Getting Started with {fibre} • fibre

library(phyf)
#> 
#> Attaching package: 'phyf'
#> The following object is masked from 'package:stats':
#> 
#>     pf
library(fibre)
library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union

We start with a phylogeny and some traits we want to model. fibre uses the phyf package to keep a phylogeny stored in the phylogenetic flow (pf) format along with the data. We will load a premade pf object for this example, but later we will see how to make your own pf object from a phylogeny stored in as an ape::phylo object.

vert_bmr
#> # A tibble: 1,712 × 8
#>    label                 is_tip phlo            lnBMR lnMass lnMass2  lnGS  endo
#>    <chr>                 <lgl>  <pfc>           <dbl>  <dbl>   <dbl> <dbl> <dbl>
#>  1 Ornithorhynchus_anat… TRUE   ◎──   7…atinus   6.33   6.54    42.8  1.12     1
#>  2 Tachyglossus_aculeat… TRUE   ◎── 71.…leatus   6.98   8.05    64.7  1.06     1
#>  3 Zaglossus_bruijni     TRUE   ◎── 71.…ruijni   7.93   9.24    85.4 NA        1
#>  4 Cyclopes_didactylus   TRUE   ◎── 71.…ctylus   5.73   5.48    30.0 NA        1
#>  5 Myrmecophaga_tridact… TRUE   ◎── 71.…actyla   8.82  10.3    107.   1.46     1
#>  6 Tamandua_mexicana     TRUE   ◎── 71.…xicana   7.81   8.29    68.7 NA        1
#>  7 Tamandua_tetradactyla TRUE   ◎── 71.…actyla   7.83   8.16    66.6  1.41     1
#>  8 Choloepus_hoffmanni   TRUE   ◎── 71.…fmanni   7.49   8.23    67.8 NA        1
#>  9 Bradypus_variegatus   TRUE   ◎── 71.…egatus   7.52   8.24    67.9  1.44     1
#> 10 Priodontes_maximus    TRUE   ◎── 71.…aximus   9.05  10.7    115.   1.50     1
#> # … with 1,702 more rows