Getting started
Source:vignettes/Getting_started_with_datelife.Rmd
Getting_started_with_datelife.RmdWhat can you get with datelife?
As a datelife user, you can get age data for your
organisms of interest in several forms:
MRCA: Get the age of the most recent common ancestor (MRCA) of your organisms.
Original chronogram: Get the chronograms from the original publications, pruned to contain your organisms only.
Biggest chronogram: Get the original chronogram with the most organisms of interest present as tips.
Summary chronogram: Obtain a single chronogram, summarized using data from the original chronograms. The summary chronogram can be calculated using different methods.
You can also apply the obtained age data to date a phylogenetic tree topology of your organisms of interest.
How do you use datelife to get these data?
1. Processing your organism names
The function make_datelife_query processes the taxon
names of your organisms of interest and structures them as a
datelifeQuery object.
A datelifeQuery object is a list of three elements:
-
$cleaned_names: a character vector of “cleaned” taxon names, -
$ott_ids: a numeric vector of OpenTree Taxonomic identifiers (OTT ids), and -
$phy: an input tree as aphyloobject orNAif none was provided.
This allows us to straightforwardly use the processed taxon names
later to perform a search for ages across the datelife
chronogram database as well as other downstream analyses.
There are two alternative ways of processing organism names with
datelife:
a) From a set of organism taxonomic names
You can provide the taxon names as a character vector or as a single comma separated string of names. For example, running the following:
datelife::make_datelife_query(input = c("Delphinus_delphis",
"Gallus gallus",
"elephas Maximus",
"felis_catus",
"homo-sapiens"))make_datelife_query output 1
#> ... Making a DateLife query.
#> ... Phylo-processing 'input'.
#> 'input' is not a phylogeny.
#> DateLife query done!
#> $cleaned_names
#> [1] "Delphinus delphis" "Gallus gallus" "elephas Maximus"
#> [4] "felis catus"
#>
#> $ott_ids
#> NULL
#>
#> $phy
#> [1] NA
#>
#> attr(,"class")
#> [1] "datelifeQuery"Gives the same result as running:
datelife::make_datelife_query(input = "Delphinus_delphis,
Gallus gallus,
elephas Maximus,
felis_catus,
homo-sapiens")make_datelife_query output 2
#> ... Making a DateLife query.
#> ... Phylo-processing 'input'.
#> 'input' is not a phylogeny.
#> DateLife query done!
#> $cleaned_names
#> [1] "Delphinus delphis" "Gallus gallus" "elephas Maximus"
#> [4] "felis catus"
#>
#> $ott_ids
#> NULL
#>
#> $phy
#> [1] NA
#>
#> attr(,"class")
#> [1] "datelifeQuery"Note that you can use underscores or spaces to separate binomial
scientific names and datelife will process them the
same.
b) From a tree with organism taxonomic names as tip labels
You can also provide the taxon names of your organisms of interest as labels on the tips of any phylogenetic tree. You can provide the tree as a newick string:
newick <- "((Elephas_maximus,(Homo_sapiens,(Delphinus_delphis, Felis_silvestris))), Gallus_gallus);"
datelife::make_datelife_query(input = newick)make_datelife_query output 3
#> ... Making a DateLife query.
#> ... Phylo-processing 'input'.
#> 'input' is a phylogeny and it is correcly formatted.
#> DateLife query done!
#> $cleaned_names
#> [1] "Elephas maximus" "Delphinus delphis" " Felis silvestris"
#> [4] " Gallus gallus"
#>
#> $ott_ids
#> NULL
#>
#> $phy
#>
#> Phylogenetic tree with 4 tips and 3 internal nodes.
#>
#> Tip labels:
#> Elephas_maximus, Delphinus_delphis, _Felis_silvestris, _Gallus_gallus
#>
#> Rooted; no branch lengths.
#>
#> attr(,"class")
#> [1] "datelifeQuery"You can also provide the tree as a phylo object. If you
already have a tree as a phylo object, you can use that
directly. For this example, we will first convert our newick string to
phylo. You can do this with the function
read.tree from the ape package:
phylo <- ape::read.tree(text = newick)
datelife::make_datelife_query(input = phylo)make_datelife_query output 4
#> ... Making a DateLife query.
