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Last data update: 2014.03.03

R: Compute tip-specific macroevolutionary rates from 'bammdata'...

getTipRates

R Documentation

Compute tip-specific macroevolutionary rates from `bammdata` object

Description

Return speciation, extinction, net diversification, or Brownian motion trait rates for all species in the phylogeny from BAMM output.

Usage

getTipRates(ephy, returnNetDiv = FALSE, statistic = "mean")

Arguments

`ephy`	An object of class `bammdata`.
`returnNetDiv`	Logical. If `TRUE`, then net diversification rates are returned, if `FALSE`, then both speciation and extinction rates are returned. If `ephy` is of type `trait`, then this is ignored.
`statistic`	Determines how the average tip rates should be calculated. Can be either `mean` or `median`.

Value

Returns a list with the following elements:

If ephy type is 'diversification':

lambda A matrix of tip speciation rates with species as rows, and posterior samples as columns.
mu A matrix of tip extinction rates with species as rows, and posterior samples as columns.
lambda.avg A vector of average tip speciation rates, averaged with mean or median, depending on selected option for statistic. The vector is named with species names.
mu.avg A vector of average tip extinction rates, averaged with mean or median, depending on selected option for statistic. The vector is named with species names.

If ephy type is 'diversification' and returnNetDiv = TRUE:

netdiv A matrix of tip net diversification rates with species as rows, and posterior samples as columns.
netdiv.avg A vector of average tip net diversification rates, averaged with mean or median, depending on selected option for statistic. The vector is named with species names.

If ephy type is 'trait':

beta A matrix of tip phenotypic rates with species as rows, and posterior samples as columns.
beta.avg A vector of average tip phenotypic rates, averaged with mean or median, depending on selected option for statistic. The vector is named with species names.

Author(s)

Pascal Title

Examples

data(whales, events.whales)
ephy <- getEventData(whales, events.whales, burnin=0.25, nsamples = 500)

# return a vector of average species-specific speciation rates.
meanlam <- getTipRates(ephy, returnNetDiv = FALSE,
                       statistic = 'mean')$lambda.avg
meanlam

# return a vector of median species-specific net diversification rates.
ndr <- getTipRates(ephy, returnNetDiv = TRUE,
                   statistic = 'median')$netdiv.avg

# Return mean species-specific speciation rates from all posterior 
# samples in the code{bamm-data} object.
lam <- getTipRates(ephy, returnNetDiv = FALSE, statistic = 'mean')$lambda
rowMeans(lam)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(BAMMtools)
Loading required package: ape
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/BAMMtools/getTipRates.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getTipRates
> ### Title: Compute tip-specific macroevolutionary rates from 'bammdata'
> ###   object
> ### Aliases: getTipRates
> ### Keywords: models
> 
> ### ** Examples
> 
> data(whales, events.whales)
> ephy <- getEventData(whales, events.whales, burnin=0.25, nsamples = 500)
Processing event data from data.frame

Discarded as burnin: GENERATIONS <  2495000
Analyzing  500  samples from posterior

Setting recursive sequence on tree...

