assign_taxa_to_bins: Assign taxa to time bins

In graemetlloyd/Claddis: Measuring Morphological Diversity and Evolutionary Tempo

Assign taxa to time bins

Description

Given a set of first and last appearances assigns a set of taxa to a series of time bins.

Usage

assign_taxa_to_bins(taxon_ages, time_bins)

Arguments

taxon_ages	A matrix of taxon ages, with columns for first ("fad") and last ("lad") appearances and rownames correspodning to taxon names.
time_bins	An object of class timeBins.

Details

The various disparity plotting functions (plot_chronophylomorphospace, plot_morphospace_stack, plot_morphospace, plot_multi_morphospace) are designed to allow assignment of taxa to named groups so that these groups may be assigned different colours when plotting. One way taxa may be grouped is temporally, by assignment to a series of time bins.

There are many ways this may be automated and this function provides a very simple one: if the first and last appearance dates of a taxon overlap with a time bin then it can be assigned to that time bin. (In practice, taxa often have multiple occurrences with "ranges" that really represent uncertainty around their true age.)

Note that it is recommended that time bins be named without special characters beyond letters and underscores.

Value

An object of class taxonGroups.

Author(s)

Graeme T. Lloyd [e-mail]

See Also

plot_chronophylomorphospace, plot_morphospace_stack, plot_morphospace, plot_multi_morphospace, ordinate_cladistic_matrix

Examples

# Build example time bins:
time_bins <- matrix(data = c(443.8, 358.9, 358.9, 298.9, 298.9, 251.9,
  251.9, 201.3, 201.3, 145.0, 145.0, 65.5, 65.5, 23.03), ncol = 2,
  byrow = TRUE, dimnames = list(c("Silurodevonian", "Carboniferous",
  "Permian", "Triassic", "Jurassic", "Cretaceous", "Paleogene"),
  c("fad", "lad")))

# Set class as timeBins:
class(time_bins) <- "timeBins"

# Build example taxon ages:
taxon_ages <- matrix(data = c(385.3, 374.5, 407, 374.5, 251, 228, 385.3,
  251, 251, 251, 391.8, 251, 251, 228, 385.3, 391.8, 391.8, 385.3, 311.7,
  359.2, 359.2, 416, 407, 407, 407, 407, 385.3, 397.5, 385.3, 161.2, 385.3,
  345.3, 318.1, 385.3, 228, 385.3, 385.3, 385.3, 385.3, 385.3, 385.3, 385.3,
  385.3, 385.3, 391.8, 407, 391.8, 374.5, 407, 70.6, 311.7, 407, 145.5, 251,
  65.5, 251, 112, 374.5, 374.5, 374.5, 385.3, 311.7, 249.7, 359.2, 391.8,
  374.5, 385.3, 83.5, 418.7, 251, 385.3, 391.8, 374.5, 345.3, 385.3, 385.3,
  407, 411.2, 397.5, 345.3, 374.5, 407, 216.5, 326.4, 411.2, 411.2, 374.5,
  359.2, 391.8, 359.2, 245, 216.5, 374.5, 245, 245, 245, 385.3, 245, 245,
  199.6, 374.5, 385.3, 385.3, 374.5, 306.5, 345.3, 345.3, 411.2, 397.5,
  397.5, 397.5, 397.5, 374.5, 391.8, 374.5, 145.5, 374.5, 326.4, 311.7,
  374.5, 199.6, 374.5, 374.5, 374.5, 374.5, 374.5, 374.5, 374.5, 374.5,
  374.5, 385.3, 397.5, 385.3, 359.2, 397.5, 65.5, 306.5, 397.5, 99.6, 245,
  23.03, 245, 99.6, 359.2, 359.2, 359.2, 374.5, 306.5, 247.4, 318.1, 385.3,
  359.2, 374.5, 70.6, 416, 250.4, 374.5, 385.3, 359.2, 326.4, 374.5, 374.5,
  397.5, 407, 391.8, 326.4, 359.2, 397.5, 203.6, 318.1, 407, 407),
  ncol = 2, dimnames = list(c("Adololopas_moyasmithae", "Adelargo_schultzei",
  "Amadeodipterus_kencampbelli", "Andreyevichthys_epitomus",
  "Aphelodus_anapes", "Archaeoceratodus_avus", "Archaeonectes_pertusus",
  "Arganodus_atlantis", "Ariguna_formosa", "Asiatoceratodus_sharovi",
  "Barwickia_downunda", "Beltanodus_ambilobensis", "Ceratodus_formosa",
  "Ceratodus_latissimus", "Chirodipterus_australis",
  "Chirodipterus_onawwayensis", "Chirodipterus_rhenanus",
  "Chirodipterus_wildungensis", "Conchopoma_gadiforme", "Ctenodus_romeri",
  "Delatitia_breviceps", "Diabolepis_speratus", "Dipnorhynch_cathlesae",
  "Dipnorhynchus_sussmilchi", "Dipnorhynchus_kiandrensis",
  "Dipnorhynchus_kurikae", "Dipterus_cf_valenciennesi",
  "Dipterus_valenciennesi", "Eoctenodus_microsoma",
  "Ferganoceratodus_jurassicus", "Fleurantia_denticulata",
  "Ganopristodus_splendens", "Gnathorhiza_serrata", "Gogodipterus_paddyensis",
  "Gosfordia_truncata", "Griphognathus_minutidens", "Griphognathus_sculpta",
  "Griphognathus_whitei", "Grossipterus_crassus", "Holodipterus_elderae",
  "Holodipterus_gogoensis", "Robinsondipterus_longi",
  "Asthenorhynchus_meemannae", "Holodipterus_santacrucensis",
  "Howidipterus_donnae", "Ichnomylax_kurnai", "Iowadipterus_halli",
  "Jarvikia_arctica", "Jessenia_concentrica", "Lepidosiren_paradoxa",
  "Megapleuron_zangerli", "Melanognathus_canadensis",
  "Metaceratodus_wollastoni", "Microceratodus_angolensis",
  "Mioceratodus_gregoryi", "Namatozodia_pitikanta", "Neoceratodus_forsteri",
  "Nielsenia_nordica", "Oervigia_nordica", "Orlovichthys_limnatis",
  "Palaeodaphus_insignis", "Palaeophichthys_parvulus", "Paraceratodus_germaini",
  "Parasagenodus_sibiricus", "Pentlandia_macroptera",
  "Phaneropleuron_andersoni", "Pillararhynchus_longi", "Protopterus_annectens",
  "Psarolepis_romeri", "Ptychoceratodus_serratus", "Rhinodipterus_secans",
  "Rhinodipterus_ulrichi", "Rhynchodipterus_elginensis", "Sagenodus_inaequalis",
  "Scaumenacia_curta", "Soederberghia_groenlandica",
  "Sorbitorhynchus_deleaskitus", "Speonesydrion_iani", "Stomiahykus_thlaodus",
  "Straitonia_waterstoni", "Sunwapta_grandiceps", "Tarachomylax_oepiki",
  "Tellerodus_sturi", "Tranodis_castrensis", "Uranolophus_wyomingensis",
  "Westollrhynchus_lehmanni"), c("fad", "lad")))

# Assign taxa to time bins:
assign_taxa_to_bins(taxon_ages = taxon_ages, time_bins = time_bins)

graemetlloyd/Claddis documentation built on May 9, 2024, 8:07 a.m.