Package 'datelife'

Get the lineage of a set of taxa. .get_ott_lineage uses rotl::taxonomy_taxon_info() with include_lineage = TRUE.

Description

Get the lineage of a set of taxa. .get_ott_lineage uses rotl::taxonomy_taxon_info() with include_lineage = TRUE.

Usage

.get_ott_lineage(input_ott_match)

Arguments

Value

A taxonomy_taxon_info object

Description

A multiPhylo object with trees resulting from a datelife search of some birds and cats species

Usage

birds_and_cats

Format

A multiPhylo object

Details

Generated with: taxa <- c("Rhea americana", "Pterocnemia pennata", "Struthio camelus", "Gallus", "Felis") birds_and_cats <- datelife_search(input = taxa, summary_format = "phylo_all", get_spp_from_taxon = TRUE) usethis::use_data(birds_and_cats)

Description

This function implements theorem 1.1 of Ané et al. (2009) doi:10.1007/s00026-009-0017-x to find a grove for a given group of chronograms.

Usage

build_grove_list(datelife_result, n = 2)

Arguments

Value

A list of vectors; each list element is a grove.

Description

This function implements theorem 1.1 of Ané et al. (2009) doi:10.1007/s00026-009-0017-x to find a grove for a given group of chronograms.

Usage

build_grove_matrix(datelife_result, n = 2)

Arguments

Value

A matrix. Each cell shows whether n-overlap exists between a pair of inputs.

References

Ané, C., Eulenstein, O., Piaggio-Talice, R., & Sanderson, M. J. (2009). "Groves of phylogenetic trees". Annals of Combinatorics, 13(2), 139-167, doi:10.1007/s00026-009-0017-x.

Description

check_conflicting_calibrations checks if calibrations are younger or older relative to descendants and ancestors, respectively.

Usage

check_conflicting_calibrations(phy, calibration_distribution)

Arguments

Details

It removes conflicting calibrations if needed, but BLADJ works as long as it has an age for the root.

Description

⁠check_ott_input is currently used in functions ⁠get_ott_clade(), get_ott_children(), and get_otol_synthetic_tree().

Usage

check_ott_input(input = NULL, ott_ids = NULL, ...)

Arguments

Details

By default, it uses the ott_id argument if it is not NULL.

Value

A named numeric vector of valid Open Tree Taxonomy (OTT) ids.

Choose an ultrametric phylo object from cluster_patristicmatrix() obtained with a particular clustering method, or the next best tree. If there are no ultrametric trees, it does not force them to be ultrametric.

Description

Choose an ultrametric phylo object from cluster_patristicmatrix() obtained with a particular clustering method, or the next best tree. If there are no ultrametric trees, it does not force them to be ultrametric.

Usage

choose_cluster(phycluster, clustering_method = "nj")

Arguments

Value

A phylo object or NA.

Description

This uses the taxize package's wrapper of the Global Names Resolver to get taxonomic paths for the vector of taxa you pass in. Sources is a vector of source labels in order (though it works best if everything uses the same taxonomy, so we recommend doing just one source). You can see options by doing taxize::gnr_datasources(). Our default is Catalogue of Life

Usage

classification_paths_from_taxonomy(taxa, sources = "Catalogue of Life")

Arguments

Details

Taxonomies supported by taxize::gnr_datasources()

1. Catalogue of Life

2. Wikispecies

3. ITIS

4. NCBI

5. Index Fungorum

6. GRIN Taxonomy for Plants

7. Union 4

8. The Interim Register of Marine and Nonmarine Genera

9. World Register of Marine Species

10. Freebase

11. GBIF Backbone Taxonomy

12. EOL

13. Passiflora vernacular names

14. Inventory of Fish Species in the Wami River Basin

15. Pheasant Diversity and Conservation in the Mt. Gaoligonshan Region

16. Finding Species

17. Birds of Lindi Forests Plantation

18. Nemertea

19. Kihansi Gorge Amphibian Species Checklist

20. Mushroom Observer

21. TaxonConcept

22. Amphibia and Reptilia of Yunnan

23. Common names of Chilean Plants

24. Invasive Species of Belgium

25. ZooKeys

26. COA Wildlife Conservation List

27. AskNature

28. China: Yunnan, Southern Gaoligongshan, Rapid Biological Inventories Report No. 04

29. Native Orchids from Gaoligongshan Mountains, China

30. Illinois Wildflowers

31. Coleorrhyncha Species File

32. /home/dimus/files/dwca/zoological names.zip

33. Peces de la zona hidrogeográfica de la Amazonia, Colombia (Spreadsheet)

34. Eastern Mediterranean Syllidae

35. Gaoligong Shan Medicinal Plants Checklist

36. birds_of_tanzania

37. AmphibiaWeb

38. tanzania_plant_sepecimens

39. Papahanaumokuakea Marine National Monument

40. Taiwanese IUCN species list

41. BioPedia

42. AnAge

43. Embioptera Species File

44. Global Invasive Species Database

45. Sendoya S., Fernández F. AAT de hormigas (Hymenoptera: Formicidae) del Neotrópico 1.0 2004 (Spreadsheet)

46. Flora of Gaoligong Mountains

47. ARKive

48. True Fruit Flies (Diptera, Tephritidae) of the Afrotropical Region

49. 3i - Typhlocybinae Database

50. CATE Sphingidae

51. ZooBank

52. Diatoms

53. AntWeb

54. Endemic species in Taiwan

55. Dermaptera Species File

56. Mantodea Species File

57. Birds of the World: Recommended English Names

58. New Zealand Animalia

59. Blattodea Species File

60. Plecoptera Species File

61. /home/dimus/files/dwca/clemens.zip

62. Coreoidea Species File

63. Freshwater Animal Diversity Assessment - Normalized export

64. Catalogue of Vascular Plant Species of Central and Northeastern Brazil

65. Wikipedia in EOL

66. Database of Vascular Plants of Canada (VASCAN)

67. Phasmida Species File

68. OBIS

69. USDA NRCS PLANTS Database

70. Catalog of Fishes

71. Aphid Species File

72. The National Checklist of Taiwan

73. Psocodea Species File

74. FishBase

75. 3i - Typhlocybinae Database

76. Belgian Species List

77. EUNIS

78. CU*STAR

79. Orthoptera Species File

80. Bishop Museum

81. IUCN Red List of Threatened Species

82. BioLib.cz

83. Tropicos - Missouri Botanical Garden

84. nlbif

85. The International Plant Names Index

86. Index to Organism Names

87. uBio NameBank

88. Arctos

89. Checklist of Beetles (Coleoptera) of Canada and Alaska. Second Edition.

90. The Paleobiology Database

91. The Reptile Database

92. The Mammal Species of The World

93. BirdLife International

94. Checklist da Flora de Portugal (Continental, Açores e Madeira)

95. FishBase Cache

96. Silva

97. Open Tree of Life Reference Taxonomy

98. iNaturalist

99. The Interim Register of Marine and Nonmarine Genera

100. Gymno

Value

A list with resolved taxa (a tibble, from taxize::gnr_resolve) and a vector of taxa not resolved

Description

Clean up some issues with Open Tree of Life chronograms For now it 1) checks unmapped taxa and maps them with tnrs_match.phylo, 2) roots the chronogram if unrooted

Usage

clean_ott_chronogram(phy)

Arguments

Details

There is no limit to the number of names that can be queried and matched.

The output will preserve all elements from original input phylo object and will add

phy$mapped

A character vector indicating the state of mapping of phy$tip.labels:

original

Tnrs matching was not attempted. Original labeling is preserved.

ott

Matching was manually made by a curator in Open Tree of Life.

tnrs

Tnrs matching was attempted and successful with no approximate matching. Original label is replaced by the matched name.

approximated

Tnrs matching was attempted and successful but with approximate matching. Original labeling is preserved.

unmatched

Tnrs matching was attempted and unsuccessful. Original labeling is preserved.

phy$original.tip.label

A character vector preserving all original labels.

phy$ott_ids

A numeric vector with ott id numbers of matched tips. Unmatched and original tips will be NaN.

if tips are duplicated, tnrs will only be run once (avoiding increases in function running time) but the result will be applied to all duplicated tip labels

Value

An object of class data frame or phylo, with the added class match_names.

NULL

NULL

Identify, extract and clean taxonomic children names from a taxonomy_taxon_info() output.

Description

clean_taxon_info_children eliminates all taxa that will give problems when trying to retrieve an induced subtree from Open Tree of Life.