#> ... Phylo-processing 'input'.
#> 'input' is a phylogeny and it is correcly formatted.
#> DateLife query done!
#> $cleaned_names
#> [1] "Elephas maximus" "Delphinus delphis" "Felis silvestris"
#> [4] "Gallus gallus"
#>
#> $ott_ids
#> NULL
#>
#> $phy
#>
#> Phylogenetic tree with 4 tips and 3 internal nodes.
#>
#> Tip labels:
#> Elephas_maximus, Delphinus_delphis, Felis_silvestris, Gallus_gallus
#>
#> Rooted; no branch lengths.
#>
#> attr(,"class")
#> [1] "datelifeQuery"Now save your datelifeQuery as an object for the next
section:
my_datelife_query <- datelife::make_datelife_query(input = phylo)
#> ... Making a DateLife query.
#> ... Phylo-processing 'input'.
#> 'input' is a phylogeny and it is correctly formatted.
#> DateLife query done!2. Searching the chronogram database
The datelife_search function takes a
datelifeQuery object and goes through the
datelife chronogram database to find all chronograms
matching at least two taxon names:
datelife::datelife_search(input = my_datelife_query)datelife_search default output
#> ... Running a DateLife search.
#> ... Getting a DateLife result.
#> DateLife result obtained!
#> Source chronograms from:
#> 1: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512
#> 2: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512
#> 3: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512
#> 4: Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, Sudhir Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32 (4): 835-845
#> Input taxa presence across source chronograms:
#> taxon chronograms
#> 1 Elephas maximus 4/4
#> 2 Delphinus delphis 4/4
#> 3 Felis silvestris 4/4
#> 4 Gallus gallus 1/4
#> Input taxa completely absent from source chronograms:
#> taxon
#> 1 None
#> DateLife search done!
#> 4 phylogenetic trees3. Summarizing chronogram search results
datelife_search will also summarize results from the
chronogram database search for you. By default, it will give you all
original chronograms matching the search, as a phylo or
multiPhylo object. You can specify the format you desire
for the summary of results with the argument
summary_format. There are different summary formats to
choose from:
Citations
summary_format = "citations" gives back the study
citations from all original chronograms matching your search:
citations <- datelife::datelife_search(input = my_datelife_query,
summary_format = "citations")datelife_search output “citations”
#> ... Running a DateLife search.
#> ... Getting a DateLife result.
#> DateLife result obtained!
#> Input taxa presence across source chronograms:
#> taxon chronograms
#> 1 Elephas maximus 4/4
#> 2 Delphinus delphis 4/4
#> 3 Felis silvestris 4/4
#> 4 Gallus gallus 1/4
#> Input taxa completely absent from source chronograms:
#> taxon
#> 1 None
#> DateLife search done!
#> [1] "Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512"
#> [2] "Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512"
#> [3] "Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512"
#> [4] "Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, Sudhir Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32 (4): 835-845"
#> attr(,"datelife_result")
#> $`Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512`
#> Elephas maximus Delphinus delphis
#> Elephas maximus 0.0 202.6
#> Delphinus delphis 202.6 0.0
#> Felis silvestris 202.6 177.0
#> Felis silvestris
#> Elephas maximus 202.6
#> Delphinus delphis 177.0
#> Felis silvestris 0.0
#>
#> $`Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512`
#> Elephas maximus Felis silvestris
#> Elephas maximus 0.0 192.2
#> Felis silvestris 192.2 0.0
#> Delphinus delphis 192.2 173.6
#> Delphinus delphis
#> Elephas maximus 192.2
#> Felis silvestris 173.6
#> Delphinus delphis 0.0
#>
#> $`Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512`
#> Delphinus delphis Felis silvestris
#> Delphinus delphis 0.0 179.6
#> Felis silvestris 179.6 0.0
#> Elephas maximus 221.6 221.6
#> Elephas maximus
#> Delphinus delphis 221.6
#> Felis silvestris 221.6
#> Elephas maximus 0.0
#>
#> $`Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, Sudhir Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32 (4): 835-845`
#> Felis silvestris Delphinus delphis
#> Felis silvestris 0.0000 156.7850
#> Delphinus delphis 156.7850 0.0000
#> Elephas maximus 210.0193 210.0193
#> Gallus gallus 641.0476 641.0476
#> Elephas maximus Gallus gallus
#> Felis silvestris 210.0193 641.0476
#> Delphinus delphis 210.0193 641.0476
#> Elephas maximus 0.0000 641.0476
#> Gallus gallus 641.0476 0.0000
#>
#> attr(,"class")
#> [1] "datelifeResult"
#> attr(,"datelife_query")
#> $cleaned_names
#> [1] "Elephas maximus" "Delphinus delphis" "Felis silvestris"
#> [4] "Gallus gallus"
#>
#> $ott_ids
#> NULL
#>
#> $phy
#>
#> Phylogenetic tree with 4 tips and 3 internal nodes.
