Name: paleobioDB
Owner: rOpenSci
Description: R interface to the Paleobiology Database
Created: 2014-01-24 17:09:05.0
Updated: 2017-10-06 15:54:54.0
Pushed: 2018-01-13 17:58:00.0
Size: 18355
Language: R
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paleobioDB is a package for downloading, visualizing and processing data from Paleobiology Database.
Install
Install paleobioDB from CRAN
all.packages("paleobioDB")
ary(paleobioDB)
Install paleobioDB developing version from github
all.packages("devtools")
ary(devtools)
all_github("ropensci/paleobioDB")
ary(paleobioDB)
General overview
paleobioDB version 0.5 has 19 functions to wrap each endpoint of the PaleobioDB API, plus 8 functions to visualize and process the fossil data. The API documentation for the Paleobiology Database can be found here.
pbdb_occurrences
e.g., to download all the fossil data that belongs to the family Canidae, set base_name = “Canidae”.
nidae<- pbdb_occurrences (limit="all",
base_name="canidae", vocab="pbdb",
interval="Quaternary",
show=c("coords", "phylo", "ident"))
(canidae)
offee
ccurrence_no record_type collection_no taxon_name taxon_rank taxon_no
50070 occurrence 13293 Cuon sp. genus 41204
86572 occurrence 18320 Canis cf. sp. genus 41198
86573 occurrence 18320 Vulpes sp. genus 41248
86574 occurrence 18320 Borophagus sp. genus 41196
92926 occurrence 19617 Canis edwardii species 44838
92927 occurrence 19617 Canis armbrusteri cf. species 44827
atched_rank early_interval late_interval early_age late_age reference_no
Middle Pleistocene Late Pleistocene 0.81 0.0117 4412
Late Hemphillian Blancan 10.300 1.8000 6086
Late Hemphillian Blancan 10.300 1.8000 6086
Late Hemphillian Blancan 10.300 1.8000 6086
Blancan Irvingtonian 4.900 0.3000 2673
Blancan Irvingtonian 4.900 0.3000 2673
ng lat family family_no order order_no class class_no phylum
11.56667 22.76667 Canidae 41189 Carnivora 36905 Mammalia 36651 Chordata
85.79195 40.45444 Canidae 41189 Carnivora 36905 Mammalia 36651 Chordata
85.79195 40.45444 Canidae 41189 Carnivora 36905 Mammalia 36651 Chordata
85.79195 40.45444 Canidae 41189 Carnivora 36905 Mammalia 36651 Chordata
112.40000 35.70000 Canidae 41189 Carnivora 36905 Mammalia 36651 Chordata
112.40000 35.70000 Canidae 41189 Carnivora 36905 Mammalia 36651 Chordata
hylum_no genus_name species_name genus_reso reid_no species_reso matched_name
3815 Cuon sp. <NA> NA <NA> <NA>
3815 Canis sp. cf. NA <NA> <NA>
3815 Vulpes sp. <NA> NA <NA> <NA>
3815 Borophagus sp. <NA> NA <NA> <NA>
3815 Canis edwardii <NA> 8376 <NA> <NA>
3815 Canis armbrusteri <NA> 8377 cf. <NA>
ubgenus_name subgenus_reso
NA> <NA>
NA> <NA>
NA> <NA>
NA> <NA>
NA> <NA>
NA> <NA>
CAUTION WITH THE RAW DATA
Beware of synonyms and errors, they could twist your estimations about species richness, evolutionary and extinction rates, etc. paleobioDB users should be critical about the raw data downloaded from the database and filter the data before analyzing it.
For instance, when using “base_name” for downloading the information with the function pbdb_occurrences, check out the synonyms and errors that could appear in “taxon_name”, “genus_name”, etc. In our example, in canidae$genus_name there are errors: “Canidae” and “Caninae” appeared as genus names. If not eliminated, they will increase the richness of genera.
pbdb_map
Returns a map with the species occurrences.
db_map(canidae)
pbdb_map_occur Returns a map and a raster object with the sampling effort (number of fossil records per cell).
db_map_occur (canidae, res= 5)
lass : RasterLayer
imensions : 34, 74, 2516 (nrow, ncol, ncell)
esolution : 5, 5 (x, y)
xtent : -179.9572, 190.0428, -86.42609, 83.57391 (xmin, ## xmax, ymin, ymax)
oord. ref. : NA
ata source : in memory
ames : layer
alues : 1, 40 (min, max)
pbdb_map_richness Returns a map and a raster object with the number of different species, genera, family, etc. per cell. The user can change the resolution of the cells.
