
rm_species_col |
A character string specifying the column name where the information on whether to remove species from the checklist before counting the number of missing species is in the checklist. This can be NULL if no species are to be removed from the checklist. This is useful when species are in the checklist because they are on the island but need to be removed as they are not in the group of interest, e.g. a migratory bird amongst terrestrial birds |
tree_size_range |
Numeric vector of two elements, the first is the smallest tree size (number of tips) and the second is the largest tree size |
num_points |
Numeric determining how many points in the sequence of smallest tree size to largest tree size |
prob_on_island |
Numeric vector of each probability on island to use in the parameter space |
prob_endemic |
Numeric vector of each probability of an island species being endemic to use in the parameter space |
replicates |
Numeric determining the number of replicates to use to account for the stochasticity in sampling the species on the island and endemic species |
log_scale |
A boolean determining whether the sequence of tree sizes are on a linear (FALSE) or log (TRUE) scale |
parameter_index |
Numeric determining which parameter set to use (i.e which row in the parameter space data frame), if this is NULL all parameter sets will be looped over |
sse_model |
either "musse" (default) or "geosse". MuSSE expects state values 1, 2, 3, which here we encode as "not_present", "endemic", "nonendemic", respectively. GeoSSE expects trait values 0, 1, 2, with 0 the widespread state (here, "nonendemic"), and 1 and 2 are "not_present" and "endemic", respectively. |
force_nonendemic_singleton |
A boolean that determines whether all
species that are classified as This argument is only active when |
... |
dots Allows arguments to be passed to |
Value
Nothing
Author(s)
Joshua W. Lambert
Convert endemicity to SSE states
Description
Convert endemicity to SSE states
Usage
endemicity_to_sse_states(endemicity_status, sse_model = "musse")
Arguments
endemicity_status |
character vector with values "endemic", "nonendemic" and/or "not_present" |
sse_model |
either "musse" (default) or "geosse". MuSSE expects state values 1, 2, 3, which here we encode as "not_present", "endemic", "nonendemic", respectively. GeoSSE expects trait values 0, 1, 2, with 0 the widespread state (here, "nonendemic"), and 1 and 2 are "not_present" and "endemic", respectively. |
Value
an integer vector of tip states, following the encoding expected by the MuSSE/GeoSSE
Extracts an island clade based on the ancestral state reconstruction of the species presence on the island, therefore this clade can contain non-endemic species as well as endemic species.
Description
Extracts an island clade based on the ancestral state reconstruction of the species presence on the island, therefore this clade can contain non-endemic species as well as endemic species.
Usage
extract_asr_clade(phylod, species_label, clade, include_not_present)
Arguments
phylod |
A |
species_label |
The tip label of the species of interest. |
clade |
A numeric vector which the indices of the species which are in the island clade. |
include_not_present |
A boolean determining whether species not present on the island should be included in island colonist when embedded within an island clade. Default is FALSE. |
Value
An object of Island_colonist class
Extract ancestral state probabilities from BioGeoBEARS output
Description
Extract the probabilities of each endemicity status for tip and internal node states from the output of an optimisation performed with BioGeoBEARS
Usage
extract_biogeobears_ancestral_states_probs(biogeobears_res)
Arguments
biogeobears_res |
a list, the output of |
Value
a data.frame with one row per node (tips and internals) and four columns: label | not_present | endemic | nonendemic, the last three columns containing the probability of each endemicity status (and summing to 1).
Creates a name for a clade depending on whether all the species of the clade have the same genus name or whether the clade is composed of multiple genera, in which case it will create a unique clade name by concatinating the genus names
Description
Creates a name for a clade depending on whether all the species of the clade have the same genus name or whether the clade is composed of multiple genera, in which case it will create a unique clade name by concatinating the genus names
Usage
extract_clade_name(clade)
Arguments
clade |
A numeric vector which the indices of the species which are in the island clade. |
Value
Character
Extracts the information for an endemic clade (i.e. more than one species on
the island more closely related to each other than other mainland species)
from a phylogeny (specifically phylo4d object from phylobase package)
and stores it in an Island_colonist class
Description
Extracts the information for an endemic clade (i.e. more than one species on
the island more closely related to each other than other mainland species)
from a phylogeny (specifically phylo4d object from phylobase package)
and stores it in an Island_colonist class
Usage
extract_endemic_clade(phylod, species_label, unique_clade_name)
Arguments
phylod |
A |
species_label |
The tip label of the species of interest. |
unique_clade_name |
Boolean determining whether a unique species identifier is used as the clade name in the Island_tbl object or a genus name which may not be unique if that genus has several independent island colonisations |
Value
An object of Island_colonist class
Examples
set.seed(
3,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
phylo <- ape::rcoal(10)
phylo$tip.label <- c("bird_a", "bird_b", "bird_c", "bird_d", "bird_e",
"bird_f", "bird_g", "bird_h", "bird_i", "bird_j")
phylo <- methods::as(phylo, "phylo4")
endemicity_status <- sample(
x = c("not_present", "endemic", "nonendemic"),
size = length(phylobase::tipLabels(phylo)),
replace = TRUE,
prob = c(0.7, 0.3, 0)
)
phylod <- phylobase::phylo4d(phylo, as.data.frame(endemicity_status))
island_colonist <- extract_endemic_clade(
phylod = phylod,
species_label = "bird_i",
unique_clade_name = TRUE
)
Extracts the information for an endemic species from a phylogeny