Done with recursive sequence

> 
> # return a vector of average species-specific speciation rates.
> meanlam <- getTipRates(ephy, returnNetDiv = FALSE,
+                        statistic = 'mean')$lambda.avg
> meanlam
         Balaena_mysticetus         Eubalaena_australis 
                 0.07350631                  0.08010124 
        Eubalaena_glacialis          Eubalaena_japonica 
                 0.08078107                  0.08200171 
          Caperea_marginata       Eschrichtius_robustus 
                 0.07397476                  0.07228203 
 Balaenoptera_acutorostrata    Balaenoptera_bonaerensis 
                 0.07080280                  0.07080280 
      Balaenoptera_physalus      Megaptera_novaeangliae 
                 0.07099425                  0.07118497 
      Balaenoptera_musculus         Balaenoptera_omurai 
                 0.07328149                  0.07193650 
      Balaenoptera_borealis         Balaenoptera_brydei 
                 0.07210983                  0.07250956 
         Balaenoptera_edeni            Physeter_catodon 
                 0.07083698                  0.07080890 
            Kogia_breviceps                 Kogia_simus 
                 0.07249179                  0.07226971 
       Platanista_gangetica            Platanista_minor 
                 0.09060065                  0.09060065 
       Tasmacetus_shepherdi           Berardius_arnuxii 
                 0.07161708                  0.07239643 
          Berardius_bairdii         Ziphius_cavirostris 
                 0.07235662                  0.07381461 
      Indopacetus_pacificus       Hyperoodon_ampullatus 
                 0.07086031                  0.07089680 
      Hyperoodon_planifrons           Mesoplodon_bidens 
                 0.07155392                  0.07288772 
       Mesoplodon_traversii       Mesoplodon_ginkgodens 
                 0.07147777                  0.07185501 
       Mesoplodon_europaeus            Mesoplodon_mirus 
                 0.07334756                  0.07147777 
        Mesoplodon_bowdoini       Mesoplodon_carlhubbsi 
                 0.07271551                  0.07147777 
        Mesoplodon_layardii          Mesoplodon_hectori 
                 0.07147777                  0.07168690 
    Mesoplodon_densirostris       Mesoplodon_stejnegeri 
                 0.07147777                  0.07153767 
           Mesoplodon_grayi          Mesoplodon_perrini 
                 0.07147777                  0.07191283 
      Mesoplodon_peruvianus          Lipotes_vexillifer 
                 0.07147777                  0.07216747 
           Inia_geoffrensis      Pontoporia_blainvillei 
                 0.07324275                  0.07167176 
      Delphinapterus_leucas           Monodon_monoceros 
                 0.11421720                  0.11382873 
   Neophocaena_phocaenoides           Phocoena_phocoena 
                 0.11526452                  0.11497718 
         Phocoenoides_dalli              Phocoena_sinus 
                 0.11704558                  0.11695435 
         Phocoena_dioptrica        Phocoena_spinipinnis 
                 0.11539118                  0.11523495 
               Orcinus_orca       Orcaella_brevirostris 
                 0.18395288                  0.20690964 
            Grampus_griseus        Pseudorca_crassidens 
                 0.20845818                  0.20672038 
           Feresa_attenuata       Peponocephala_electra 
                 0.20702529                  0.20878570 
 Globicephala_macrorhynchus          Globicephala_melas 
                 0.20750534                  0.20734939 
 Lagenorhynchus_albirostris       Lagenorhynchus_acutus 
                 0.20925967                  0.21083272 
      Lissodelphis_borealis        Lissodelphis_peronii 
                 0.20899274                  0.20899274 
    Cephalorhynchus_hectori Cephalorhynchus_commersonii 
                 0.20889205                  0.20922540 
   Cephalorhynchus_eutropia     Lagenorhynchus_obscurus 
                 0.20922540                  0.20947731 
 Lagenorhynchus_obliquidens  Cephalorhynchus_heavisidii 
                 0.21001787                  0.20951550 
   Lagenorhynchus_australis     Lagenorhynchus_cruciger 
                 0.21070240                  0.20911650 
          Steno_bredanensis         Sotalia_fluviatilis 
                 0.20988384                  0.20891775 
         Sotalia_guianensis         Lagenodelphis_hosei 
                 0.20922540                  0.20964552 
      Stenella_longirostris          Stenella_attenuata 
                 0.20964552                  0.20975303 
           Tursiops_aduncus          Tursiops_truncatus 
                 0.20978923                  0.20975303 
            Sousa_chinensis            Stenella_clymene 
                 0.20974937                  0.20964552 
      Stenella_coeruleoalba          Stenella_frontalis 
                 0.20964552                  0.20964552 
       Delphinus_tropicalis          Delphinus_capensis 
                 0.21127939                  0.21127939 
          Delphinus_delphis 
                 0.21127939 
> 
> # return a vector of median species-specific net diversification rates.
> ndr <- getTipRates(ephy, returnNetDiv = TRUE,