#>
#> Tip labels:
#> Elephas_maximus, Delphinus_delphis, Felis_silvestris, Gallus_gallus
#>
#> Rooted; no branch lengths.
#>
#> attr(,"class")
#> [1] "datelifeQuery"MRCA ages
summary_format = "mrca" gives back the age of the MRCA
of your organisms of interest:
mrca <- datelife::datelife_search(input = my_datelife_query,
summary_format = "mrca")datelife_search output “mrca”
#> ... Running a DateLife search.
#> ... Getting a DateLife result.
#> DateLife result obtained!
#> Source chronograms from:
#> 1: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512
#> 2: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512
#> 3: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512
#> 4: Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, Sudhir Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32 (4): 835-845
#> Input taxa presence across source chronograms:
#> taxon chronograms
#> 1 Elephas maximus 4/4
#> 2 Delphinus delphis 4/4
#> 3 Felis silvestris 4/4
#> 4 Gallus gallus 1/4
#> Input taxa completely absent from source chronograms:
#> taxon
#> 1 None
#> DateLife search done!
#> Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512
#> 101.3000
#> Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512
#> 96.1000
#> Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512
#> 110.8000
#> Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, Sudhir Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32 (4): 835-845
#> 320.5238
#> attr(,"datelife_result")
#> $`Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512`
#> Elephas maximus Delphinus delphis
#> Elephas maximus 0.0 202.6
#> Delphinus delphis 202.6 0.0
#> Felis silvestris 202.6 177.0
#> Felis silvestris
#> Elephas maximus 202.6
#> Delphinus delphis 177.0
#> Felis silvestris 0.0
#>
#> $`Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512`
#> Elephas maximus Felis silvestris
#> Elephas maximus 0.0 192.2
#> Felis silvestris 192.2 0.0
#> Delphinus delphis 192.2 173.6
#> Delphinus delphis
#> Elephas maximus 192.2
#> Felis silvestris 173.6
#> Delphinus delphis 0.0
#>
#> $`Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512`
#> Delphinus delphis Felis silvestris
#> Delphinus delphis 0.0 179.6
#> Felis silvestris 179.6 0.0
#> Elephas maximus 221.6 221.6
#> Elephas maximus
#> Delphinus delphis 221.6
#> Felis silvestris 221.6
#> Elephas maximus 0.0
#>
#> $`Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, Sudhir Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32 (4): 835-845`
#> Felis silvestris Delphinus delphis
#> Felis silvestris 0.0000 156.7850
#> Delphinus delphis 156.7850 0.0000
#> Elephas maximus 210.0193 210.0193
#> Gallus gallus 641.0476 641.0476
#> Elephas maximus Gallus gallus
#> Felis silvestris 210.0193 641.0476
#> Delphinus delphis 210.0193 641.0476
#> Elephas maximus 0.0000 641.0476
#> Gallus gallus 641.0476 0.0000
#>
#> attr(,"class")
#> [1] "datelifeResult"
#> attr(,"datelife_query")
#> $cleaned_names
#> [1] "Elephas maximus" "Delphinus delphis" "Felis silvestris"
#> [4] "Gallus gallus"
#>
#> $ott_ids
#> NULL
#>
#> $phy
#>
#> Phylogenetic tree with 4 tips and 3 internal nodes.