(specifically phylo4d object from phylobase package) and stores it in
in an Island_colonist class
Description
Extracts the information for an endemic species from a phylogeny
(specifically phylo4d object from phylobase package) and stores it in
in an Island_colonist class
Usage
extract_endemic_singleton(phylod, species_label)
Arguments
phylod |
A |
species_label |
The tip label of the species of interest. |
Value
An object of Island_colonist class
Examples
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
phylo <- ape::rcoal(10)
phylo$tip.label <- c("bird_a", "bird_b", "bird_c", "bird_d", "bird_e",
"bird_f", "bird_g", "bird_h", "bird_i", "bird_j")
phylo <- phylobase::phylo4(phylo)
endemicity_status <- sample(
x = c("not_present", "endemic", "nonendemic"),
size = length(phylobase::tipLabels(phylo)),
replace = TRUE,
prob = c(0.6, 0.2, 0.2)
)
phylod <- phylobase::phylo4d(phylo, as.data.frame(endemicity_status))
extract_endemic_singleton(phylod = phylod, species_label = "bird_i")
Extracts the colonisation, diversification, and endemicty data from
phylogenetic and endemicity data and stores it in an Island_tbl object
Description
Extracts the colonisation, diversification, and endemicty data from
phylogenetic and endemicity data and stores it in an Island_tbl object
Usage
extract_island_species(
phylod,
extraction_method,
island_tbl = NULL,
include_not_present = FALSE,
nested_asr_species = c("split", "group"),
force_nonendemic_singleton = FALSE,
unique_clade_name = TRUE
)
Arguments
phylod |
A |
extraction_method |
A character string specifying whether the
colonisation time extracted is the minimum time ( |
island_tbl |
An instance of the |
include_not_present |
A boolean determining whether species not present on the island should be included in island colonist when embedded within an island clade. Default is FALSE. |
nested_asr_species |
A |
force_nonendemic_singleton |
A boolean that determines whether all
species that are classified as This argument is only active when |
unique_clade_name |
Boolean determining whether a unique species identifier is used as the clade name in the Island_tbl object or a genus name which may not be unique if that genus has several independent island colonisations |
Value
An object of Island_tbl class
Examples
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
phylo <- ape::rcoal(10)
phylo$tip.label <- c("bird_a", "bird_b", "bird_c", "bird_d", "bird_e",
"bird_f", "bird_g", "bird_h", "bird_i", "bird_j")
phylo <- phylobase::phylo4(phylo)
endemicity_status <- sample(
c("not_present", "endemic", "nonendemic"),
size = length(phylobase::tipLabels(phylo)),
replace = TRUE,
prob = c(0.6, 0.2, 0.2)
)
phylod <- phylobase::phylo4d(phylo, as.data.frame(endemicity_status))
extract_island_species(phylod, extraction_method = "min")
Extracts the information for a species (endemic or non-endemic) which has
multiple tips in the phylogeny (i.e. more than one sample per species) from
a phylogeny (specifically phylo4d object from phylobase package)
and stores it in an Island_colonist class
Description
Extracts the information for a species (endemic or non-endemic) which has
multiple tips in the phylogeny (i.e. more than one sample per species) from
a phylogeny (specifically phylo4d object from phylobase package)
and stores it in an Island_colonist class
Usage
extract_multi_tip_species(phylod, species_label, species_endemicity)
Arguments
phylod |
A |
species_label |
The tip label of the species of interest. |
species_endemicity |
A character string with the endemicity, either "endemic" or "nonendemic" of an island species, or "not_present" if not on the island. |
Value
An object of Island_colonist class
Examples
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
phylo <- ape::rcoal(10)
phylo$tip.label <- c("bird_a", "bird_b", "bird_c", "bird_d", "bird_e",
"bird_f", "bird_g", "bird_h_1", "bird_h_2", "bird_i")
phylo <- phylobase::phylo4(phylo)
endemicity_status <- c("not_present", "not_present", "not_present",
"not_present", "not_present", "not_present",
"not_present", "endemic", "endemic", "not_present")
phylod <- phylobase::phylo4d(phylo, as.data.frame(endemicity_status))
extract_multi_tip_species(
phylod = phylod,
species_label = "bird_h_1",
species_endemicity = "endemic"
)
Extracts the information for a non-endemic species from a phylogeny
(specifically phylo4d object from phylobase package) and stores it in
in an island_colonist class
Description
Extracts the information for a non-endemic species from a phylogeny
(specifically phylo4d object from phylobase package) and stores it in
in an island_colonist class
Usage
extract_nonendemic(phylod, species_label)
Arguments
phylod |
A |
species_label |
The tip label of the species of interest. |
Value
An object of island_colonist class
Examples
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
phylo <- ape::rcoal(10)
phylo$tip.label <- c("bird_a", "bird_b", "bird_c", "bird_d", "bird_e",
"bird_f", "bird_g", "bird_h", "bird_i", "bird_j")
phylo <- phylobase::phylo4(phylo)
endemicity_status <- sample(
x = c("not_present", "endemic", "nonendemic"),
size = length(phylobase::tipLabels(phylo)),
replace = TRUE,
prob = c(0.6, 0.2, 0.2)
)
phylod <- phylobase::phylo4d(phylo, as.data.frame(endemicity_status))
extract_nonendemic(phylod = phylod, species_label = "bird_g")
Extract non-endemic colonist that is forced to be a singleton by user
Description
Extract non-endemic colonist that is forced to be a singleton by user
Usage
extract_nonendemic_forced(phylod, species_label, island_tbl)
Arguments
phylod |
A |
species_label |
The tip label of the species of interest. |
island_tbl |
An instance of the |
Value
An object of phylo4d class with tip and node data
Extracts the colonisation, diversification, and endemicty data from
phylogenetic and endemicity data and stores it in an Island_tbl object
using the "asr" algorithm that extract island species given their ancestral
states of either island presence or absence.
Description
Extracts the colonisation, diversification, and endemicty data from
phylogenetic and endemicity data and stores it in an Island_tbl object
using the "asr" algorithm that extract island species given their ancestral
states of either island presence or absence.
