This function takes a data.frame of information downloaded from the Paleobiology Database and converts it into .inp format to be used in subsequent analyses. For example, those demonstrated by Liow and Finarelli (2014, Proc. Roy. Soc. B). First, let’s take a look at the format of the data.
load("valid.aves.spp.RData")
head(valid.aves.spp)## oid typ cid tna rnk tid
## 1:3 149835 occ 13264 Ornimegalonyx oteroi 3 290147
## 1:4 150093 occ 18597 Phalacrocorax subvolans n. sp. 3 53350
## 1:5 150094 occ 18597 Proictinia floridana n. sp. 3 53301
## 1:6 150133 occ 13296 Buteo fluviaticus n. sp. 3 100015
## 1:7 150134 occ 13297 Hadrogyps n. gen. aigialeus n. sp. 3 53351
## 1:8 150135 occ 13298 Primapus n. gen. lacki n. sp. 3 53337
## mna mra mid oei oli eag lag
## 1:3 Ornimegalonyx oteroi 3 290147 Pleistocene <NA> 2.588 0.0117
## 1:4 Anhinga subvolans 3 110890 Hemingfordian <NA> 20.430 15.9700
## 1:5 Promilio floridanus 3 117615 Hemingfordian <NA> 20.430 15.9700
## 1:6 Buteo fluviaticus 3 100015 Orellan <NA> 33.900 33.3000
## 1:7 Hadrogyps aigialeus 3 53351 Langhian <NA> 15.970 13.8200
## 1:8 Primapus lacki 3 53337 Ypresian <NA> 56.000 47.8000
## rid cll cln phl phn idt ids eag.1
## 1:3 4396;4396 Aves 36616 Chordata 33815 Ornimegalonyx oteroi NA
## 1:4 4414;4414 Aves 36616 Chordata 33815 Phalacrocorax subvolans NA
## 1:5 4414;4414 Aves 36616 Chordata 33815 Proictinia floridana NA
## 1:6 4415;4415 Aves 36616 Chordata 33815 Buteo fluviaticus NA
## 1:7 4416;4416 Aves 36616 Chordata 33815 Hadrogyps aigialeus NA
## 1:8 4417;4417 Aves 36616 Chordata 33815 Primapus lacki NA
## lag.1 cxi ein lin lng lat gnl gnn
## 1:3 NA 33 33 33 -83.666664 22.58333 Ornimegalonyx 39405
## 1:4 NA 102 102 102 -82.599998 29.70000 Anhinga 39686
## 1:5 NA 102 102 102 -82.599998 29.70000 Promilio 117610
## 1:6 NA 105 105 105 -104.866669 40.90000 Buteo 39325
## 1:7 NA 101 101 101 -118.500000 35.30000 Hadrogyps 53352
## 1:8 NA 109 109 109 -0.683333 50.78333 Primapus 39422
## fml fmn odl odn rss rst eid idf
## 1:3 Strigidae 39403 Strigiformes 39397 <NA> <NA> NA <NA>
## 1:4 Anhingidae 39685 Pelecaniformes 36634 n. sp. <NA> NA <NA>
## 1:5 Accipitridae 39323 Falconiformes 39316 n. sp. <NA> NA <NA>
## 1:6 Accipitridae 39323 Falconiformes 39316 n. sp. <NA> NA <NA>
## 1:7 Cathartidae 99060 <NA> NA n. sp. n. gen. NA <NA>
## 1:8 Aegialornithidae 39419 Apodiformes 39417 n. sp. n. gen. NA <NA>
## rsf
## 1:3 <NA>
## 1:4 <NA>
## 1:5 <NA>
## 1:6 <NA>
## 1:7 <NA>
## 1:8 <NA>The function is provided here, and it takes a few arguments:
- pbdb.data - a
data.frameof data downloaded from the PBDB - age.interval - a
numericargument of length 1 specifying the duration of each age interval - max.age - a
numericvector of length 1 specifying the maximum age of the analysis - file.out - a
charactervector for the file name to export. Note, you don’t need to specify ‘.inp’ at the end. - target.orders - a
charactervector specifying a clade of interest. This will be a 1 in the first grouping column, with all other orders in the second grouping column
The function automatically writes the output to the current working directory, with the name specified when the function is called.
source("make.inp.format.R")
library(dplyr)
make.inp.format(pbdb.data = valid.aves.spp,
age.interval=2,
max.age = 66,
file.out="myFile",
target.orders = "Passeriformes")We can load the output back into R to have a look at it
output <- readLines("myFile.inp")
head(output)## [1] "000000000000000000000000000000011 0 1 ;"
## [2] "000000000000000000000011110000000 0 1 ;"
## [3] "000000000000000000000011110000000 0 1 ;"
## [4] "000000000000000010000000000000000 0 1 ;"
## [5] "000000000000000000000000011000000 0 1 ;"
## [6] "000001111100000000000000000000000 0 1 ;"