db_map_richness (canidae, res= 5, rank="species")
lass : RasterLayer
imensions : 34, 74, 2516 (nrow, ncol, ncell)
esolution : 5, 5 (x, y)
xtent : -179.9572, 190.0428, -86.42609, 83.57391 (xmin, xmax, ymin, ymax)
oord. ref. : NA
ata source : in memory
ames : layer
alues : 1, 12 (min, max)
pbdb_temporal_range
Returns a dataframe and a plot with the time span of the species, genera, families, etc. in your query.
db_temp_range (canidae, rank="species")
max min
anis brevirostris 5.3330 0.0000
anis mesomelas 5.3330 0.
lopex praeglacialis 5.3330 0.0117
yctereutes megamastoides 5.3330 0.0117
ulpes atlantica 5.3330 0.0117
anis latrans 4.9000 0.0000
pbdb_richness
Returns a dataframe and a plot with the number of species (or genera, families, etc.) across time. You should set the temporal extent and the temporal resolution for the steps.
db_richness (canidae, rank="species", temporal_extent=c(0,10), res=1)
offee
abels2 richness
=1 23
-2 56
-3 53
-4 19
-5 18
-6 5
-7 0
-8 0
-9 0
-10 0
10 0
pbdb_orig_ext
Returns a dataframe and a plot with the number of new appearances and last appearances of species, genera, families, etc. in your query across the time. You should set the temporal extent and the resolution of the steps.
olutionary rates= orig_ext=1
db_orig_ext (canidae, rank="species", orig_ext=1, temporal_extent=c(0,10), res=1)
new ext
-2 to 0-1 0 28
-3 to 1-2 34 6
-4 to 2-3 1 0
-5 to 3-4 13 0
-6 to 4-5 5 0
-7 to 5-6 0 0
-8 to 6-7 0 0
-9 to 7-8 0 0
-10 to 8-9 0 0
tinction rates= orig_ext=2
_orig_ext(canidae, rank="species", orig_ext=2, temporal_extent=c(0,10), res=1)
new ext
-2 to 0-1 0 28
-3 to 1-2 34 6
-4 to 2-3 1 0
-5 to 3-4 13 0
-6 to 4-5 5 0
-7 to 5-6 0 0
-8 to 6-7 0 0
-9 to 7-8 0 0
-10 to 8-9 0 0
pbdb_subtaxa
Returns a plot and a dataframe with the number of species, genera, families, etc. in your dataset.
db_subtaxa (canidae, do.plot=TRUE)
pecies genera families orders classes phyla
5 24 1 1 1 1
pbdb_temporal_resolution
Returns a plot and a dataframe with a main summary of the temporal resolution of the fossil records
db_temporal_resolution (canidae)
offee
summary
in. 1st Qu. Median Mean 3rd Qu. Max.
.0117 0.1143 1.5000 1.5360 2.5760 23.0200
temporal_resolution
1] 0.7693 8.5000 8.5000 8.5000 4.6000
6] 4.6000 4.6000 3.1000 3.1000 3.1000
11] 3.1000 4.6000 3.1000 3.1000 3.1000
16] 3.1000 3.1000 3.1000 3.1000 3.1000
21] 3.1000 3.1000 3.1000 3.1000 3.1000
26] 3.1000 3.1000 3.1000 3.1000 3.1000
Please report any issues or bugs.
License: GPL-2
To cite package paleobioDB in publications use:
ite package `paleobioDB` in publications use:
Varela, Javier Gonzalez-Hernandez and Luciano Fabris Sgarbi (2016). paleobioDB: an R-package for downloading, visualizing and processing data from the Paleobiology Database. R package version 0.5. https://github.com/ropensci/paleobioDB
bTeX entry for LaTeX users is
anual{,
title = {paleobioDB: an R-package for downloading, visualizing and processing data from the Paleobiology Database},
author = {{Sara Varela} and {Javier Gonzalez-Hernandez} and {Luciano Fabris Sgarbi}},
year = {2014},
note = {R package version 0.5},
base = {https://github.com/ropensci/paleobioDB},
This package is part of the rOpenSci project.