Usage
extract_species_asr(
phylod,
species_label,
species_endemicity,
island_tbl,
include_not_present
)
Arguments
phylod |
A |
species_label |
The tip label of the species of interest. |
species_endemicity |
A character string with the endemicity, either "endemic" or "nonendemic" of an island species, or "not_present" if not on the island. |
island_tbl |
An instance of the |
include_not_present |
A boolean determining whether species not present on the island should be included in island colonist when embedded within an island clade. Default is FALSE. |
Value
An object of island_tbl class
Examples
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
phylo <- ape::rcoal(10)
phylo$tip.label <- c("bird_a", "bird_b", "bird_c", "bird_d", "bird_e",
"bird_f", "bird_g", "bird_h", "bird_i", "bird_j")
phylo <- phylobase::phylo4(phylo)
endemicity_status <- sample(c("not_present", "endemic", "nonendemic"),
size = length(phylobase::tipLabels(phylo)),
replace = TRUE, prob = c(0.8, 0.1, 0.1))
phylod <- phylobase::phylo4d(phylo, as.data.frame(endemicity_status))
phylod <- add_asr_node_states(
phylod = phylod,
asr_method = "parsimony"
)
island_tbl <- island_tbl()
extract_species_asr(
phylod = phylod,
species_label = "bird_i",
species_endemicity = "endemic",
island_tbl = island_tbl,
include_not_present = FALSE
)
Extracts the colonisation, diversification, and endemicty data from
phylogenetic and endemicity data and stores it in an Island_tbl object
using the "min" algorithm that extract island species as the shortest time
to the present.
Description
Extracts the colonisation, diversification, and endemicty data from
phylogenetic and endemicity data and stores it in an Island_tbl object
using the "min" algorithm that extract island species as the shortest time
to the present.
Usage
extract_species_min(
phylod,
species_label,
species_endemicity,
island_tbl,
unique_clade_name
)
Arguments
phylod |
A |
species_label |
The tip label of the species of interest. |
species_endemicity |
A character string with the endemicity, either "endemic" or "nonendemic" of an island species, or "not_present" if not on the island. |
island_tbl |
An instance of the |
unique_clade_name |
Boolean determining whether a unique species identifier is used as the clade name in the Island_tbl object or a genus name which may not be unique if that genus has several independent island colonisations |
Value
An object of island_tbl class
Examples
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
phylo <- ape::rcoal(10)
phylo$tip.label <- c("bird_a", "bird_b", "bird_c", "bird_d", "bird_e",
"bird_f", "bird_g", "bird_h", "bird_i", "bird_j")
phylo <- phylobase::phylo4(phylo)
endemicity_status <- sample(
c("not_present", "endemic", "nonendemic"),
size = length(phylobase::tipLabels(phylo)),
replace = TRUE,
prob = c(0.6, 0.2, 0.2)
)
phylod <- phylobase::phylo4d(phylo, as.data.frame(endemicity_status))
island_tbl <- island_tbl()
extract_species_min(
phylod = phylod,
species_label = "bird_g",
species_endemicity = "nonendemic",
island_tbl = island_tbl,
unique_clade_name = TRUE
)
Extracts the stem age from the phylogeny when the a species is known to
belong to a genus but is not itself in the phylogeny and there are members
of the same genus are in the phylogeny. The stem age can either be for the
genus (or several genera) in the tree (stem = "genus") or use an extraction
algorithm to find the stem of when the species colonised the island
(stem = "island_presence), either 'min' or 'asr' as in
extract_island_species(). When stem = "island_presence"
the reconstructed node states are used
to determine the stem age.
Description
Extracts the stem age from the phylogeny when the a species is known to
belong to a genus but is not itself in the phylogeny and there are members
of the same genus are in the phylogeny. The stem age can either be for the
genus (or several genera) in the tree (stem = "genus") or use an extraction
algorithm to find the stem of when the species colonised the island
(stem = "island_presence), either 'min' or 'asr' as in
extract_island_species(). When stem = "island_presence"
the reconstructed node states are used
to determine the stem age.
Usage
extract_stem_age(genus_name, phylod, stem, extraction_method = NULL)
Arguments
genus_name |
Character string of genus name to be matched with a genus name from the tip labels in the phylogeny |
phylod |
A |
stem |
Character string, either "genus" or "island_presence". The former will extract the stem age of the genussbased on the genus name provided, the latter will extract the stem age based on the ancestral presence on the island either based on the "min" or "asr" extraction algorithms. |
extraction_method |
A character string specifying whether the
colonisation time extracted is the minimum time ( |
Value
Numeric
Examples
# In this example the parrot clade is the genus of interest only the parrots
# are endemic to the island and all the passerines are not on the island
set.seed(1)
tree <- ape::rcoal(10)
tree$tip.label <- c(
"passerine_a", "passerine_b", "passerine_c", "passerine_d", "passerine_e",
"passerine_f", "parrot_a", "parrot_b", "parrot_c", "passerine_j")
tree <- phylobase::phylo4(tree)
endemicity_status <- c(
"not_present", "not_present", "not_present", "not_present", "not_present",
"not_present", "endemic", "endemic", "endemic", "not_present")
phylod <- phylobase::phylo4d(tree, as.data.frame(endemicity_status))
DAISIEprep::plot_phylod(phylod)
# the species 'parrot_a' is removed and becomes the missing species we want
# to the know the stem age for
phylod <- phylobase::subset(x = phylod, tips.exclude = "parrot_a")
DAISIEprep::plot_phylod(phylod)
extract_stem_age(
genus_name = "parrot",
phylod = phylod,
stem = "island_presence",
extraction_method = "min"
)