#>
#> Tip labels:
#> Elephas_maximus, Delphinus_delphis, Felis_silvestris, Gallus_gallus
#>
#> Rooted; no branch lengths.
#>
#> attr(,"class")
#> [1] "datelifeQuery"Newick strings
summary_format = "newick_all"
newick_all <- datelife::datelife_search(input = my_datelife_query,
summary_format = "newick_all")datelife_search output “newick_all”
#> ... Running a DateLife search.
#> ... Getting a DateLife result.
#> DateLife result obtained!
#> Source chronograms from:
#> 1: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512
#> 2: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512
#> 3: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512
#> 4: Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, Sudhir Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32 (4): 835-845
#> Input taxa presence across source chronograms:
#> taxon chronograms
#> 1 Elephas maximus 4/4
#> 2 Delphinus delphis 4/4
#> 3 Felis silvestris 4/4
#> 4 Gallus gallus 1/4
#> Input taxa completely absent from source chronograms:
#> taxon
#> 1 None
#> DateLife search done!
#> Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512
#> "((Felis_silvestris:88.5,Delphinus_delphis:88.5):12.8,Elephas_maximus:101.3);"
#> Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512
#> "((Delphinus_delphis:86.8,Felis_silvestris:86.8):9.3,Elephas_maximus:96.1);"
#> Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512
#> "((Felis_silvestris:89.8,Delphinus_delphis:89.8):21,Elephas_maximus:110.8);"
#> Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, Sudhir Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32 (4): 835-845
#> "((Elephas_maximus:105.009658,(Felis_silvestris:78.392518,Delphinus_delphis:78.392517):26.617141):215.5141645,Gallus_gallus:320.5238235);"
#> attr(,"datelife_result")
#> $`Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512`
#> Elephas maximus Delphinus delphis
#> Elephas maximus 0.0 202.6
#> Delphinus delphis 202.6 0.0
#> Felis silvestris 202.6 177.0
#> Felis silvestris
#> Elephas maximus 202.6
#> Delphinus delphis 177.0
#> Felis silvestris 0.0
#>
#> $`Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512`
#> Elephas maximus Felis silvestris
#> Elephas maximus 0.0 192.2
#> Felis silvestris 192.2 0.0
#> Delphinus delphis 192.2 173.6
#> Delphinus delphis
#> Elephas maximus 192.2
#> Felis silvestris 173.6
#> Delphinus delphis 0.0
#>
#> $`Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512`
#> Delphinus delphis Felis silvestris
#> Delphinus delphis 0.0 179.6
#> Felis silvestris 179.6 0.0
#> Elephas maximus 221.6 221.6
#> Elephas maximus
#> Delphinus delphis 221.6
#> Felis silvestris 221.6
#> Elephas maximus 0.0
#>
#> $`Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, Sudhir Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32 (4): 835-845`
#> Felis silvestris Delphinus delphis
#> Felis silvestris 0.0000 156.7850
#> Delphinus delphis 156.7850 0.0000
#> Elephas maximus 210.0193 210.0193
#> Gallus gallus 641.0476 641.0476
#> Elephas maximus Gallus gallus
#> Felis silvestris 210.0193 641.0476
#> Delphinus delphis 210.0193 641.0476
#> Elephas maximus 0.0000 641.0476
#> Gallus gallus 641.0476 0.0000
#>
#> attr(,"class")
#> [1] "datelifeResult"
#> attr(,"datelife_query")
#> $cleaned_names
#> [1] "Elephas maximus" "Delphinus delphis" "Felis silvestris"
#> [4] "Gallus gallus"
#>
#> $ott_ids
#> NULL
#>
#> $phy
#>
#> Phylogenetic tree with 4 tips and 3 internal nodes.
#>
#> Tip labels:
#> Elephas_maximus, Delphinus_delphis, Felis_silvestris, Gallus_gallus
#>
#> Rooted; no branch lengths.