Usage

clean_taxon_info_children(
  taxon_info,
  invalid = c("barren", "extinct", "uncultured", "major_rank_conflict", "incertae_sedis",
    "unplaced", "conflict", "environmental", "not_otu", "hidden", "hybrid")
)

Arguments

Value

A list with valid children unique OTT names, OTT ids and taxonomic ranks.

Eliminates unmatched (NAs) and invalid taxa from a rotl::tnrs_match_names() or tnrs_match() output Useful to get ott ids to retrieve an induced synthetic Open Tree of Life. Needed because using include_suppressed = FALSE in rotl::tnrs_match_names() does not drop all invalid taxa.

Description

Eliminates unmatched (NAs) and invalid taxa from a rotl::tnrs_match_names() or tnrs_match() output Useful to get ott ids to retrieve an induced synthetic Open Tree of Life. Needed because using include_suppressed = FALSE in rotl::tnrs_match_names() does not drop all invalid taxa.

Usage

clean_tnrs(
  tnrs,
  invalid = c("barren", "extinct", "uncultured", "major_rank_conflict", "incertae",
    "unplaced", "conflict", "environmental", "not_otu"),
  remove_nonmatches = FALSE
)

Arguments

Details

Input can be any data frame or named list that relates taxa stored in an element named "unique" to a validity category stored in "flags".

Value

A data frame or named list (depending on the input) with valid taxa only.

Description

Cluster a patristic matrix into a tree with various methods.

Usage

cluster_patristicmatrix(patristic_matrix, variance_matrix = NULL)

Arguments

Details

If clustering method fails, NA is returned.

Value

A list of trees obtained with clustering methods detailed in patristic_matrix_to_phylo().

Description

Congruify and Check.

Usage

congruify_and_check(
  reference,
  target,
  taxonomy = NULL,
  tol = 0.01,
  option = 2,
  scale = "pathd8",
  attempt_fix = TRUE
)

Arguments

Description

congruify_and_mrca_multiPhylo congruifies a target tree against all source chronograms in a multiPhylo object, and gets nodes of target tree that correspond to the most recent common ancestor (mrca) of taxon pairs in the congruified calibrations. It calls congruify_and_mrca_phylo(), and phytools::findMRCA() to get mrca nodes.

Usage

congruify_and_mrca_multiPhylo(phy, source_chronograms)

Arguments

Value

a data.frame of node ages from source_chronograms and corresponding mrca nodes in target tree phy. attributes(return)$phy stores the congruified and mrca matched phylogeny.

Description

congruify_and_mrca congruifies a target tree against a single source chronogram, and gets nodes of target tree that correspond to the most recent common ancestor (mrca) of taxon pairs from the congruified calibrations. It uses phytools::findMRCA() to get mrca nodes.

Usage

congruify_and_mrca_phylo(phy, source_chronogram, reference)

Arguments

Value

a data.frame of node ages from source_chronograms and corresponding mrca nodes in target tree phy.

Description

Information on contributors, authors, study ids and clades from studies with chronograms in Open Tree of Life (Open Tree)

Usage

contributor_cache

Format

A list of five data sets.

author.pretty

A character vector with the author names from studies with chronograms that are in Open Tree.

author.results

A dataframe with three variables: authors, study ids and clades.

curator.pretty

A character vector with the names of curators of chronograms that are in Open Tree.

curator.results

A data.frame with three variables: curators, study ids and clades.

missed_doi

A character vector with study ids whose "doi" could not be retrieved.

Details

Generated with make_contributor_cache().

Source

http://opentreeoflife.org

Description

This will take a topology, look up information about fossils for taxa on the tree, and use paleotree::timePaleoPhy() to compute branch lengths.

Usage

date_with_pbdb(phy, recent = FALSE, assume_recent_if_missing = TRUE)

Arguments

Value

A dated tree.

Examples

## Not run:  # This is a flag for package development. You are welcome to run the example.

taxa <- c(
  "Archaeopteryx", "Pinus", "Quetzalcoatlus", "Homo sapiens",
  "Tyrannosaurus rex", "Megatheriidae", "Metasequoia", "Aedes", "Panthera"
)
phy <- tree_from_taxonomy(taxa, sources = "The Paleobiology Database")$phy

## End(Not run) # end dontrun

Description

Return the relevant authors for a set of studies.

Usage

datelife_authors_tabulate(results.index, cache = "opentree_chronograms")

Arguments

Value

A vector with counts of each author, with names equal to author names.

Description

Get a median summary chronogram from a datelifeResult object.

Usage

datelife_result_median(datelife_result, ...)

Arguments

Value

A phylo object.

Description

Compute a median matrix of a datelifeResult object.

Usage

datelife_result_median_matrix(datelife_result)

Arguments

Value

A patristic distance summary matrix from a datelifeResult object.

Get a numeric vector of MRCAs from a datelifeResult object. Used in summarize_datelife_result().

Description

Get a numeric vector of MRCAs from a datelifeResult object. Used in summarize_datelife_result().

Usage

datelife_result_MRCA(datelife_result, na_rm = TRUE)

Arguments

Value

A named numeric vector of MRCA ages for each element given in datelife_result.

Description

Go from a datelifeResult object to a Super Distance Matrix (SDM) using weighting = "flat"

Usage

datelife_result_sdm_matrix(datelife_result)

Arguments

Value

A numeric matrix.

Description

Reconstruct a supertree from a datelifeResult object using the Super Distance Matrix (SDM) method.

Usage

datelife_result_sdm_phylo(datelife_result, weighting = "flat", ...)

Arguments

Details

Chronograms given as input in datelife_result are summarized with the Super Distance Matrix (SDM) method described in Criscuolo et al. (2006) doi:10.1080/10635150600969872, implemented with the function ape::SDM(). The resulting summary SDM is clustered with summary_matrix_to_phylo().

Value

A supertree with branch lengths proportional to time, obtained by summarizing individual chronograms given as input in datelife_result. It is returned as an object of class datelifeSDM, which is a phylo object with an additional ⁠$data⁠ element storing the input chronograms as a datelifeResult object, and a ⁠$citation⁠ element containing citations of studies from input chronograms.

References

Criscuolo A, Berry V, Douzery EJ, Gascuel O. (2006) "SDM: a fast distance-based approach for (super) tree building in phylogenomics" doi:10.1080/10635150600969872.

Description

datelife_result_study_index is used in summarize_datelife_result().

Usage

datelife_result_study_index(datelife_result, cache = "opentree_chronograms")

Arguments

Value

A vector of indices of studies that have relevant information.

Description

Compute a variance matrix of a datelifeResult object.

Usage

datelife_result_variance_matrix(datelife_result)

Arguments

Value

A variance matrix from a datelifeResult object.

Description

datelife_search is the core DateLife function to find and get all openly available, peer-reviewed scientific information on time of lineage divergence for a set of input taxon names given as a character vector, a newick character string, a phylo or multiPhylo object or as a an already processed datelifeQuery object obtained with make_datelife_query().

Usage

datelife_search(
  input = c("Rhea americana", "Pterocnemia pennata", "Struthio camelus"),
  use_tnrs = FALSE,
  get_spp_from_taxon = FALSE,
  partial = TRUE,
  cache = "opentree_chronograms",
  summary_format = "phylo_all",
  na_rm = FALSE,
  summary_print = c("citations", "taxa"),
  taxon_summary = c("none", "summary", "matrix"),
  criterion = "taxa"
)

Arguments

Details

If only one taxon name is given as input, get_spp_from_taxon is always set to TRUE.

Value

The output is determined by the argument summary_format:

If summary_format = "citations"

The function returns a character vector of references.

If summary_format = "mrca"

The function returns a named numeric vector of most recent common ancestor (mrca) ages.

If summary_format = "newick_[all, sdm, or median]"

The function returns output chronograms as newick strings.

If summary_format = "phylo_[all, sdm, median, or biggest]"

The function returns output chronograms as phylo or multiPhylo objects.

If ⁠summary_format = "html" or "data_frame"⁠

The function returns a 4 column table with data on mrca ages, number of taxa, references, and output chronograms as newick strings.