# here we use the extraction_method = "asr" which requires ancestral node
# states in the tree.
phylod <- add_asr_node_states(
phylod = phylod,
asr_method = "parsimony",
tie_preference = "mainland"
)
DAISIEprep::plot_phylod(phylod)
extract_stem_age(
genus_name = "parrot",
phylod = phylod,
stem = "island_presence",
extraction_method = "asr"
)
# lastly we extract the stem age based on the genus name
extract_stem_age(
genus_name = "parrot",
phylod = phylod,
stem = "genus",
extraction_method = NULL
)
Extracts the stem age from the phylogeny when the a species is known to belong to a genus but is not itself in the phylogeny and there are members of the same genus are in the phylogeny using the 'asr' extraction method
Description
Extracts the stem age from the phylogeny when the a species is known to belong to a genus but is not itself in the phylogeny and there are members of the same genus are in the phylogeny using the 'asr' extraction method
Usage
extract_stem_age_asr(genus_in_tree, phylod)
Arguments
genus_in_tree |
A numeric vector that indicates which species in the genus are in the tree |
phylod |
A |
Value
Numeric
Extracts the stem age from the phylogeny when the a species is known to belong to a genus but is not itself in the phylogeny and there are members of the same genus are in the phylogeny
Description
Extracts the stem age from the phylogeny when the a species is known to belong to a genus but is not itself in the phylogeny and there are members of the same genus are in the phylogeny
Usage
extract_stem_age_genus(genus_in_tree, phylod)
Arguments
genus_in_tree |
A numeric vector that indicates which species in the genus are in the tree |
phylod |
A |
Value
Numeric
Extracts the stem age from the phylogeny when the a species is known to belong to a genus but is not itself in the phylogeny and there are members of the same genus are in the phylogeny using the 'min' extraction method
Description
Extracts the stem age from the phylogeny when the a species is known to belong to a genus but is not itself in the phylogeny and there are members of the same genus are in the phylogeny using the 'min' extraction method
Usage
extract_stem_age_min(genus_in_tree, phylod)
Arguments
genus_in_tree |
A numeric vector that indicates which species in the genus are in the tree |
phylod |
A |
Value
Numeric
A phylogenetic tree of finches species with endemicity status as tip states.
Description
A phylogenetic tree of finches species with endemicity status as tip states.
Usage
finches_phylod
Format
finches_phylod
A phylo4d object (from the phylobase package) with
16 tips and
15 internal
nodes.
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.
Accessor functions for the data (slots) in objects of the
Island_colonist class
Description
Accessor functions for the data (slots) in objects of the
Island_colonist class
Usage
get_clade_name(x)
## S4 method for signature 'Island_colonist'
get_clade_name(x)
set_clade_name(x) <- value
## S4 replacement method for signature 'Island_colonist'
set_clade_name(x) <- value
get_status(x)
## S4 method for signature 'Island_colonist'
get_status(x)
set_status(x) <- value
## S4 replacement method for signature 'Island_colonist'
set_status(x) <- value
get_missing_species(x)
## S4 method for signature 'Island_colonist'
get_missing_species(x)
set_missing_species(x) <- value
## S4 replacement method for signature 'Island_colonist'
set_missing_species(x) <- value
get_col_time(x)
## S4 method for signature 'Island_colonist'
get_col_time(x)
set_col_time(x) <- value
## S4 replacement method for signature 'Island_colonist'
set_col_time(x) <- value
get_col_max_age(x)
## S4 method for signature 'Island_colonist'
get_col_max_age(x)
set_col_max_age(x) <- value
## S4 replacement method for signature 'Island_colonist'
set_col_max_age(x) <- value
get_branching_times(x)
## S4 method for signature 'Island_colonist'
get_branching_times(x)
set_branching_times(x) <- value
## S4 replacement method for signature 'Island_colonist'
set_branching_times(x) <- value
get_min_age(x)
## S4 method for signature 'Island_colonist'
get_min_age(x)
set_min_age(x) <- value
## S4 replacement method for signature 'Island_colonist'
set_min_age(x) <- value
get_species(x)
## S4 method for signature 'Island_colonist'
get_species(x)
set_species(x) <- value
## S4 replacement method for signature 'Island_colonist'
set_species(x) <- value
get_clade_type(x)
## S4 method for signature 'Island_colonist'
get_clade_type(x)
set_clade_type(x) <- value
## S4 replacement method for signature 'Island_colonist'
set_clade_type(x) <- value
Arguments
x |
An object whose class is determined by the signature. |
value |
A value which can take several forms to be assigned to an object of a class. |
Value
Getter functions (get_) return a variable from the Island_colonist class, the setter functions (set_) return the modified Island_colonist class.
Author(s)
Joshua W. Lambert
Examples
colonist <- island_colonist()
get_clade_name(colonist)
set_clade_name(colonist) <- "abc"
get_status(colonist)
set_status(colonist) <- "abc"
get_missing_species(colonist)
set_missing_species(colonist) <- 0
get_col_time(colonist)
set_col_time(colonist) <- 1
get_col_max_age(colonist)
set_col_max_age(colonist) <- FALSE
get_branching_times(colonist)
set_branching_times(colonist) <- 0
get_min_age(colonist)
set_min_age(colonist) <- 0.1
get_species(colonist)
set_species(colonist) <- "abc_a"
get_clade_type(colonist)
set_clade_type(colonist) <- 1
Checks whether the focal species (given by its tip lable in species_label argument) is part of an endemic clade on the island and a vector of the endemic species, either a single species for a singleton or multiple species in an endemic clade.
Description
Checks whether the focal species (given by its tip lable in species_label argument) is part of an endemic clade on the island and a vector of the endemic species, either a single species for a singleton or multiple species in an endemic clade.