#>
#> attr(,"class")
#> [1] "datelifeQuery"summary_format = "newick_sdm"
newick_sdm <- datelife::datelife_search(input = my_datelife_query,
summary_format = "newick_sdm")datelife_search output “newick_sdm”
summary_format = "newick_median"
newick_median <- datelife::datelife_search(input = my_datelife_query,
summary_format = "newick_median")datelife_search output “newick_median”
#> ... Running a DateLife search.
#> ... Getting a DateLife result.
#> DateLife result obtained!
#> Trying with overlap = 2
#> Registered S3 method overwritten by 'compare':
#> method from
#> print.comparison testthat
#> Success!
#> ... Calculating a median summary chronogram.
#> Source chronograms from:
#> 1: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512
#> 2: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512
#> 3: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512
#> 4: Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, Sudhir Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32 (4): 835-845
#> Input taxa presence across source chronograms:
#> taxon chronograms
#> 1 Elephas maximus 4/4
#> 2 Delphinus delphis 4/4
#> 3 Felis silvestris 4/4
#> 4 Gallus gallus 1/4
#> Input taxa completely absent from source chronograms:
#> taxon
#> 1 None
#> DateLife search done!
#> [1] "((Elephas_maximus:103.154831,(Delphinus_delphis:87.650002,Felis_silvestris:87.650002)n3:15.504829)n2:217.369003,Gallus_gallus:320.523834)n1:1;"
#> attr(,"datelife_result")
#> $`Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512`
#> Elephas maximus Delphinus delphis
#> Elephas maximus 0.0 202.6
#> Delphinus delphis 202.6 0.0
#> Felis silvestris 202.6 177.0
#> Felis silvestris
#> Elephas maximus 202.6
#> Delphinus delphis 177.0
#> Felis silvestris 0.0
#>
#> $`Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512`
#> Elephas maximus Felis silvestris
#> Elephas maximus 0.0 192.2
#> Felis silvestris 192.2 0.0
#> Delphinus delphis 192.2 173.6
#> Delphinus delphis
#> Elephas maximus 192.2
#> Felis silvestris 173.6
#> Delphinus delphis 0.0
#>
#> $`Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512`
#> Delphinus delphis Felis silvestris
#> Delphinus delphis 0.0 179.6
#> Felis silvestris 179.6 0.0
#> Elephas maximus 221.6 221.6
#> Elephas maximus
#> Delphinus delphis 221.6
#> Felis silvestris 221.6
#> Elephas maximus 0.0
#>
#> $`Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, Sudhir Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32 (4): 835-845`
#> Felis silvestris Delphinus delphis
#> Felis silvestris 0.0000 156.7850
#> Delphinus delphis 156.7850 0.0000
#> Elephas maximus 210.0193 210.0193
#> Gallus gallus 641.0476 641.0476
#> Elephas maximus Gallus gallus
#> Felis silvestris 210.0193 641.0476
#> Delphinus delphis 210.0193 641.0476
#> Elephas maximus 0.0000 641.0476
#> Gallus gallus 641.0476 0.0000
#>
#> attr(,"class")
#> [1] "datelifeResult"
#> attr(,"datelife_query")
#> $cleaned_names
#> [1] "Elephas maximus" "Delphinus delphis" "Felis silvestris"
#> [4] "Gallus gallus"
#>
#> $ott_ids
#> NULL
#>
#> $phy
#>
#> Phylogenetic tree with 4 tips and 3 internal nodes.
#>
#> Tip labels:
#> Elephas_maximus, Delphinus_delphis, Felis_silvestris, Gallus_gallus
#>
#> Rooted; no branch lengths.
#>
#> attr(,"class")
#> [1] "datelifeQuery"
phylo objects
summary_format = "phylo_sdm"
phylo_sdm <- datelife::datelife_search(input = my_datelife_query,
summary_format = "phylo_sdm")datelife_search output
summary_format = "phylo_median"
phylo_median <- datelife::datelife_search(input = my_datelife_query,
summary_format = "phylo_median")datelife_search output “phylo_median”
#> ... Running a DateLife search.
#> ... Getting a DateLife result.
#> DateLife result obtained!
#> Trying with overlap = 2
#> Success!
#> ... Calculating a median summary chronogram.