Examples

## Not run: 

# For this example, we will set a temp working directory, but you can set
# your working directory as needed:
# we will use the tempdir() function to get a temporary directory:
tempwd <- tempdir()

# Obtain median ages from a set of source chronograms in newick format:
ages <- datelife_search(c(
  "Rhea americana", "Pterocnemia pennata", "Struthio camelus",
  "Mus musculus"
), summary_format = "newick_median")

# Save the tree in the temp working directory in newick format:
write(ages, file = file.path(tempwd, "some.bird.ages.txt"))

# Obtain median ages from a set of source chronograms in phylo format
# Will produce same tree as above but in "phylo" format:
ages.again <- datelife_search(c(
  "Rhea americana", "Pterocnemia pennata", "Struthio camelus",
  "Mus musculus"
), summary_format = "phylo_median")
plot(ages.again)
library(ape)
ape::axisPhylo()
mtext("Time (million years ago)", side = 1, line = 2, at = (max(get("last_plot.phylo",
  envir = .PlotPhyloEnv
)$xx) * 0.5))

# Save "phylo" object in newick format
write.tree(ages.again, file = file.path(tempwd, "some.bird.tree.again.txt"))

# Obtain MRCA ages and target chronograms from all source chronograms
# Generate an htm"l output readable in any web browser:
ages.html <- datelife_search(c(
  "Rhea americana", "Pterocnemia pennata", "Struthio camelus",
  "Mus musculus"
), summary_format = "html")
write(ages.html, file = file.path(tempwd, "some.bird.trees.html"))
system(paste("open", file.path(tempwd, "some.bird.trees.html")))

## End(Not run) # end dontrun

Description

datelife_use gets secondary calibrations available for any pair of given taxon names, mined from the opentree_chronograms object, congruifies them, and uses them to date a given tree topology with the algorithm defined in dating_method. If no tree topology is provided, it will attempt to get one for the given taxon names from Open Tree of Life synthetic tree, using make_bold_otol_tree().

Usage

datelife_use(input = NULL, each = FALSE, dating_method = "bladj", ...)

Arguments

Details

If input is a vector of taxon names, the function will attempt to reconstruct a BOLD tree with make_bold_otol_tree() to get a tree with branch lengths. If it fails, it will get an Open Tree of Life synthetic tree topology. The function then calls use_calibrations().

Value

A phylo or multiPhylo object with branch lengths proportional to time.

More

The output object stores the used calibrations and dating_method as attributes(output)$datelife_calibrations and attributes(output)$dating_method.

Description

datelife_use gets secondary calibrations available for any pair of given taxon names, mined from the opentree_chronograms object, congruifies them, and uses them to date a given tree topology with the algorithm defined in dating_method. If no tree topology is provided, it will attempt to get one for the given taxon names from Open Tree of Life synthetic tree, using make_bold_otol_tree().

Usage

datelife_use_datelifequery(
  datelife_query = NULL,
  dating_method = "bladj",
  each = FALSE
)

Arguments

Details

If phy has no branch lengths, dating_method is ignores, and the function applies secondary calibrations to date the tree with the BLADJ algorithm. See make_bladj_tree() and use_calibrations_bladj(). If phy has branch lengths, the function can use the PATHd8 algorithm. See use_calibrations_pathd8().

Value

A phylo or multiPhylo object with branch lengths proportional to time.

More

The output object stores the used calibrations and dating_method as attributes(output)$datelife_calibrations and attributes(output)$dating_method.

Description

This function extracts node ages for each taxon pair given in input$tip.labels. It applies the congruification method described in Eastman et al. (2013) doi:10.1111/2041-210X.12051, implemented with the function geiger::congruify.phylo(), to create a data.frame of taxon pair node ages that can be used as secondary calibrations.

Usage

extract_calibrations_dateliferesult(input = NULL, each = FALSE)

Arguments

Details

The function takes a datelifeResult object and calls summarize_datelife_result() with ⁠summary_format = "phylo_all". This goes from a ⁠datelifeResult⁠object to a⁠phyloormultiPhylo' object that is passed to extract_calibrations_phylo().

Value

An object of class calibrations, which is a data.frame (if each = FALSE) or a list of data.frames (if each = TRUE) of node ages for each pair of taxon names. You can access the input data from which the calibrations were extracted with attributes(output)$chronograms.

Description

This function extracts node ages for each taxon pair given in input$tip.labels. It applies the congruification method described in Eastman et al. (2013) doi:10.1111/2041-210X.12051, implemented with the function geiger::congruify.phylo(), to create a data.frame of taxon pair node ages that can be used as secondary calibrations.

Usage

extract_calibrations_phylo(input = NULL, each = FALSE)

Arguments

Value

An object of class calibrations, which is a data.frame (if each = FALSE) or a list of data.frames (if each = TRUE) of node ages for each pair of taxon names. You can access the input data from which the calibrations were extracted with attributes(output)$chronograms.

References

Eastman et al. (2013) "Congruification: support for time scaling large phylogenetic trees". Methods in Ecology and Evolution, 4(7), 688-691, doi:10.1111/2041-210X.12051.

Description

Extract numeric OTT ids from a character vector that combines taxon names and OTT ids.

Usage

extract_ott_ids(x, na.rm = TRUE)

## Default S3 method:
extract_ott_ids(x, na.rm = TRUE)

Arguments

Value

An object of class numeric containing OTT ids only.

NULL

Examples

## Not run:  # This is a flag for package development. You are welcome to run the example.

canis <- rotl::tnrs_match_names("canis")
canis_taxonomy <- rotl::taxonomy_subtree(canis$ott_id)
my_ott_ids <- extract_ott_ids(x = canis_taxonomy$tip_label)
# Get the problematic elements from input
canis_taxonomy$tip_label[attr(my_ott_ids, "na.action")]


## End(Not run) # end dontrun

Description

datelifeSummary of a datelifeResult object of all Felidae species.

Usage

felid_gdr_phylo_all

Format

A list of three elements, containing the summary of a datelifeResult object

phylo_all

List of subset chronograms in phylo format

taxon_distribution

A data frame with taxon presence across subset chronograms

absent_taxa

A dataframe with names of taxon not found in any chronogram

Details

Generated with: felid_spp <- make_datelife_query(input = "felidae", get_spp_from_taxon = TRUE) felid_gdr <- get_datelife_result(input = felid_spp, get_spp_from_taxon = TRUE) felid_gdr_phylo_all <- summarize_datelife_result(datelife_result = felid_gdr, taxon_summary = "summary", summary_format = "phylo_all", datelife_query = felid_spp) usethis::use_data(felid_gdr_phylo_all)

Source

http://opentreeoflife.org

Description

SDM tree of a datelifeResult object of all Felidae species.

Usage

felid_sdm

Format

A list of two elements, containing the summary of a datelifeResult object

phy

An ultrametric phylo object with the SDM tree.

data

A datelifeResult object with data used to construct phy

Details

Generated with: felid_spp <- make_datelife_query(input = "felidae", get_spp_from_taxon = TRUE) felid_gdr <- get_datelife_result(input = felid_spp, get_spp_from_taxon = TRUE) felid_sdm <- datelife_result_sdm_phylo(felid_gdr) usethis::use_data(felid_sdm)

Source

http://opentreeoflife.org

Description

Filter a datelifeResult object to find the largest grove.

Usage

filter_for_grove(datelife_result, criterion = "taxa", n = 2)

Arguments

Value

A datelifeResult object filtered to only include one grove of trees.

Force a non-ultrametric phylo object to be ultrametric with phytools::force.ultrametric().

Description

Force a non-ultrametric phylo object to be ultrametric with phytools::force.ultrametric().

Usage

force_ultrametric(phy)

Arguments

Value

A phylo object.

Description

get_all_calibrations performs a datelife_search() and gets divergence times (i.e., secondary calibrations) from a chronogram database for each taxon name pair given as input.

get_all_calibrations performs a datelife_search() and gets divergence times (i.e., secondary calibrations) from a chronogram database for each taxon name pair given as input.

Usage

get_all_calibrations(input = NULL, each = FALSE)

get_all_calibrations(input = NULL, each = FALSE)

Arguments

Value

An object of class calibrations, which is a data.frame (if each = FALSE) or a list of data.frames (if each = TRUE) of node ages for each pair of taxon names. You can access the input data from which the calibrations were extracted with attributes(output)$chronograms.

Description

This is less thorough than get_open_tree_species(), but much faster. It uses the fact that something has just two names (genus and species) to assume that something is a single species; if it has more than two names, it is assumed to be a subspecies so it goes up one level in the hierarchy. It will return the subspecies and the species.

Usage

get_all_descendant_species(taxon_name, ott_id)

Arguments

Value

A list of unique OTT names and OTT ids of species within the provided taxon.

Description

Get grove from a datelifeResult object that can be converted to phylo from a median summary matrix

Usage

get_best_grove(datelife_result, criterion = "taxa", n = 2)

Arguments

Value

A list of two elements:

best_grove

A datelifeResult object filtered to only include one grove of trees that can be summarized with median or sdm.

overlap

The degree of taxon names overlap among trees in the best grove.

