A versioned and dynamically updating taxonomic lookup table for land plants
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README.md

taxonlookup: a taxonomic lookup table for land plants

Build Status codecov.io DOI GitHub version

How to use this package

Install the required packages

#istall.packages("devtools") # if necessary
devtools::install_github("ropenscilabs/datastorr")
devtools::install_github("wcornwell/taxonlookup")
library(taxonlookup)

Find the higher taxonomy for your species list

lookup_table(c("Pinus ponderosa","Quercus agrifolia"), by_species=TRUE)
##                     genus   family   order       group
## Pinus ponderosa     Pinus Pinaceae Pinales Gymnosperms
## Quercus agrifolia Quercus Fagaceae Fagales Angiosperms

There are a few other functions to get species diversity numbers and other (non-Linnean) high clades if you want that information. If you use this package in a published paper, please note the version number and the appropriate doi via Zenodo. This will allow others to reproduce your work later.

That's it, really. Below is information about the data sources and the versioned data distribution system (which we think is really cool), feel free to check it out, but you don't need to read the rest of this to use the package.

Reproducing a specific version

If you are publishing a paper with this library, or you want the results of your analysis to be reproducable for any other reason, include the version number in your call to lookup table. This will always pull the specific version of the taxonomy lookup that you used. If you leave this out, on a new machine the library will download the most recent version of the database rather than the specific one that you used.

lookup_table(c("Pinus ponderosa", "Quercus agrifolia"), by_species=TRUE, version="1.1.0")
##                     genus   family   order       group
## Pinus ponderosa     Pinus Pinaceae Pinales Gymnosperms
## Quercus agrifolia Quercus Fagaceae Fagales Angiosperms

Higher taxonomy lookup

If you want different taxonomic levels, use add_higher_order. Because of the incomplete nesting of many taxonomic levels, this resource has a non-intuitive format. If a genus is within a specific group, that column includes the name of the clade. If it is not, then that cell is left blank. This shows the format of the resource:

knitr::kable(head(add_higher_order()))
number.of.accepted.species number.of.accepted.and.unresolved.species genus family order group Spermatophyta Angiospermae Mesangiospermae Monocotyledoneae Nartheciidae Petrosaviidae Commelinidae Eudicotyledoneae Gunneridae Superasteridae Pentapetalae Asteridae Campanulidae Lamiidae Superrosidae Rosidae Malvidae Fabidae Magnoliidae Acrogymnospermae Cycadophyta Coniferae Cupressophyta Gnetophyta
2 5 Acorus Acoraceae Acorales Angiosperms Spermatophyta Angiospermae Mesangiospermae Monocotyledoneae
1 1 Albidella Alismataceae Alismatales Angiosperms Spermatophyta Angiospermae Mesangiospermae Monocotyledoneae Nartheciidae
8 16 Alisma Alismataceae Alismatales Angiosperms Spermatophyta Angiospermae Mesangiospermae Monocotyledoneae Nartheciidae
1 1 Astonia Alismataceae Alismatales Angiosperms Spermatophyta Angiospermae Mesangiospermae Monocotyledoneae Nartheciidae
3 5 Baldellia Alismataceae Alismatales Angiosperms Spermatophyta Angiospermae Mesangiospermae Monocotyledoneae Nartheciidae
1 1 Burnatia Alismataceae Alismatales Angiosperms Spermatophyta Angiospermae Mesangiospermae Monocotyledoneae Nartheciidae

This could for example, return orders within the Rosidae:

# load the data.frame into memory
ho<-add_higher_order()
unique(ho$order[ho$Rosidae=="Rosidae"])
##  [1] "Brassicales"     "Celastrales"     "Crossosomatales"
##  [4] "Cucurbitales"    "Fabales"         "Fagales"        
##  [7] "Geraniales"      "Huerteales"      "Malpighiales"   
## [10] "Malvales"        "Myrtales"        "Oxalidales"     
## [13] "Picramniales"    "Rosales"         "Sapindales"     
## [16] "Vitales"         "Zygophyllales"

Combined with the species counts from the plant list this can be used to get the current estimates of diversity. For example, find the number of accepted Conifer species in the world:

sum(ho$number.of.accepted.species[ho$Coniferae=="Coniferae"])
## [1] 760

Compare with the number of accepted plus the number of unresolved species:

sum(ho$number.of.accepted.and.unresolved.species[ho$Coniferae=="Coniferae"])
## [1] 877

Data sources

  1. The Plant List for accepted genera to families

  2. APWeb for family-level synonymies and family to order as curated by Peter Stevens

  3. A higher-level taxonomy lookup compiled by Dave Tank and colleagues

We have a complete genus-family-order mapping for vascular plants. For bryophytes, there is only genus-family mapping at present; if anyone has a family-order map for bryophytes, please let me know. We also correct some spelling errors, special character issues, and other errors from The Plant List. We will try to keep this curation up-to-date, but there may new errors introduced as the cannonical data sources shift to future versions.