Usage
get_endemic_species(phylod, species_label)
Arguments
phylod |
A |
species_label |
The tip label of the species of interest. |
Value
Named numeric vector
Accessor functions for the data (slots) in objects of the
Island_tbl class
Description
Accessor functions for the data (slots) in objects of the
Island_tbl class
Usage
get_island_tbl(x)
## S4 method for signature 'Island_tbl'
get_island_tbl(x)
set_island_tbl(x) <- value
## S4 replacement method for signature 'Island_tbl'
set_island_tbl(x) <- value
get_extracted_species(x)
## S4 method for signature 'Island_tbl'
get_extracted_species(x)
set_extracted_species(x) <- value
## S4 replacement method for signature 'Island_tbl'
set_extracted_species(x) <- value
get_num_phylo_used(x)
## S4 method for signature 'Island_tbl'
get_num_phylo_used(x)
set_num_phylo_used(x) <- value
## S4 replacement method for signature 'Island_tbl'
set_num_phylo_used(x) <- value
Arguments
x |
An object whose class is determined by the signature. |
value |
A value which can take several forms to be assigned to an object of a class. |
Value
Getter function (get_) returns a data frame, the setter function (set_) returns the modified Island_tbl class.
Author(s)
Joshua W. Lambert
Examples
island_tbl <- island_tbl()
get_island_tbl(island_tbl)
set_island_tbl(island_tbl) <- data.frame(
clade_name = "birds",
status = "endemic",
missing_species = 0,
branching_times = I(list(c(1.0, 0.5)))
)
Extract tip states from a phylod object
Description
Extract tip states from a phylod object
Usage
get_sse_tip_states(phylod, sse_model = "musse")
Arguments
phylod |
A |
sse_model |
either "musse" (default) or "geosse". MuSSE expects state values 1, 2, 3, which here we encode as "not_present", "endemic", "nonendemic", respectively. GeoSSE expects trait values 0, 1, 2, with 0 the widespread state (here, "nonendemic"), and 1 and 2 are "not_present" and "endemic", respectively. |
Value
an integer vector of tip states, as expected by SSE models
Checks whether species has undergone back-colonisation from
Description
Checks whether species has undergone back-colonisation from
Usage
is_back_colonisation(phylod, node_label)
Arguments
phylod |
A |
node_label |
A numeric label for a node within a phylogeny. |
Value
A character string or FALSE. Character string is in the format ancestral_node -> focal_node, where the ancestral node is not on mainland but the focal node is.
Examples
set.seed(
3,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
phylo <- ape::rcoal(5)
phylo$tip.label <- c("bird_a", "bird_b", "bird_c", "bird_d", "bird_e")
phylo <- phylobase::phylo4(phylo)
endemicity_status <- c("endemic", "endemic", "not_present",
"endemic", "not_present")
phylod <- phylobase::phylo4d(phylo, as.data.frame(endemicity_status))
phylod <- add_asr_node_states(phylod = phylod, asr_method = "parsimony")
# aritificially modify data to produce back-colonisation
phylobase::tdata(phylod)$island_status[8] <- "endemic"
# Example without back colonisation
is_back_colonisation(phylod = phylod, node_label = 2)
# Example with back colonisation
is_back_colonisation(phylod = phylod, node_label = 3)
Determines if colonist has already been stored in Island_tbl class. This is
used to stop endemic clades from being stored multiple times in the island
table by checking if the endemicity status and branching times are identical.
Description
Determines if colonist has already been stored in Island_tbl class. This is
used to stop endemic clades from being stored multiple times in the island
table by checking if the endemicity status and branching times are identical.
Usage
is_duplicate_colonist(island_colonist, island_tbl)
Arguments
island_colonist |
An instance of the |
island_tbl |
An instance of the |
Value
Boolean
Examples
# with empty island_tbl
island_colonist <- island_colonist(
clade_name = "bird",
status = "endemic",
missing_species = 0,
col_time = 1.0,
col_max_age = FALSE,
branching_times = 0.5,
species = "bird_a",
clade_type = 1
)
island_tbl <- island_tbl()
is_duplicate_colonist(
island_colonist = island_colonist,
island_tbl = island_tbl
)
# with non-empty island_tbl
island_colonist <- island_colonist(
clade_name = "bird",
status = "endemic",
missing_species = 0,
col_time = 1.0,
col_max_age = FALSE,
branching_times = 0.5,
species = c("bird_a", "bird_b"),
clade_type = 1
)
island_tbl <- island_tbl()
island_tbl <- bind_colonist_to_tbl(
island_colonist = island_colonist,
island_tbl = island_tbl
)
island_colonist <- island_colonist(
clade_name = "bird",
status = "endemic",
missing_species = 0,
col_time = 1.0,
col_max_age = FALSE,
branching_times = 0.5,
species = c("bird_a", "bird_b"),
clade_type = 1
)
is_duplicate_colonist(
island_colonist = island_colonist,
island_tbl = island_tbl
)
Checks whether two Island_tbl objects are identical. If they are different
comparisons are made to report which components of the Island_tbls are
different.
Description
Checks whether two Island_tbl objects are identical. If they are different
comparisons are made to report which components of the Island_tbls are
different.
Usage
is_identical_island_tbl(island_tbl_1, island_tbl_2)
Arguments
island_tbl_1 |
An object of |
island_tbl_2 |
An object of |
Value
Either TRUE or a character string with the differences
Examples
multi_island_tbl <- multi_extract_island_species(
multi_phylod = list(
create_test_phylod(test_scenario = 1),
create_test_phylod(test_scenario = 1)),
extraction_method = "min")
is_identical_island_tbl(multi_island_tbl[[1]], multi_island_tbl[[2]])
Checks if a species is represented in the tree has multiple tips and those tips form a monophyletic group (i.e. one species with multiple samples) all labeled as with the same endemicity status
Description
Checks if a species is represented in the tree has multiple tips and those tips form a monophyletic group (i.e. one species with multiple samples) all labeled as with the same endemicity status
Usage
is_multi_tip_species(phylod, species_label)
Arguments
phylod |
A |
species_label |
The tip label of the species of interest. |
Details
is_multi_tip_species() only returns TRUE if all tips for each sample
of the species (i.e. conspecific tips) are labelled the same. It is
possible that a phylogeny has multiple tips for the same species but only
the island samples are labelled as "endemic" or "nonendemic" as the
other tips are from samples from the mainland, and are labelled
"not_present", see
vignette("Multi_tip_extraction", package = "DAISIEprep").