Description

Get the tree with the most tips from a multiPhylo object: the biggest tree.

Usage

get_biggest_multiphylo(trees)

Arguments

Value

The largest tree from those given in trees, as a phylo object with an additional ⁠$citation⁠ element containing the reference of the original publication.

Description

get_bold_data uses taxon names from a tree topology, a character vector of names or a datelifeQuery object, to search for genetic markers in the Barcode of Life Database (BOLD).

Usage

get_bold_data(
  input = c("Rhea americana", "Struthio camelus", "Gallus gallus"),
  marker = "COI",
  ...
)

Arguments

Details

If input is a phylo object or a newick string, it is used as backbone topology. If input is a character vector of taxon names, an induced synthetic OpenTree subtree is used as backbone.

Value

A phylo object. If there are enough BOLD sequences available for the input taxon names, the function returns a tree with branch lengths proportional to relative substitution rate. If not enough BOLD sequences are available for the input taxon names, the function returns the topology given as input, or a synthetic Open Tree of Life for the taxon names given in input, obtained with get_otol_synthetic_tree().

Description

The function searches DateLife's local database of phylogenetic trees with branch lengths proportional to time (chronograms) with datelife_search(), and extracts available node ages for each pair of given taxon names with extract_calibrations_phylo().

Usage

get_calibrations_datelifequery(datelife_query = NULL, each = FALSE)

Arguments

Details

The function calls datelife_search() with summary_format = "phylo_all" to get all chronograms in the database containing at least two taxa in input, and generates a phylo or multiPhylo object object that will be passed to extract_calibrations_phylo().

Value

An object of class calibrations, which is a data.frame (if each = FALSE) or a list of data.frames (if each = TRUE) of node ages for each pair of taxon names. You can access the input data from which the calibrations were extracted with attributes(output)$chronograms.

Description

The function searches DateLife's local database of phylogenetic trees with branch lengths proportional to time (chronograms) with datelife_search(), and extracts available node ages for each pair of given taxon names with extract_calibrations_phylo().

Usage

get_calibrations_vector(input = NULL, each = FALSE)

Arguments

Details

The function calls datelife_search() with summary_format = "phylo_all" to get all chronograms in the database containing at least two taxa in input, and generates a phylo or multiPhylo object object that will be passed to extract_calibrations_phylo().

Value

An object of class calibrations, which is a data.frame (if each = FALSE) or a list of data.frames (if each = TRUE) of node ages for each pair of taxon names. You can access the input data from which the calibrations were extracted with attributes(output)$chronograms.

Description

Get a dated OpenTree induced synthetic subtree from a set of given taxon names, from blackrim's FePhyFoFum service.

Usage

get_dated_otol_induced_subtree(input = NULL, ott_ids = NULL, ...)

Arguments

Details

OpenTree dated tree from Stephen Smith's OpenTree scaling service at https://github.com/FePhyFoFum/gophy if you want to make an LTT plot of a dated OpenTree tree you'll need to get rid of singleton nodes with ape::collapse.singles() and also probably do phytools::force.ultrametric().

Value

A phylo object with edge length proportional to time in Myrs. It will return NA if any ott_id is invalid.

Description

get_datelife_result takes as input a vector of taxon names, a newick string, a phylo object, or adatelifeQuery object. It searches the chronogram database specified in cache for chronograms matching two or more given taxon names. For each matching chronogram, it extracts time of lineage divergence data and stores it as a patristic matrix. It then lists all resulting patristic matrices. Each list element is named with the study citation of the source chronogram.

Usage

get_datelife_result(
  input = NULL,
  partial = TRUE,
  cache = "opentree_chronograms",
  update_opentree_chronograms = FALSE,
  ...
)

Arguments

Value

A datelifeResult object – a named list of patristic matrices.

Description

Get a list of patristic matrices from a given datelifeQuery object

Usage

get_datelife_result_datelifequery(
  datelife_query = NULL,
  partial = TRUE,
  cache = "opentree_chronograms",
  update_opentree_chronograms = FALSE,
  ...
)

Arguments

Details

If there is just one taxon name in input$cleaned_names, the function will run make_datelife_query() setting get_spp_from_taxon = TRUE. The datelifeQuery used as input can be accessed with attributes(datelifeResult)$query.

Value

A datelifeResult object – a named list of patristic matrices.

Description

This uses the Paleobiology Database's API to gather information on the ages for all specimens of a taxon. It will also look for all descendants of the taxon. It fixes name misspellings if possible.

Usage

get_fossil_range(taxon, recent = FALSE, assume_recent_if_missing = TRUE)

Arguments

Value

a data.frame of max_ma and min_ma for the specimens

Get indices of good matrices to apply Super Distance Matrix (SDM) method with make_sdm().

Description

Get indices of good matrices to apply Super Distance Matrix (SDM) method with make_sdm().

Usage

get_goodmatrices(unpadded.matrices)

Arguments

Value

A numeric vector of good matrix indices in unpadded.matrices.

Description

Makes a block of node constraints and node calibrations for a MrBayes run file from a list of taxa and ages, or from a dated tree

Usage

get_mrbayes_node_constraints(
  constraint = NULL,
  taxa = NULL,
  missing_taxa = NULL,
  ncalibration = NULL,
  age_distribution = "fixed",
  root_calibration = FALSE,
  mrbayes_constraints_file = NULL,
  clockratepr = "prset clockratepr = fixed(1);"
)

Arguments

Value

A set of MrBayes constraints and/or calibration commands printed in console as character strings or as a text file specified in mrbayes_constraints_file.

Description

Get all chronograms from Open Tree of Life database using direct call from Open Tree API

Usage

get_opentree_chronograms(max_tree_count = "all")

get_otol_chronograms(max_tree_count = "all")

Arguments

Value

A list of 4 elements:

authors

A list of lists of author names of the original studies that published chronograms currently stored in the Open Tree of Life database.

curators

A list of lists of curator names that uploaded chronograms to the Open Tree of Life database.

studies

A list of study identifiers from original studies that published chronograms currently stored in the Open Tree of Life database.

trees

A multiPhylo object storing the chronograms from Open Tree of Life database.

update

A character vector indicating the time when the database object was last updated.

version

A character vector indicating the datelife package version when the object was last updated.

Description

Get all chronograms from Open Tree of Life database

Usage

get_opentree_chronograms_slow(max_tree_count = "all")

Arguments

Value

A list of 4 elements:

authors

A list of lists of author names of the original studies that published chronograms currently stored in the Open Tree of Life database.

curators

A list of lists of curator names that uploaded chronograms to the Open Tree of Life database.

studies

A list of study identifiers from original studies that published chronograms currently stored in the Open Tree of Life database.

trees

A multiPhylo object storing the chronograms from Open Tree of Life database.

update

A character vector indicating the time when the database object was last updated.

version

A character vector indicating the datelife package version when the object was last updated.

Description

Get all species belonging to a taxon from the Open Tree of Life Taxonomy (OTT)

Usage

get_opentree_species(taxon_name, ott_id, synth_tree_only = TRUE)

Arguments

Value

A list of unique OTT names and OTT ids of species within the provided taxon.

Description

Get an Open Tree of Life synthetic subtree of a set of given taxon names.

Usage

get_otol_synthetic_tree(
  input = NULL,
  ott_ids = NULL,
  otol_version = "v3",
  resolve = FALSE,
  ...
)

Arguments

Value

A phylo object

Use this instead of rotl::tol_subtree() when taxa are not in synthesis tree and you still need to get all species or an induced OpenTree subtree

Description

Use this instead of rotl::tol_subtree() when taxa are not in synthesis tree and you still need to get all species or an induced OpenTree subtree

Usage

get_ott_children(input = NULL, ott_ids = NULL, ott_rank = "species", ...)

Arguments

Value

A data.frame object.

Examples

# An example with the dog genus:

# It is currently not possible to get an OpenTree subtree of a taxon that is
#  missing from the OpenTree synthetic tree.
# The dog genus is not monophyletic in the OpenTree synthetic tree, so in
#  practice, it has no node to extract a subtree from.
tnrs <- tnrs_match("Canis")

## Not run:  # This is a flag for package development. You are welcome to run the example.
rotl::tol_subtree(tnrs$ott_id[1])
#> Error: HTTP failure: 400
#> [/v3/tree_of_life/subtree] Error: node_id was not found (broken taxon).