#> Source chronograms from:
#> 1: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512
#> 2: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512
#> 3: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512
#> 4: Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, Sudhir Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32 (4): 835-845
#> Input taxa presence across source chronograms:
#> taxon chronograms
#> 1 Elephas maximus 4/4
#> 2 Delphinus delphis 4/4
#> 3 Felis silvestris 4/4
#> 4 Gallus gallus 1/4
#> Input taxa completely absent from source chronograms:
#> taxon
#> 1 None
#> DateLife search done!
#>
#> Phylogenetic tree with 4 tips and 3 internal nodes.
#>
#> Tip labels:
#> Elephas_maximus, Delphinus_delphis, Felis_silvestris, Gallus_gallus
#> Node labels:
#> n1, n2, n3
#>
#> Rooted; includes branch lengths.summary_format = "phylo_all"
phylo_all <- datelife::datelife_search(input = my_datelife_query,
summary_format = "phylo_all")datelife_search output “phylo_all”
#> ... Running a DateLife search.
#> ... Getting a DateLife result.
#> DateLife result obtained!
#> Source chronograms from:
#> 1: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512
#> 2: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512
#> 3: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512
#> 4: Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, Sudhir Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32 (4): 835-845
#> Input taxa presence across source chronograms:
#> taxon chronograms
#> 1 Elephas maximus 4/4
#> 2 Delphinus delphis 4/4
#> 3 Felis silvestris 4/4
#> 4 Gallus gallus 1/4
#> Input taxa completely absent from source chronograms:
#> taxon
#> 1 None
#> DateLife search done!
#> 4 phylogenetic treessummary_format = "phylo_biggest"
phylo_biggest <- datelife::datelife_search(input = my_datelife_query,
summary_format = "phylo_biggest")datelife_search output “phylo_biggest”
#> ... Running a DateLife search.
#> ... Getting a DateLife result.
#> DateLife result obtained!
#> Source chronograms from:
#> 1: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512
#> 2: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512
#> 3: Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512
#> 4: Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, Sudhir Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32 (4): 835-845
#> Input taxa presence across source chronograms:
#> taxon chronograms
#> 1 Elephas maximus 4/4
#> 2 Delphinus delphis 4/4
#> 3 Felis silvestris 4/4
#> 4 Gallus gallus 1/4
#> Input taxa completely absent from source chronograms:
#> taxon
#> 1 None
#> DateLife search done!
#>
#> Phylogenetic tree with 4 tips and 3 internal nodes.
#>
#> Tip labels:
#> Gallus_gallus, Felis_silvestris, Delphinus_delphis, Elephas_maximus
#>
#> Rooted; includes branch lengths.Summary tables
summary_format = "html" returns a summary table in
“html” format that cns be open and read with any web browser.
html <- datelife::datelife_search(input = my_datelife_query,
summary_format = "html")datelife_search output “html”
#> ... Running a DateLife search.
#> ... Getting a DateLife result.
#> DateLife result obtained!
#> Input taxa presence across source chronograms:
#> taxon chronograms
#> 1 Elephas maximus 4/4
#> 2 Delphinus delphis 4/4
#> 3 Felis silvestris 4/4
#> 4 Gallus gallus 1/4
#> Input taxa completely absent from source chronograms:
#> taxon
#> 1 None
#> DateLife search done!