Value
Boolean
Constructor for Island_colonist
Description
Constructor for Island_colonist
Usage
island_colonist(
clade_name = NA_character_,
status = NA_character_,
missing_species = NA_real_,
col_time = NA_real_,
col_max_age = NA,
branching_times = NA_real_,
min_age = NA_real_,
species = NA_character_,
clade_type = NA_integer_
)
Arguments
clade_name |
Character name of the colonising clade. |
status |
Character endemicity status of the colonising clade. Either
|
missing_species |
Numeric number of missing species from the phylogeny
that belong to the colonising clade. For a clade with missing species this
is |
col_time |
Numeric with the colonisation time of the island colonist |
col_max_age |
Boolean determining whether colonisation time should be considered a precise time of colonisation or a maximum time of colonisation |
branching_times |
Numeric vector of one or more elements which are the branching times on the island. |
min_age |
Numeric minimum age (time before the present) that the species must have colonised the island by. This is known when there is a branching on the island, either in species or subspecies. |
species |
Character vector of one or more elements containing the name of the species included in the colonising clade. |
clade_type |
Numeric determining which type of clade the island colonist
is, this determines which macroevolutionary regime (parameter set) the island
colonist is in. After formatting the |
Value
Object of Island_colonist class.
Examples
# Without initial values
colonist <- island_colonist()
# With initial values
colonist <- island_colonist(
clade_name = "bird",
status = "endemic",
missing_species = 0,
col_time = 0.5,
col_max_age = FALSE,
branching_times = 0.5,
min_age = NA_real_,
species = "bird_a",
clade_type = 1
)
Constructor function for Island_tbl class
Description
Constructor function for Island_tbl class
Usage
island_tbl()
Value
An Island_tbl object.
A phylogenetic tree of mimus species with endemicity status as tip states.
Description
A phylogenetic tree of mimus species with endemicity status as tip states.
Usage
mimus_phylod
Format
mimus_phylod
A phylo4d object (from the phylobase package) with
29 tips and
28 internal
nodes.
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.
Extracts the colonisation, diversification, and endemicty data from multiple
phylod (phylo4d class from phylobase) objects (composed of phylogenetic
and endemicity data) and stores each in an Island_tbl object which are
stored in a Multi_island_tbl object.
Description
Extracts the colonisation, diversification, and endemicty data from multiple
phylod (phylo4d class from phylobase) objects (composed of phylogenetic
and endemicity data) and stores each in an Island_tbl object which are
stored in a Multi_island_tbl object.
Usage
multi_extract_island_species(
multi_phylod,
extraction_method,
island_tbl = NULL,
include_not_present = FALSE,
verbose = FALSE,
unique_clade_name = TRUE
)
Arguments
multi_phylod |
A list of phylod objects. |
extraction_method |
A character string specifying whether the
colonisation time extracted is the minimum time ( |
island_tbl |
An instance of the |
include_not_present |
A boolean determining whether species not present on the island should be included in island colonist when embedded within an island clade. Default is FALSE. |
verbose |
Boolean. States if intermediate results should be printed to console. Defaults to FALSE |
unique_clade_name |
Boolean determining whether a unique species identifier is used as the clade name in the Island_tbl object or a genus name which may not be unique if that genus has several independent island colonisations |
Value
An object of Multi_island_tbl class
Examples
multi_phylod <- list()
multi_phylod[[1]] <- create_test_phylod(test_scenario = 1)
multi_phylod[[2]] <- create_test_phylod(test_scenario = 2)
multi_island_tbl <- multi_extract_island_species(
multi_phylod = multi_phylod,
extraction_method = "min",
island_tbl = NULL,
include_not_present = FALSE
)
Constructor function for Multi_island_tbl class
Description
Constructor function for Multi_island_tbl class
Usage
multi_island_tbl()
Value
A Multi_island_tbl object.
A phylogenetic tree of myiarchus species with endemicity status as tip states.
Description
A phylogenetic tree of myiarchus species with endemicity status as tip states.
Usage
myiarchus_phylod
Format
myiarchus_phylod
A phylo4d object (from the phylobase package) with
13 tips and
12 internal
nodes.
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.
A phylogenetic tree of plant species.
Description
This is a mock dataset for demonstrating the DAISIEprep package.
Usage
plant_phylo
Format
plant_phylo
A phylo object (from the ape package) with 10 tips and 9 internal
nodes. Each tip label is formatted "Plant_*" with the letters a, b,
etc. used as species names.
Plots a dot plot (cleveland dot plot when include_crown_age = TRUE) of the stem and potentially crown ages of a community of island colonists.
Description
Plots a dot plot (cleveland dot plot when include_crown_age = TRUE) of the stem and potentially crown ages of a community of island colonists.