## End(Not run) # end dontrun

ids <- tnrs$ott_id[1]
names(ids) <- tnrs$unique_name
children <- get_ott_children(ott_ids = ids) # or
children <- get_ott_children(input = "Canis")
if (!is.na(children)) {
str(children)
ids <- children$Canis$ott_id
names(ids) <- rownames(children$Canis)
tree_children <- datelife::get_otol_synthetic_tree(ott_ids = ids)
plot(tree_children, cex = 0.3)
}

# An example with flowering plants:

## Not run:  # This is a flag for package development. You are welcome to run the example.

oo <- get_ott_children(input = "magnoliophyta", ott_rank = "order")
# Get the number of orders of flowering plants that we have
sum(oo$Magnoliophyta$rank == "order")


## End(Not run) # end dontrun

Description

Get the Open Tree of Life Taxonomic identifiers (OTT ids) and name of one or several given taxonomic ranks from one or more input taxa.

Usage

get_ott_clade(input = NULL, ott_ids = NULL, ott_rank = "family")

Arguments

Value

A list of named numeric vectors with OTT ids from input and all requested ranks.

Description

Get the Open Tree of Life Taxonomic identifier (OTT id) and name of all lineages from one or more input taxa.

Usage

get_ott_lineage(input = NULL, ott_ids = NULL)

Arguments

Value

A list of named numeric vectors of ott ids from input and all the clades it belongs to.

Examples

## Not run:  # This is a flag for package development. You are welcome to run the example.

taxa <- c("Homo", "Bacillus anthracis", "Apis", "Salvia")
lin <- get_ott_lineage(taxa)
lin

# Look up an unknown OTT id:
get_ott_lineage(ott_id = 454749)


## End(Not run) # end dontrun

Description

get_subset_array_dispatch is used inside get_datelife_result()

Usage

get_subset_array_dispatch(
  study_element,
  taxa,
  phy = NULL,
  phy4 = NULL,
  dating_method = "PATHd8"
)

Arguments

Value

A patristic matrix with ages for the target taxa.

Description

Get a taxon summary of a datelifeResult object.

Usage

get_taxon_summary(datelife_result = NULL, datelife_query = NULL)

Arguments

Value

A datelifeTaxonSummary object, which is a list of 4 elements:

$matrix

Data as a presence/absence matrix of taxon names across chronograms.

$summary

A data.frame with taxon names as row.names() and two columns, one with the number of chronograms that contain a taxon name and the other one with the total number of chronograms that have at least 2 taxon names.

$summary2

A data.frame with chronogram citations as row.names() and two columns, one with the number of taxon names found in each chronogram and the other one with the total number of taxon names.

$absent_taxa

A character vector of taxon names that are not found in the chronogram database.

Description

make_datelife_query2 always uses TNRS (Taxonomic Name Resolution Service to process input taxon names, to correct misspellings and taxonomic name variations with tnrs_match(), a wrapper of rotl::tnrs_match_names()).

Usage

get_tnrs_names(
  input = c("Rhea americana", "Pterocnemia pennata", "Struthio camelus"),
  reference_taxonomy = "ott",
  ...
)

Arguments

Value

A datelifeTNRS object, which is a list of three elements:

$cleaned_names

A character vector of names provided as input.

$tnrs_names

A character vector of taxon names processed with TNRS.

$ott_ids

A numeric vector of Open Tree of Life Taxonomy (OTT) ids.

Description

Extract valid children from given taxonomic name(s) or Open Tree of Life Taxonomic identifiers (OTT ids) from a taxonomic source.

Usage

get_valid_children(input = NULL, ott_ids = NULL, reference_taxonomy = "ncbi")

Arguments

Details

GBIF and other taxonomies contain deprecated taxa that are not marked as such in the Open Tree of Life Taxonomy. We are relying mainly in the NCBI taxonomy for now.

Value

A named list containing valid taxonomic children of given taxonomic name(s).

Examples

# genus Dictyophyllidites with ott id = 6003921 has only extinct children
# in cases like this the same name will be returned

tti <- rotl::taxonomy_taxon_info(6003921, include_children = TRUE)
gvc <- get_valid_children(ott_ids = 6003921)

# More examples:

get_valid_children(ott_ids = 769681) # Psilotopsida
get_valid_children(ott_ids = 56601) # Marchantiophyta

Description

Process a phylo object or a character string to determine if it's correct newick

Usage

input_process(input)

Arguments

Value

A phylo object or NA if input is not a tree .

Description

is_datelife_query checks for two things to be TRUE or FALSE. First, that input is of class datelifeQuery. Second, that input is a list that contains at least two elements of a datelifeQuery object:

cleaned_names

A character vector of taxon names.

phy

Either NA or a phylo object.

Usage

is_datelife_query(input)

Arguments

Details

If the object has the correct format but it has a class different than datelifeQuery, the class is not modified.

Value

Is determined by the second condition.

Description

Check if we obtained an empty search with the given taxon name(s).

Usage

is_datelife_result_empty(datelife_result, use_tnrs = FALSE)

Arguments

Value

Boolean. If TRUE, no chronograms were found for the given taxon name(s). If FALSE, the chronogram search was successful.

Description

Check if a tree is a valid chronogram.

Usage

is_good_chronogram(phy)

Arguments

Value

TRUE if it is a valid tree.

Description

This function implements definition 2.8 for n-overlap from Ané et al. (2009) doi:10.1007/s00026-009-0017-x.

Usage

is_n_overlap(names_1, names_2, n = 2)

Arguments

Value

Boolean for whether the degree of overlap was met or not.

References

Ané, C., Eulenstein, O., Piaggio-Talice, R., & Sanderson, M. J. (2009). "Groves of phylogenetic trees". Annals of Combinatorics, 13(2), 139-167, doi:10.1007/s00026-009-0017-x.

Description

Find all authors and where they have deposited their trees

Usage

make_all_associations(outputfile = "depositorcache.RData")

Arguments

Value

a data.frame of "person" and "urls".

Description

The function takes a tree topology and uses the BLADJ algorithm implemented with phylocomr::ph_bladj() to assign node ages and branch lengths, given a set of fixed node ages and respective node names.

Usage

make_bladj_tree(tree = NULL, nodenames = NULL, nodeages = NULL)

Arguments

Details

Input tree can be dated or not, ⁠$edge.length⁠ is ignored. Ages given in nodeages are fixed on their corresponding nodes given in nodenames.

Value

A phylo object.

Description

make_bold_otol_tree takes taxon names from a tree topology or a vector of names to search for genetic markers in the Barcode of Life Database (BOLD), create an alignment, and reconstruct branch lengths on a tree topology with Maximum Likelihood.

Usage

make_bold_otol_tree(
  input = c("Rhea americana", "Struthio camelus", "Gallus gallus"),
  marker = "COI",
  otol_version = "v3",
  chronogram = TRUE,
  doML = FALSE,
  aligner = "muscle",
  ...
)

Arguments

Details

If input is a phylo object or a newick string, it is used as backbone topology. If input is a character vector of taxon names, an induced synthetic OpenTree subtree is used as backbone.

Value

A phylo object. If there are enough BOLD sequences available for the input taxon names, the function returns a tree with branch lengths proportional to relative substitution rate. If not enough BOLD sequences are available for the input taxon names, the function returns the topology given as input, or a synthetic Open Tree of Life for the taxon names given in input, obtained with get_otol_synthetic_tree().

Description

Create a cache from Open Tree of Life

Usage

make_contributor_cache(outputfile = "contributorcache.RData")

Arguments

Value

List containing author and curator results

Description

Go from taxon names to a datelifeQuery object

Usage

make_datelife_query(
  input = c("Rhea americana", "Pterocnemia pennata", "Struthio camelus"),
  use_tnrs = TRUE,
  get_spp_from_taxon = FALSE,
  reference_taxonomy = "ott"
)

Arguments

Details

It processes phylo objects and newick character string inputs with input_process(). If input is a multiPhylo object, only the first phylo element will be used. Similarly, if an input newick character string has multiple trees, only the first one will be used.

Value

A datelifeQuery object, which is a list of three elements:

$phy

A phylo object or NA, if input is not a tree.

$cleaned_names

A character vector of cleaned taxon names.

$ott_ids

A numeric vector of OTT ids if use_tnrs = TRUE, or NULL if use_tnrs = FALSE.

Description

Go from taxon names to a datelifeQuery object

Usage

make_datelife_query2(
  input = c("Rhea americana", "Pterocnemia pennata", "Struthio camelus"),
  get_spp_from_taxon = FALSE,
  reference_taxonomy = "ott",
  ...
)

Arguments

Details

It processes phylo objects and newick character string inputs with input_process(). If input is a multiPhylo object, only the first phylo element will be used. Similarly, if an input newick character string has multiple trees, only the first one will be used.

