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DESCRIPTION
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Package: DAISIEprep
Type: Package
Title: Extracts Phylogenetic Island Community Data from Phylogenetic Trees
Version: 1.0.0
Authors@R: c(
person(given = "Joshua W.",
family = "Lambert",
email = "[email protected]",
role = c("aut", "cre"),
comment = c(ORCID = "0000-0001-5218-3046")),
person(given = "Luis",
family = "Valente",
email = "[email protected]",
role = c("aut"),
comment = c(ORCID = "0000-0003-4247-8785")),
person(given = "Pedro",
family = "Santos Neves",
role = c("aut"),
email = "[email protected]",
comment = c(ORCID = "0000-0003-2561-4677")),
person(given = "Lizzie",
family = "Roeble",
email = "[email protected]",
role = c("aut"),
comment = c(ORCID = "0000-0003-3664-4222")),
person(given = "Theo",
family = "Pannetier",
email = "[email protected]",
role = c("aut"),
comment = c(ORCID = "0000-0002-8424-3573"))
)
Maintainer: Joshua W. Lambert <[email protected]>
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
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
Depends: R (>= 4.0)
biocViews:
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'