Usage
plot_colonisation(island_tbl, island_age, include_crown_age = TRUE)
Arguments
island_tbl |
An instance of the |
island_age |
Age of the island in appropriate units. |
include_crown_age |
A boolean determining whether the crown age gets plotted with the stem age. |
Value
ggplot object
Examples
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
phylo <- ape::rcoal(10)
phylo$tip.label <- c("bird_a", "bird_b", "bird_c", "bird_d", "bird_e",
"bird_f", "bird_g", "bird_h", "bird_i", "bird_j")
phylo <- phylobase::phylo4(phylo)
endemicity_status <- sample(
c("not_present", "endemic", "nonendemic"),
size = length(phylobase::tipLabels(phylo)),
replace = TRUE,
prob = c(0.6, 0.2, 0.2)
)
phylod <- phylobase::phylo4d(phylo, as.data.frame(endemicity_status))
island_tbl <- extract_island_species(phylod, extraction_method = "min")
plot_colonisation(island_tbl, island_age = 2)
Plots performance results for a grouping variable (prob_on_island or prob_endemic).
Description
Plots performance results for a grouping variable (prob_on_island or prob_endemic).
Usage
plot_performance(performance_data, group_by)
Arguments
performance_data |
Tibble of collated performance results |
group_by |
A variable to partition by for plotting. Uses data masking so variable does not need to be quoted. |
Value
ggplot2 object
Plots the phylogenetic tree and its associated tip and/or node data
Description
Plots the phylogenetic tree and its associated tip and/or node data
Usage
plot_phylod(phylod, node_pies = FALSE)
Arguments
phylod |
A |
node_pies |
Boolean determining if pie charts of the probabilities of a species being present on the island. If TRUE the correct data is required in the phylod object. |
Value
ggplot object
Examples
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
phylo <- ape::rcoal(10)
phylo$tip.label <- c("bird_a", "bird_b", "bird_c", "bird_d", "bird_e",
"bird_f", "bird_g", "bird_h", "bird_i", "bird_j")
phylo <- phylobase::phylo4(phylo)
endemicity_status <- sample(
c("not_present", "endemic", "nonendemic"),
size = length(phylobase::tipLabels(phylo)),
replace = TRUE,
prob = c(0.6, 0.2, 0.2)
)
phylod <- phylobase::phylo4d(phylo, as.data.frame(endemicity_status))
plot_phylod(phylod)
Plots
Description
Plots
Usage
plot_sensitivity(sensitivity_data, pairwise_diffs = FALSE)
Value
ggplot2 object
A phylogenetic tree of progne species with endemicity status as tip states.
Description
A phylogenetic tree of progne species with endemicity status as tip states.
Usage
progne_phylod
Format
progne_phylod
A phylo4d object (from the phylobase package) with
19 tips and
18 internal
nodes.
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.
A phylogenetic tree of pyrocephalus species with endemicity status as tip states.
Description
A phylogenetic tree of pyrocephalus species with endemicity status as tip states.
Usage
pyrocephalus_phylod
Format
pyrocephalus_phylod
A phylo4d object (from the phylobase package) with
66 tips and
65 internal
nodes.
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.
Reads in performance analysis results from inst/performance_data and formats the data ready for plotting
Description
Reads in performance analysis results from inst/performance_data and formats the data ready for plotting
Usage
read_performance()
Value
List of two data frames
Reads in the results from the sensitivity analysis saved in the inst/sensitivity_data folder
Description
Reads in the results from the sensitivity analysis saved in the inst/sensitivity_data folder
Usage
read_sensitivity()
Value
List of of lists with parameter estimates for the mammal DNA-only phylogeny, mammal complete phylogeny and the parameter set used
Remove any duplicated species from the island_tbl after "asr" extraction
Description
Removes any duplicates species from the island_tbl by choosing to either
have duplicated species be in smaller, more recently colonised clade(s) and
removing them from the larger, older clade(s)
(nested_asr_species = "split"), or removing the smaller, more recently
colonised clade(s) in favour of leaving them in the larger, older clade(s)
(nested_asr_species = "group").
Usage
rm_duplicate_island_species(
island_tbl,
phylod,
nested_asr_species,
include_not_present
)
Arguments
island_tbl |
An instance of the |
phylod |
A |
nested_asr_species |
A |
include_not_present |
A boolean determining whether species not present on the island should be included in island colonist when embedded within an island clade. Default is FALSE. |
Value
An object of Island_tbl class
Removes an island colonist from an Island_tbl object
Description
Removes an island colonist from an Island_tbl object
Usage
rm_island_colonist(island_tbl, clade_name)
Arguments
island_tbl |
An instance of the |
clade_name |
Character name of the colonising clade. |
Value
Object of Island_tbl class
Examples
phylod <- create_test_phylod(test_scenario = 1)
island_tbl <- extract_island_species(
phylod = phylod,
extraction_method = "min"
)
island_tbl <- rm_island_colonist(
island_tbl = island_tbl,
clade_name = "bird_b"
)
Loops through the genera that have missing species and removes the ones that
are found in the missing genus list which have phylogenetic data. This is
useful when wanting to know which missing species have not been assigned to
the island_tbl using add_multi_missing_species().
Description
Loops through the genera that have missing species and removes the ones that
are found in the missing genus list which have phylogenetic data. This is
useful when wanting to know which missing species have not been assigned to
the island_tbl using add_multi_missing_species().
Usage
rm_multi_missing_species(missing_species, missing_genus, island_tbl)
Arguments
missing_species |
Numeric number of missing species from the phylogeny
that belong to the colonising clade. For a clade with missing species this
is |
missing_genus |
A list of character vectors containing the genera in each island clade |
island_tbl |
An instance of the |
Value
Data frame
Examples
phylod <- create_test_phylod(test_scenario = 6)
island_tbl <- suppressWarnings(extract_island_species(
phylod = phylod,
extraction_method = "asr",
))
phylod <- create_test_phylod(test_scenario = 7)
island_tbl <- suppressWarnings(extract_island_species(
phylod = phylod,
extraction_method = "asr",
island_tbl = island_tbl
))
missing_species <- data.frame(
clade_name = "bird",
missing_species = 1,
endemicity_status = "endemic"
)
missing_genus <- list("bird", character(0))
rm_missing_species <- rm_multi_missing_species(
missing_species = missing_species,
missing_genus = missing_genus,
island_tbl = island_tbl
)
Rounds numbers using the round up method, rather than the round to the
nearest even number method used by the base function round.