Value

A datelifeQuery object, which is a list of four elements:

$input_names

A character vector of input taxon names.

$tnrs_names

A character vector of taxon names processed with TNRS.

$ott_ids

A numeric vector of OTT ids.

$phy

A phylo object or NA, if input is not a tree.

Description

Make a mrBayes run block file with a constraint topology and a set of node calibrations and missing taxa

Usage

make_mrbayes_runfile(
  constraint = NULL,
  taxa = NULL,
  ncalibration = NULL,
  missing_taxa = NULL,
  age_distribution = "fixed",
  root_calibration = FALSE,
  mrbayes_output_file = "mrbayes_run.nexus"
)

Arguments

Value

A MrBayes block run file in nexus format.

Description

Take a constraint tree and use mrBayes to get node ages and branch lengths given a set of node calibrations without any data.

Usage

make_mrbayes_tree(
  constraint = NULL,
  taxa = NULL,
  ncalibration = NULL,
  missing_taxa = NULL,
  age_distribution = "fixed",
  root_calibration = FALSE,
  mrbayes_output_file = "mrbayes_run.nexus"
)

Arguments

Value

A phylo object with branch lengths proportional to time. It saves all mrBayes outputs in the working directory.

Description

Associate Open Tree of Life authors with studies

Usage

make_otol_associations()

Value

data.frame with author last name, author first and other names, and comma delimited URLs for OToL studies

Description

Create an overlap table

Usage

make_overlap_table(results_table)

Arguments

Value

A data.frame with information on curators and what clades they've worked on

Make a Super Distance Matrix (SDM) from a list of good matrices obtained with get_goodmatrices()

Description

Make a Super Distance Matrix (SDM) from a list of good matrices obtained with get_goodmatrices()

Usage

make_sdm(unpadded.matrices, weighting = "flat")

Arguments

Value

A matrix.

Description

Associate TreeBase authors with studies

Usage

make_treebase_associations()

Value

data.frame with author last name, author first and other names, and comma delimited URLs for TreeBase studies

Description

Create a cache from TreeBase

Usage

make_treebase_cache(outputfile = "treebasecache.RData")

Arguments

Value

List containing author and curator results

Description

Add Open Tree of Life Taxonomy to tree nodes.

Usage

map_nodes_ott(tree)

Arguments

Value

A phylo object with "nodelabels".

Examples

## Not run:  # This is a flag for package development. You are welcome to run the example.

# Load the Open Tree chronograms database cached in datelife:
utils::data(opentree_chronograms)

# Get the small chronograms (i.e., chronograms with less that ten tips) to generate a pretty plot:
small <- opentree_chronograms$trees[unlist(sapply(opentree_chronograms$trees, ape::Ntip)) < 10]

# Now, map the Open Tree taxonomy to the nodes of the first tree
phy <- map_nodes_ott(tree = small[[1]])
# and plot it:
# plot_phylo_all(phy)
library(ape)
plot(phy)
nodelabels(phy$node.label)


## End(Not run) #end dontrun

Description

match_all_calibrations searches a given tree for the most recent common ancestor (mrca) of all taxon name pairs in a datelifeCalibration. It uses phytools::findMRCA().

Usage

match_all_calibrations(phy, calibrations)

Arguments

Details

The function takes pairs of taxon names in a secondary calibrations data frame, and looks for them in the vector of tip labels of the tree. If both are present, then it gets the node that represents the most recent common ancestor (mrca) for that pair of taxa in the tree. Nodes of input phy can be named or not.

Value

A list of two elements:

phy

A phylo object with nodes renamed with tree_add_nodelabels().

matched_calibrations

A matchedCalibrations object, which is the input calibrations object with two additional columns storing results from the mrca search with phytools::findMRCA(): ⁠$mrca_node_number⁠ and ⁠$mrca_node_name⁠.

Description

Go from a list of patristic distance matrix to a table of node ages

Usage

matrices_to_table(matrices)

Arguments

Value

A single data.frame of "taxonA", "taxonB", and "age".

Description

Go from a patristic distance matrix to a node ages table

Usage

matrix_to_table(matrix, reference)

Arguments

Value

A data.frame of "taxonA", "taxonB", and "age".

Description

Message for a multiPhylo input

Usage

message_multiphylo()

Value

A relevant message as a character string.

Description

Checks that missing_taxa argument is ok to be used by make_mrbayes_runfile inside tree_add_dates functions.

Usage

missing_taxa_check(missing_taxa = NULL, dated_tree = NULL)

Arguments

Value

A phylo object, a newick character string or a dataframe with taxonomic assignations

Description

mrca_calibrations get nodes of a tree topology given in phy that correspond to the most recent common ancestor (mrca) of taxon pairs given in calibrations. It uses phytools::findMRCA() to get mrca nodes.

Usage

mrca_calibrations(phy, calibrations)

Arguments

Details

The function takes pairs of taxon names in a calibrations data frame, and looks for them in the vector of tip labels of the tree. If both are present, then it gets the node that represents the most recent common ancestor (mrca) for that pair of taxa in the tree. Nodes of input phy can be named or not. They will be renamed.

Value

A list of two elements:

matched_phy

A phylo object with nodes renamed to match results of the mrca search. Nodes are renamed using tree_add_nodelabels().

matched_calibrations

A matchedCalibrations object, which is the input calibrations object with two additional columns storing results from the mrca search with phytools::findMRCA(): ⁠$mrca_node_number⁠ and ⁠$mrca_node_name⁠.

Description

Now storing >200 chronograms from Open Tree of Life

Usage

opentree_chronograms

Format

A list of four elements, containing data from Open Tree of Life chronograms

authors

A list of lists of author names of the original studies that published chronograms in the Open Tree of Life database.

curators

A list of lists of curator names that uploaded chronograms to the Open Tree of Life database.

studies

A list of study identifiers.

trees

A multiPhylo object storing the chronograms from Open Tree of Life database.

update

A character vector indicating the time when the database object was last updated.

version

A character vector indicating the datelife utils::packageVersion() when the database was last updated.

Details

Generated with opentree_chronograms <- get_opentree_chronograms() opentree_chronograms$version <- '2023.12.30' usethis::use_data(opentree_chronograms, overwrite = T, compress = "xz") and updated with update_datelife_cache()

Source

http://opentreeoflife.org

Description

patristic_matrix_array_congruify is used for patristic_matrix_array_subset_both and patristic_matrix_array_congruify.

Usage

patristic_matrix_array_congruify(
  patristic_matrix_array,
  taxa,
  phy = NULL,
  dating_method = "PATHd8"
)

Arguments

Value

A patristic matrix with ages for the target taxa.

Description

Congruify a patristic matrix array from a given phylo object.

Usage

patristic_matrix_array_phylo_congruify(
  patristic_matrix,
  target_tree,
  dating_method = "PATHd8",
  attempt_fix = TRUE
)

Arguments

Value

A matrix.

Description

Split a patristic matrix array Used inside: patristic_matrix_array_congruify

Usage

patristic_matrix_array_split(patristic_matrix_array)

Arguments

Value

A patristic matrix 3d array.

Description

Subset a patristic matrix array

Usage

patristic_matrix_array_subset(patristic_matrix_array, taxa, phy4 = NULL)

Arguments

Value

A list with a patristic matrix array and a ⁠$problem⁠ if any.

Description

patristic_matrix_array_subset_both is used inside get_subset_array_dispatch().

Usage

patristic_matrix_array_subset_both(
  patristic_matrix_array,
  taxa,
  phy = NULL,
  phy4 = NULL,
  dating_method = "PATHd8"
)

Arguments

Value

A patristic matrix with ages for the target taxa.

Description

patristic_matrix_list_to_array us ised inside summarize_datelife_result(), patristic_matrix_array_congruify().

Usage

patristic_matrix_list_to_array(patristic_matrix_list, pad = TRUE)

Arguments

Value

A 3d array of patristic matrices

Get time of MRCA from patristic matrix. Used in datelife_result_MRCA().

Description

Get time of MRCA from patristic matrix. Used in datelife_result_MRCA().

Usage

patristic_matrix_MRCA(patristic_matrix, na_rm = TRUE)

Arguments

Value

The depth of the MRCA as a numeric vector.

Description

patristic_matrix_name_order_test is only used in patristic_matrix_list_to_array().

Usage

patristic_matrix_name_order_test(
  patristic_matrix,
  standard.rownames,
  standard.colnames
)

Arguments

Value

Boolean.

Description

patristic_matrix_name_reorder is only used in: patristic_matrix_pad().

Usage

patristic_matrix_name_reorder(patristic_matrix)

Arguments

Value

A patristic matrix with row and column names for taxa in alphabetical order.