#> [1] "<table border='1'><tr><th>MRCA Age (MY)</th><th>Ntax</th><th>Citation</th><th>Newick</th></tr><tr><td>101.3</td><td>3</td><td>Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512</td><td>((Felis_silvestris:88.5,Delphinus_delphis:88.5):12.8,Elephas_maximus:101.3);</td></tr><tr><td>96.1</td><td>3</td><td>Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512</td><td>((Delphinus_delphis:86.8,Felis_silvestris:86.8):9.3,Elephas_maximus:96.1);</td></tr><tr><td>110.8</td><td>3</td><td>Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512</td><td>((Felis_silvestris:89.8,Delphinus_delphis:89.8):21,Elephas_maximus:110.8);</td></tr><tr><td>320.5238235</td><td>4</td><td>Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, Sudhir Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32 (4): 835-845</td><td>((Elephas_maximus:105.009658,(Felis_silvestris:78.392518,Delphinus_delphis:78.392517):26.617141):215.5141645,Gallus_gallus:320.5238235);</td></tr></table>"
#> attr(,"datelife_result")
#> $`Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512`
#> Elephas maximus Delphinus delphis
#> Elephas maximus 0.0 202.6
#> Delphinus delphis 202.6 0.0
#> Felis silvestris 202.6 177.0
#> Felis silvestris
#> Elephas maximus 202.6
#> Delphinus delphis 177.0
#> Felis silvestris 0.0
#>
#> $`Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512`
#> Elephas maximus Felis silvestris
#> Elephas maximus 0.0 192.2
#> Felis silvestris 192.2 0.0
#> Delphinus delphis 192.2 173.6
#> Delphinus delphis
#> Elephas maximus 192.2
#> Felis silvestris 173.6
#> Delphinus delphis 0.0
#>
#> $`Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512`
#> Delphinus delphis Felis silvestris
#> Delphinus delphis 0.0 179.6
#> Felis silvestris 179.6 0.0
#> Elephas maximus 221.6 221.6
#> Elephas maximus
#> Delphinus delphis 221.6
#> Felis silvestris 221.6
#> Elephas maximus 0.0
#>
#> $`Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, Sudhir Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32 (4): 835-845`
#> Felis silvestris Delphinus delphis
#> Felis silvestris 0.0000 156.7850
#> Delphinus delphis 156.7850 0.0000
#> Elephas maximus 210.0193 210.0193
#> Gallus gallus 641.0476 641.0476
#> Elephas maximus Gallus gallus
#> Felis silvestris 210.0193 641.0476
#> Delphinus delphis 210.0193 641.0476
#> Elephas maximus 0.0000 641.0476
#> Gallus gallus 641.0476 0.0000
#>
#> attr(,"class")
#> [1] "datelifeResult"
#> attr(,"datelife_query")
#> $cleaned_names
#> [1] "Elephas maximus" "Delphinus delphis" "Felis silvestris"
#> [4] "Gallus gallus"
#>
#> $ott_ids
#> NULL
#>
#> $phy
#>
#> Phylogenetic tree with 4 tips and 3 internal nodes.
#>
#> Tip labels:
#> Elephas_maximus, Delphinus_delphis, Felis_silvestris, Gallus_gallus
#>
#> Rooted; no branch lengths.
#>
#> attr(,"class")
#> [1] "datelifeQuery"summary_format = "data_frame"
data_frame <- datelife::datelife_search(input = my_datelife_query,
summary_format = "data_frame")datelife_search output “data_frame”
#> ... Running a DateLife search.
#> ... Getting a DateLife result.
#> DateLife result obtained!
#> Input taxa presence across source chronograms:
#> taxon chronograms
#> 1 Elephas maximus 4/4
#> 2 Delphinus delphis 4/4
#> 3 Felis silvestris 4/4
#> 4 Gallus gallus 1/4
#> Input taxa completely absent from source chronograms:
#> taxon
#> 1 None
#> DateLife search done!
#> Age Ntax
#> 1 101.3000 3
#> 2 96.1000 3
#> 3 110.8000 3
#> 4 320.5238 4
#> Citation
#> 1 Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512
#> 2 Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512
#> 3 Bininda-Emonds, Olaf R. P., Marcel Cardillo, Kate E. Jones, Ross D. E. MacPhee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis. 2007. The delayed rise of present-day mammals. Nature 446 (7135): 507-512
#> 4 Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, Sudhir Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32 (4): 835-845
#> Newick
#> 1 ((Felis_silvestris:88.5,Delphinus_delphis:88.5):12.8,Elephas_maximus:101.3);
#> 2 ((Delphinus_delphis:86.8,Felis_silvestris:86.8):9.3,Elephas_maximus:96.1);
#> 3 ((Felis_silvestris:89.8,Delphinus_delphis:89.8):21,Elephas_maximus:110.8);
#> 4 ((Elephas_maximus:105.009658,(Felis_silvestris:78.392518,Delphinus_delphis:78.392517):26.617141):215.5141645,Gallus_gallus:320.5238235);