Description
Rounds numbers using the round up method, rather than the round to the
nearest even number method used by the base function round.
Usage
round_up(n, digits = 0)
Arguments
n |
A numeric to be rounded. |
digits |
A numeric specifying which decimal places to round to |
Value
Numeric
Select endemicity status from ancestral states probabilities
Description
Selects a state for each node (both internal nodes, i.e. ancestral states, and tips, if included) from a table of probabilities.
Usage
select_endemicity_status(asr_df, method = "max")
Arguments
asr_df |
a data frame containing at least these three columns: not_present_prob | endemic_prob | nonendemic_prob (in any order). Each column should contain the estimated probability of the state for each node (rows) and these columns should sum to 1. |
method |
"max" or "random". "max" will select the state with highest probability (selecting last state in event of a tie), while "random" will sample the states randomly with the probabilities as weight for each state. |
Value
a character vector, with the selected endemicity status for each node.
Runs a sensitivity analysis to test the influences of changing the data on the parameter estimates for the DAISIE maximum likelihood inference model
Description
Runs a sensitivity analysis to test the influences of changing the data on the parameter estimates for the DAISIE maximum likelihood inference model
Usage
sensitivity(
phylo,
island_species,
extraction_method,
asr_method,
tie_preference,
island_age,
num_mainland_species,
verbose = FALSE
)
Arguments
phylo |
A phylogeny either as a |
island_species |
Data frame with two columns. The first is a character string of the tip_labels with the tip names of the species on the island. The second column a character string of the endemicity status of the species, either endemic or nonendemic. |
extraction_method |
A character string specifying whether the
colonisation time extracted is the minimum time ( |
asr_method |
A character string, either "parsimony" or "mk" determines
whether a maximum parsimony or continuous-time markov model reconstructs the
ancestral states at each node. See documentation in
|
tie_preference |
Character string, either "island" or "mainland" to
choose the most probable state at each node using the |
island_age |
Age of the island in appropriate units. |
num_mainland_species |
The size of the mainland pool, i.e. the number of species that can potentially colonise the island. |
verbose |
Boolean. States if intermediate results should be printed to console. Defaults to FALSE |
Value
Data frame of parameter estimates and the parameter setting used when inferring them
A phylogenetic tree of setophaga species with endemicity status as tip states.
Description
A phylogenetic tree of setophaga species with endemicity status as tip states.
Usage
setophaga_phylod
Format
setophaga_phylod
A phylo4d object (from the phylobase package) with
19 tips and
18 internal
nodes.
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.
Convert SSE states back to endemicity status
Description
Convert SSE states back to endemicity status
Usage
sse_states_to_endemicity(states, sse_model = "musse")
Arguments
states |
integer vector of tip states, as expected by SSE models |
sse_model |
either "musse" (default) or "geosse". MuSSE expects state values 1, 2, 3, which here we encode as "not_present", "endemic", "nonendemic", respectively. GeoSSE expects trait values 0, 1, 2, with 0 the widespread state (here, "nonendemic"), and 1 and 2 are "not_present" and "endemic", respectively. |
Value
character vector with values "endemic", "nonendemic" and/or "not_present"
Takes a string of the various ways the island species status can be and returns a uniform all lower-case string of the same status to make handling statuses easier in other function
Description
Takes a string of the various ways the island species status can be and returns a uniform all lower-case string of the same status to make handling statuses easier in other function
Usage
translate_status(status)
Arguments
status |
Character endemicity status of the colonising clade. Either
|
Value
Character string
Examples
translate_status("Endemic")
Determines the unique endemic genera that are included in the island clades contained within the island_tbl object and stores them as a list with each genus only occuring once in the first island clade it appears in
Description
Determines the unique endemic genera that are included in the island clades contained within the island_tbl object and stores them as a list with each genus only occuring once in the first island clade it appears in
Usage
unique_island_genera(island_tbl)
Arguments
island_tbl |
An instance of the |
Value
list of character vectors
Examples
phylod <- create_test_phylod(test_scenario = 6)
island_tbl <- suppressWarnings(extract_island_species(
phylod = phylod,
extraction_method = "asr",
))
phylod <- create_test_phylod(test_scenario = 7)
island_tbl <- suppressWarnings(extract_island_species(
phylod = phylod,
extraction_method = "asr",
island_tbl = island_tbl
))
unique_genera <- unique_island_genera(island_tbl = island_tbl)
Write input files for BioGeoBEARS
Description
Write input files for a BioGeoBEARS analysis, i.e. a phlyogenetic tree in Newick format and occurrence data in PHYLIP format.
Usage
write_biogeobears_input(phylod, path_to_phylo, path_to_biogeo)
Arguments
phylod |
A |
path_to_phylo |
string specifying the path and name to write the phylogeny file to. |
path_to_biogeo |
string specifying the path and name to write the biogeography file to. |
Value
Nothing, called for side-effects
Write tree input file for BioGeoBEARS
Description
Write a text file containing a phylogenetic tree in the Newick format expected by BioGeoBEARS
Usage
write_newick_file(phylod, path_to_phylo)
Arguments
phylod |
A |
path_to_phylo |
string specifying the path and name to write the file to. |
Value
Nothing, called for side-effects.
Write biogeography input file for BioGeoBEARS
Description
Write a text file containing occurrence data for all tips in the PHYLIP format expected by BioGeoBEARS
Usage
write_phylip_biogeo_file(phylod, path_to_biogeo)
Arguments
phylod |
A |
path_to_biogeo |
string specifying the path and name to write the file to. |
Value
Nothing, called for side-effects.