Description

Used in: patristic_matrix_list_to_array().

Usage

patristic_matrix_pad(patristic_matrix, all_taxa)

Arguments

Value

A patristic matrix, with NA for entries between taxa where at least one was not in the original patristic matrix.

Description

patristic_matrix_taxa_all_matching is used inside: results_list_process().

Usage

patristic_matrix_taxa_all_matching(patristic_matrix, taxa)

Arguments

Value

A Boolean.

Description

Convert patristic matrix to a newick string. Used inside: summarize_datelife_result.

Usage

patristic_matrix_to_newick(patristic_matrix)

Arguments

Value

A newick string

Description

Function patristic_matrix_to_phylo is used inside summarize_datelife_result().

Usage

patristic_matrix_to_phylo(
  patristic_matrix,
  clustering_method = "nj",
  fix_negative_brlen = TRUE,
  fixing_method = 0,
  ultrametric = TRUE,
  variance_matrix = NULL
)

Arguments

Details

We might add the option to insert a function as clustering_method in the future. Before, we had hard-coded the function to try Neighbor-Joining (NJ) first; if it errors, it will try UPGMA. Now, it uses NJ for a "phylo_all" summary, and we are using our own algorithm to get a tree from a summary matrix.

Value

A rooted phylo object.

Description

Used in datelife_result_sdm_phylo().

Usage

patristic_matrix_unpad(patristic_matrix)

Arguments

Value

patristic_matrix for all_taxa

Description

Checks if phy is a phylo object and/or a chronogram.

Usage

phylo_check(phy = NULL, brlen = FALSE, dated = FALSE)

Arguments

Value

Nothing

Description

Congruify a reference tree and a target tree given as phylo objects.

Usage

phylo_congruify(
  reference_tree,
  target_tree,
  dating_method = "PATHd8",
  attempt_fix = TRUE
)

Arguments

Value

A matrix.

Description

Generate uncertainty in branch lengths using a lognormal.

Usage

phylo_generate_uncertainty(
  phy,
  size = 100,
  uncertainty_method = "other",
  age_distribution = "uniform",
  age_sd = NULL,
  age_var = 0.1,
  age_scale = 0,
  alpha = 0.025,
  rescale = TRUE
)

Arguments

Details

If you want to change the size of sampled trees you do not need to run mrbayes again. Just use sample_trees("mrbayes_trees_file_directory", size = new_size) and you will get a multiPhylo object with a new tree sample.

Value

A phylo or multiPhylo object with the same topology as phy but different branch lengths

Examples

## Not run: 
# Generate uncertainty over feline species SDM chronogram.
# Load the data:

data(felid_sdm)

# By default, generates a sample of 100 trees with var = 0.1:

unc <- phylo_generate_uncertainty(felid_sdm$phy)
length(unc)

# Make an LTT plot:

max_age <- max(sapply(unc, ape::branching.times))
ape::ltt.plot(phy = unc[[1]], xlim = c(-max_age, 0), col = "#cce5ff50")
for (i in 2:100) {
  ape::ltt.lines(phy = unc[[i]], col = "#cce5ff50")
}
ape::ltt.lines(felid_sdm$phy, col = "red")
title(c("fake uncertainty", "in Felidae SDM chronogram"))

## End(Not run) # end dontrun

Description

Gets node numbers from any phylogeny

Usage

phylo_get_node_numbers(phy)

Arguments

Value

A numeric vector with node numbers

Description

Get a subset array from a phylo object

Usage

phylo_get_subset_array(
  reference_tree,
  taxa,
  phy4 = NULL,
  dating_method = "PATHd8"
)

Arguments

Value

A list with a patristic matrix array and a ⁠$problem⁠ if any.

Description

Get a congruified subset array from a phylo object

Usage

phylo_get_subset_array_congruify(
  reference_tree,
  taxa,
  phy = NULL,
  dating_method = "PATHd8"
)

Arguments

Value

A list with a patristic matrix array and a ⁠$problem⁠ if any.

Description

Check if a tree has branch lengths

Usage

phylo_has_brlen(phy)

Arguments

Value

A TRUE or FALSE

Description

Prune missing taxa from a phylo object Used inside phylo_get_subset_array and phylo_get_subset_array_congruify.

Usage

phylo_prune_missing_taxa(phy, taxa)

Arguments

Value

A phylo object.

Description

Subset a reference and a target tree given as phylo objects.

Usage

phylo_subset_both(
  reference_tree,
  taxa,
  phy = NULL,
  phy4 = NULL,
  dating_method = "PATHd8"
)

Arguments

Value

A list with a patristic matrix array and a ⁠$problem⁠ if any.

Description

phylo_tiplabel_space_to_underscore is used in: make_mrbayes_runfile(), tree_get_singleton_outgroup(), congruify_and_check(), patristic_matrix_array_phylo_congruify().

Usage

phylo_tiplabel_space_to_underscore(phy)

Arguments

Value

A phylo object.

Description

phylo_tiplabel_underscore_to_space is used inside patristic_matrix_array_phylo_congruify(), congruify_and_check().

Usage

phylo_tiplabel_underscore_to_space(phy)

Arguments

Value

A phylo object.

Description

Get a patristic matrix from a phylo object.

Usage

phylo_to_patristic_matrix(phy, test = TRUE, tol = 0.01, option = 2)

Arguments

Value

A patristic matrix.

Description

Pick a grove in the case of multiple groves in a set of trees.

Usage

pick_grove(grove_list, criterion = "taxa", datelife_result)

Arguments

Value

A numeric vector of the elements of the picked grove.

Description

Some plants chronogram

Usage

plant_bold_otol_tree

Format

A phylo object with 6 tips and 5 internal nodes

edge

Integer vector with edge (branch) numbers

tip.label

Character vector with species names of plants

Nnode

Integer vector with the number of nodes

node.label

Character vector with node names

edge.length

Numeric vector with edge (branch) lengths

Details

Generated with make_bold_otol_tree(input = "((Zea mays,Oryza sativa),((Arabidopsis thaliana,(Glycine max,Medicago sativa)),Solanum lycopersicum)Pentapetalae);") usethis::use_data(plant_bold_otol_tree)

Author(s)

Luna L. Sanchez-Reyes [email protected]

Brian O'Meara [email protected]

Source

http://opentreeoflife.org

http://www.boldsystems.org

Description

Problematic chronograms from Open Tree of Life.

Usage

problems

Format

A list of trees with unmapped taxa

Details

Before we developed tools to clean and map tip labels for our cached trees we found some trees that were stored with unmapped tip labels we extracted them and saved them to be used for testing functions. Generated with problems <- opentree_chronograms$trees[sapply(sapply(opentree_chronograms$trees, "[", "tip.label"), function(x) any(grepl("not.mapped", x)))] usethis::use_data(problems) opentree_chronograms object from commit https://github.com/phylotastic/datelife/tree/be894448f6fc437241cd0916fab45e84ac3e09c6

[", "tip.label"), function(x) any(grepl("not.mapped", x)))]: R:%22,%20%22tip.label%22),%20function(x)%20any(grepl(%22not.mapped%22,%20x)))

Source

http://opentreeoflife.org

Description

Get an mrcaott tag from an OpenTree induced synthetic tree and get its name and ott id

Usage

recover_mrcaott(tag)

Arguments

Value

A numeric vector with ott id from original taxon named with the corresponding ott name

Description

Return the relevant curators for a set of studies.

Usage

relevant_curators_tabulate(results.index, cache = "opentree_chronograms")

Arguments

Value

A vector with counts of each curator, with names equal to curator names.

Description

results_list_process is used inside: get_datelife_result()

Usage

results_list_process(results_list, taxa = NULL, partial = FALSE)

Arguments

Value

A list with the patristic.matrices that are not NA.

Description

Core function to generate results

Usage

run(
  input = c("Rhea americana", "Pterocnemia pennata", "Struthio camelus"),
  format = "citations",
  partial = "yes",
  plot.width = 600,
  plot.height = 600,
  use_tnrs = "no",
  opentree_chronograms = NULL
)

Arguments

Value

results in the desired format

Description

Runs MrBayes from R

Usage

run_mrbayes(mrbayes_output_file = NULL)

Arguments

Value

A phylo object with the consensus tree. MrBayes output files are stored in the working directory.

Description

Sample trees from a file containing multiple trees. Usually from a bayesian analysis output trees file.

Usage

sample_trees(trees_file, trees_object = NULL, burnin = 0.25, size = 100)

Arguments

Value

A multiPhylo object with a random sample of trees.