+                    statistic = 'median')$netdiv.avg
> 
> # Return mean species-specific speciation rates from all posterior 
> # samples in the code{bamm-data} object.
> lam <- getTipRates(ephy, returnNetDiv = FALSE, statistic = 'mean')$lambda
> rowMeans(lam)
         Balaena_mysticetus         Eubalaena_australis 
                 0.07350631                  0.08010124 
        Eubalaena_glacialis          Eubalaena_japonica 
                 0.08078107                  0.08200171 
          Caperea_marginata       Eschrichtius_robustus 
                 0.07397476                  0.07228203 
 Balaenoptera_acutorostrata    Balaenoptera_bonaerensis 
                 0.07080280                  0.07080280 
      Balaenoptera_physalus      Megaptera_novaeangliae 
                 0.07099425                  0.07118497 
      Balaenoptera_musculus         Balaenoptera_omurai 
                 0.07328149                  0.07193650 
      Balaenoptera_borealis         Balaenoptera_brydei 
                 0.07210983                  0.07250956 
         Balaenoptera_edeni            Physeter_catodon 
                 0.07083698                  0.07080890 
            Kogia_breviceps                 Kogia_simus 
                 0.07249179                  0.07226971 
       Platanista_gangetica            Platanista_minor 
                 0.09060065                  0.09060065 
       Tasmacetus_shepherdi           Berardius_arnuxii 
                 0.07161708                  0.07239643 
          Berardius_bairdii         Ziphius_cavirostris 
                 0.07235662                  0.07381461 
      Indopacetus_pacificus       Hyperoodon_ampullatus 
                 0.07086031                  0.07089680 
      Hyperoodon_planifrons           Mesoplodon_bidens 
                 0.07155392                  0.07288772 
       Mesoplodon_traversii       Mesoplodon_ginkgodens 
                 0.07147777                  0.07185501 
       Mesoplodon_europaeus            Mesoplodon_mirus 
                 0.07334756                  0.07147777 
        Mesoplodon_bowdoini       Mesoplodon_carlhubbsi 
                 0.07271551                  0.07147777 
        Mesoplodon_layardii          Mesoplodon_hectori 
                 0.07147777                  0.07168690 
    Mesoplodon_densirostris       Mesoplodon_stejnegeri 
                 0.07147777                  0.07153767 
           Mesoplodon_grayi          Mesoplodon_perrini 
                 0.07147777                  0.07191283 
      Mesoplodon_peruvianus          Lipotes_vexillifer 
                 0.07147777                  0.07216747 
           Inia_geoffrensis      Pontoporia_blainvillei 
                 0.07324275                  0.07167176 
      Delphinapterus_leucas           Monodon_monoceros 
                 0.11421720                  0.11382873 
   Neophocaena_phocaenoides           Phocoena_phocoena 
                 0.11526452                  0.11497718 
         Phocoenoides_dalli              Phocoena_sinus 
                 0.11704558                  0.11695435 
         Phocoena_dioptrica        Phocoena_spinipinnis 
                 0.11539118                  0.11523495 
               Orcinus_orca       Orcaella_brevirostris 
                 0.18395288                  0.20690964 
            Grampus_griseus        Pseudorca_crassidens 
                 0.20845818                  0.20672038 
           Feresa_attenuata       Peponocephala_electra 
                 0.20702529                  0.20878570 
 Globicephala_macrorhynchus          Globicephala_melas 
                 0.20750534                  0.20734939 
 Lagenorhynchus_albirostris       Lagenorhynchus_acutus 
                 0.20925967                  0.21083272 
      Lissodelphis_borealis        Lissodelphis_peronii 
                 0.20899274                  0.20899274 
    Cephalorhynchus_hectori Cephalorhynchus_commersonii 
                 0.20889205                  0.20922540 
   Cephalorhynchus_eutropia     Lagenorhynchus_obscurus 
                 0.20922540                  0.20947731 
 Lagenorhynchus_obliquidens  Cephalorhynchus_heavisidii 
                 0.21001787                  0.20951550 
   Lagenorhynchus_australis     Lagenorhynchus_cruciger 
                 0.21070240                  0.20911650 
          Steno_bredanensis         Sotalia_fluviatilis 
                 0.20988384                  0.20891775 
         Sotalia_guianensis         Lagenodelphis_hosei 
                 0.20922540                  0.20964552 
      Stenella_longirostris          Stenella_attenuata 
                 0.20964552                  0.20975303 
           Tursiops_aduncus          Tursiops_truncatus 
                 0.20978923                  0.20975303 
            Sousa_chinensis            Stenella_clymene 
                 0.20974937                  0.20964552 
      Stenella_coeruleoalba          Stenella_frontalis 
                 0.20964552                  0.20964552 
       Delphinus_tropicalis          Delphinus_capensis 
                 0.21127939                  0.21127939 
          Delphinus_delphis 
                 0.21127939 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>

Compute tip-specific macroevolutionary rates from bammdata object