Case study: the Fringillidae

str(dquery) #> List of 3 #> $ cleaned_names: Named chr [1:289] "Crithagra sulphurata" "Crithagra #> citrinelloides" "Crithagra mozambica" "Crithagra capistrata" ... #> ..- attr(*, "names")= chr [1:289] "Fringillidae1" "Fringillidae2" #> "Fringillidae3" "Fringillidae4" ... #> $ ott_ids : Named int [1:289] 903281 328908 1083721 901359 318589 #> 455546 903271 405220 242220 455541 ... #> ..- attr(*, "names")= chr [1:289] "Crithagra sulphurata" "Crithagra #> citrinelloides" "Crithagra mozambica" "Crithagra capistrata" ... #> $ phy : logi NA #> - attr(*, "class")= chr "datelifeQuery"

2. Search the species names across a chronogram database

Load the prebuilt OpenTree chronogram database object names opentree_chronograms:

utils::data("opentree_chronograms", package = "datelife")

Use your datelifeQuery object named dquery to search the chronogram database:

dres <- datelife::get_datelife_result(input = dquery, cache = opentree_chronograms)

#> ... Searching the chronogram database.
#> Search done!
#>
#> Input taxon names were found in 13 chronograms.

Results from the chronogram search are returned as a datelifeResult object, which is a named list of patristic matrices. Each element of the list corresponds to a chronogram that has been translated to a distance matrix or patristic matrix. The main reason for this is that pruning is much faster on a matrix than on a phylo object:

class(dres)
#> [1] "datelifeResult"

typeof(dres)
#> [1] "list"

names(dres)

names on our datelifeResult object

#> [1] "Hooper, Daniel M., Trevor D. Price. 2017. Chromosomal inversion differences correlate with range overlap in passerine birds. Nature Ecology & Evolution 1 (10): 1526-1534"

#> [2] "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"

#> [3] "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"

#> [4] "Claramunt, Santiago, Joel Cracraft. 2015. A new time tree reveals Earth historys imprint on the evolution of modern birds. Science Advances 1 (11): e1501005-e1501005"

#> [5] "Gibb, Gillian C., Ryan England, Gerrit Hartig, P.A. (Trish) McLenachan, Briar L. Taylor Smith, Bennet J. McComish, Alan Cooper, David Penny. 2015. New Zealand passerines help clarify the diversification of major songbird lineages during the Oligocene. Genome Biology and Evolution 7 (11): 2983-2995."

#> [6] "Barker, F. Keith, Kevin J. Burns, John Klicka, Scott M. Lanyon, Irby J. Lovette. 2015. New insights into New World biogeography: An integrated view from the phylogeny of blackbirds, cardinals, sparrows, tanagers, warblers, and allies. The Auk 132 (2): 333-348."
#> [7] "Barker, F. Keith, Kevin J. Burns, John Klicka, Scott M. Lanyon, Irby J. Lovette. 2015. New insights into New World biogeography: An integrated view from the phylogeny of blackbirds, cardinals, sparrows, tanagers, warblers, and allies. The Auk 132 (2): 333-348."
#> [8] "Jetz, W., G. H. Thomas, J. B. Joy, K. Hartmann, A. O. Mooers. 2012. The global diversity of birds in space and time. Nature 491 (7424): 444-448"

#> [9] "Jetz, W., G. H. Thomas, J. B. Joy, K. Hartmann, A. O. Mooers. 2012. The global diversity of birds in space and time. Nature 491 (7424): 444-448"

#> [10] "Barker, F. K., K. J. Burns, J. Klicka, S. M. Lanyon, I. J. Lovette. 2013. Going to extremes: contrasting rates of diversification in a recent radiation of New World passerine birds. Systematic Biology 62 (2): 298-320."
#> [11] "Burns, Kevin J., Allison J. Shultz, Pascal O. Title, Nicholas A. Mason, F. Keith Barker, John Klicka, Scott M. Lanyon, Irby J. Lovette. 2014. Phylogenetics and diversification of tanagers (Passeriformes: Thraupidae), the largest radiation of Neotropical songbirds. Molecular Phylogenetics and Evolution 75: 41-77."
#> [12] "Price, Trevor D., Daniel M. Hooper, Caitlyn D. Buchanan, Ulf S. Johansson, D. Thomas Tietze, Per Alström, Urban Olsson, Mousumi Ghosh-Harihar, Farah Ishtiaq, Sandeep K. Gupta, Jochen Martens, Bettina Harr, Pratap Singh, Dhananjai Mohan. 2014. Niche filling slows the diversification of Himalayan songbirds. Nature 509: 222-225."

#> [13] "Price, Trevor D., Daniel M. Hooper, Caitlyn D. Buchanan, Ulf S. Johansson, D. Thomas Tietze, Per Alström, Urban Olsson, Mousumi Ghosh-Harihar, Farah Ishtiaq, Sandeep K. Gupta, Jochen Martens, Bettina Harr, Pratap Singh, Dhananjai Mohan. 2014. Niche filling slows the diversification of Himalayan songbirds. Nature 509: 222-225."

class(dres[[1]])
#> [1] "matrix" "array"

dsumm <- summary(dres) #> Trying with overlap = 2 #> #> Success! #> #> ... Calculating a median summary chronogram. #> |==========================================================| 100% #> |==========================================================| 100% #> |==========================================================| 100% #> 1 out of 13 chronograms tried: Ok. #> 2 out of 13 chronograms tried: Ok. #> 3 out of 13 chronograms tried: Ok. #> 4 out of 13 chronograms tried: Ok. #> 5 out of 13 chronograms tried: Ok. #> 6 out of 13 chronograms tried: Ok. #> 7 out of 13 chronograms tried: Ok. #> 8 out of 13 chronograms tried: Ok. #> 9 out of 13 chronograms tried: Ok. #> 10 out of 13 chronograms tried: Ok. #> 11 out of 13 chronograms tried: Ok. #> 12 out of 13 chronograms tried: Failed. #> 13 out of 13 chronograms tried: Ok. #> #> Synthesizing 12 chronograms with SDM #> |==========================================================| 100% #> |==========================================================| 100% #> |==========================================================| 100%

Case study: the Fringillidae

1. Processing Fringillidae names

2. Search the species names across a chronogram database

3. Summarizing a `datelifeResult` object

Case study: the Fringillidae

1. Processing Fringillidae names

2. Search the species names across a chronogram database

3. Summarizing a datelifeResult object

3. Summarizing a `datelifeResult` object