Description

datelifeResult object of some ants

Usage

some_ants_datelife_result

Format

A list of one element, containing a named patristic matrix

Details

Generated with: some_ants_input <- "(Aulacopone_relicta,(((Myrmecia_gulosa,(Aneuretus_simoni,Dolichoderus_mariae)),((Ectatomma_ruidum,Huberia_brounii),Formica_rufa)),Apomyrma_stygia),Martialis_heureka)Formicidae;" some_ants_datelife_query <- make_datelife_query(input = some_ants_input) some_ants_datelife_result <- get_datelife_result(input = some_ants_datelife_query) usethis::use_data(some_ants_datelife_result)

Source

http://opentreeoflife.org

Description

A list with datelifeQuery and datelifeResult objects from a search of taxon names from subset2_taxa

Usage

subset2_search

Format

A list with two named elements. datelifeResult object with 24 patristic matrices

datelife_query

A datelifeQuery object using names_subset 2 as input.

datelife_result

A datelifeResult object resulting from a search of names in datelifeQuery

Details

Generated with: datelife_query <- make_datelife_query(subset2_taxa) datelife_result <- get_datelife_result(datelife_query) subset2_search <- list(query = datelife_query, result = datelife_result) usethis::use_data(subset2_search, overwrite = TRUE)

Description

Long list of >2.7k virus, bacteria, plant and animal taxon names

Usage

subset2_taxa

Format

A character vector of length 2778

Details

Generated with: subset2_taxa <- rphylotastic::url_get_scientific_names("https://github.com/phylotastic/rphylotastic/blob/master/tests/testthat/subset2.txt") usethis::use_data(subset2_taxa)

Source

https://github.com/phylotastic/rphylotastic/tree/master/tests/testthat

Description

Function summarize_congruifiedCalibrations returns a table of summary statistics for each node in congruified_calibrations argument.

Usage

summarize_congruifiedCalibrations(congruified_calibrations, age_column)

Arguments

Value

A data.frame of summarized ages.

Description

Get different types of summaries from a datelifeResult object, an output from get_datelife_result(). This allows rapid processing of data. If you need a list of chronograms from your datelifeResult object, this is the function you are looking for.

Usage

summarize_datelife_result(
  datelife_result = NULL,
  datelife_query = NULL,
  summary_format = "phylo_all",
  na_rm = TRUE,
  summary_print = c("citations", "taxa"),
  taxon_summary = c("none", "summary", "matrix"),
  criterion = "taxa"
)

Arguments

Value

The output is determined by the argument summary_format:

If summary_format = "citations"

The function returns a character vector of references.

If summary_format = "mrca"

The function returns a named numeric vector of most recent common ancestor (mrca) ages.

If summary_format = "newick_[all, sdm, or median]"

The function returns output chronograms as newick strings.

If summary_format = "phylo_[all, sdm, median, or biggest]"

The function returns output chronograms as phylo or multiPhylo objects.

If ⁠summary_format = "html" or "data_frame"⁠

The function returns a 4 column table with data on mrca ages, number of taxa, references, and output chronograms as newick strings.

References

Ané, C., Eulenstein, O., Piaggio-Talice, R., & Sanderson, M. J. (2009). "Groves of phylogenetic trees". Annals of Combinatorics, 13(2), 139-167, doi:10.1007/s00026-009-0017-x.

Description

This uses the Paleobiology Database's API to gather information on the ages for all specimens of a taxon. It will also look for all descendants of the taxon. It fixes name misspellings if possible. It is basically a wrapper for get_fossil_range.

Usage

summarize_fossil_range(taxon, recent = FALSE, assume_recent_if_missing = TRUE)

Arguments

Value

a single row data.frame of max_ma and min_ma for the specimens, with rowname equal to taxon input

Description

Gets all ages per taxon pair from a distance matrix Internal function used in summary_matrix_to_phylo_all().

Usage

summarize_summary_matrix(summ_matrix)

Arguments

Value

A data.frame of pairwise ages, with row number equal to the combinatory of column names (or row names), estimated as ncol(summ_matrix)^2 - sum(1:(ncol(summ_matrix)-1)).

Description

Go from a summary matrix to an ultrametric phylo object.

Usage

summary_matrix_to_phylo(
  summ_matrix,
  datelife_query = NULL,
  target_tree = NULL,
  total_distance = TRUE,
  use = "mean",
  ...
)

Arguments

Details

It can take a regular patristic distance matrix, but there are simpler methods for that implemented in patristic_matrix_to_phylo().

Value

An ultrametric phylo object.

Description

Get minimum, median, mean, midpoint, and maximum summary chronograms from a summary matrix of a datelifeResult object.

Usage

summary_matrix_to_phylo_all(
  summ_matrix,
  datelife_query = NULL,
  target_tree = NULL,
  total_distance = TRUE,
  ...
)

Arguments

Details

With this function users can choose the minimum, mean or maximum ages from the summary matrix as calibration points to get a single summary chronogram. Users get all three summary chronograms in a multiPhylo object.

Value

A multiPhylo object of length 5. It contains min, mean, median, midpoint, and max summary chronograms.

Description

Summarize patristic matrix array (by default, median). Used inside: summarize_datelife_result.

Usage

summary_patristic_matrix_array(patristic_matrix_array, fn = stats::median)

Arguments

Value

A 2d array with the median (or max, or mean, etc) of the input array

Description

Summarize a datelifeResult object.

Usage

## S3 method for class 'datelifeResult'
summary(object, datelife_query, na_rm = TRUE, ...)

Arguments

Value

A named list of 11 elements:

"citations"

A character vector of references where chronograms with some or all of the target taxa are published (source chronograms).

"mrca"

A named numeric vector of most recent common ancestor (mrca) ages of target taxa defined in input, obtained from the source chronograms. Names of mrca vector are equal to citations.

"newick_all"

A named character vector of newick strings corresponding to target chronograms derived from source chronograms. Names of newick_all vector are equal to citations.

"newick_sdm"

Only if multiple source chronograms are available. A character vector with a single newick string corresponding to a target chronogram obtained with SDM supertree method (Criscuolo et al. 2006).

"newick_median"

Only if multiple source chronograms are available. A character vector with a single newick string corresponding to a target chronogram from the median of all source chronograms.

"phylo_sdm"

Only if multiple source chronograms are available. A phylo object with a single target chronogram obtained with SDM supertree method (Criscuolo et al. 2006).

"phylo_median"

Only if multiple source chronograms are available. A phylo object with a single target chronogram obtained from source chronograms with median method.

"phylo_all"

A named list of phylo objects corresponding to each target chronogram obtained from available source chronograms. Names of phylo_all list correspond to citations.

"phylo_biggest"

The chronogram with the most taxa. In the case of a tie, the chronogram with clade age closest to the median age of the equally large trees is returned.

"html"

A character vector with an html string that can be saved and then opened in any web browser. It contains a 4 column table with data on target taxa: mrca, number of taxa, citations of source chronogram and newick target chronogram.

"data_frame"

A 4 column data.frame with data on target taxa: mrca, number of taxa, citations of source chronograms and newick string.

Description

Summarize a matchedCalibrations object summary.matchedCalibrations gets the node age distribution from a matchedCalibrations object.

Usage

## S3 method for class 'matchedCalibrations'
summary(object, ...)

Arguments

Details

Columns in_phy$mrca_node_name and in_phy$reference are factors.

Value

A summaryMatchedCalibrations object, which is a list of two matchedCalibrations objects:

not_in_phy

A data.frame subset of input matchedCalibrations object containing taxon name pairs that were not present in the given tree. NULL if all input taxon names are found in the given tree.

in_phy

A data.frame subset of input matchedCalibrations object containing all taxon name pairs that were present in the given tree.

Description

datelifeResult object of three birds "Rhea americana", "Pterocnemia pennata", and "Struthio camelus"

Usage

threebirds_dr

Format

A list of 9 named patristic matrix

Details

Generated with: threebirds_dr <- get_datelife_result(input=c("Rhea americana", "Pterocnemia pennata", "Struthio camelus"), partial = TRUE, use_tnrs = FALSE, approximate_match = TRUE, cache = "opentree_chronograms") use_data(threebirds_dr)

Source

http://opentreeoflife.org

Description

Taxon name resolution service (tnrs) applied to a vector of names by batches

Usage

tnrs_match(input, reference_taxonomy, tip, ...)

## Default S3 method:
tnrs_match(input, reference_taxonomy = "ott", ...)

## S3 method for class 'phylo'
tnrs_match(input, reference_taxonomy = "ott", tip = NULL, ...)

Arguments