Notes on genus-to-family mapping

Taxonlookup is strictly constrained to a one-to-one genus-to-family (Linnean) mapping of taxa. The Plant List v1.1, which itself assembles data from multiple sources, is not strict about following implementing this rule and so this creates a few conflicts, which hopefully will be resolved in v1.2. In the meantime, taxonlookup resolves these conflicts (one genus name mapping to multiple families) using the following rules:

  1. For conflicts where two "accepted species" with the same genus name are mapped to different families, the genus is mapped to the family with more accepted species. This seemed to solve a somewhat common error in which one species is mistakenly given the wrong genus name. For example, there could be one moss species with the genus mistakenly listed as Pinus. In this case we want a behavior that maintains the clearly legitimate mapping of Pinus to Pinaceae.

  2. For conflicts in which some species are accepted and others unresolved, the genus is mapped to the family of the accepted species.

  3. For conflicts where all the species are unresolved it drops the genus entirely from both (or in some cases all three) families

The full list of TPL genus--family pairs that get dropped based on these criteria is here.

Details about the data distribution system

This is designed to be a living database--it will update as taxonomy changes (which it always will). These updates will correspond with changes to the version number of this resource, and each version of the database will be available via travis-ci and Github Releases. If you use this resource for published analysis, please note the version number in your publication. This will allow anyone in the future to go back and find exactly the same version of the data that you used.

Because Releases can be altered after the fact, we use zenodo-github integration to mint a DOI for each release. This will both give a citable DOI and help with the logevity of each version of the database. (Read more about this here.)

Details about the data distribution system

The core of this repository is a set of scripts that dynamically build a genus-family-order-higher taxa look-up table for land plants with the data lookup primarily coming from three sources (with most of the web-scraping done by taxize):

The scripts are in the repository but not in the package. Only the data and ways to access the data are in the package; the reason for this design will become clear further down the readme.

You can download and load the data into R using the plant_lookup() function:

head(plant_lookup())
##       genus       family       order       group
## 1    Acorus    Acoraceae    Acorales Angiosperms
## 2 Albidella Alismataceae Alismatales Angiosperms
## 3    Alisma Alismataceae Alismatales Angiosperms
## 4   Astonia Alismataceae Alismatales Angiosperms
## 5 Baldellia Alismataceae Alismatales Angiosperms
## 6  Burnatia Alismataceae Alismatales Angiosperms

The first call to plant_lookup will download the data, but subsequent calls will be essentially instantaneous. If you are interested in diversity data, the data object also stores the number of accepted species within each genus as per the plant list:

head(plant_lookup(include_counts = TRUE)[,c(1,3,4)])
##   number.of.accepted.species     genus       family
## 1                          2    Acorus    Acoraceae
## 2                          1 Albidella Alismataceae
## 3                          8    Alisma Alismataceae
## 4                          1   Astonia Alismataceae
## 5                          3 Baldellia Alismataceae
## 6                          1  Burnatia Alismataceae

For taxonomic groups higher than order, use the add_higher_order() function. Because currently the higher taxonomy of plants does not have a nested structure, the format of that lookup table is a little more complicated. Check the help file for more details. To get the version number of the dataset run:

plant_lookup_version_current()
## [1] "1.1.5"

For most uses, the latest release should be sufficient, and this is all that is necessary to use the data. However, if there have been some recent changes to taxonomy that are both important for your project and incorporated in the cannical sources (the plant list or APWeb) but are more recent than the last release of this package, you might want to rebuild the lookup table from the sources. Because this requires downloading the data from the web sources, this will run slowly, depending on your internet connection.

Rebuilding the lookup table

To build the lookup table, first clone this repository. Then download and install remake from github:

devtools::install_github("richfitz/remake")

Then run the following commands from within R. Make sure the home directory is within the repository:

remake::install_missing_packages()
remake::make()

This requires a working internet connection and that the plant list, mobot, and datadryad servers are up and working properly. This will dynamically re-create the lookup tables within your local version of the package, as well as save the main file as a .csv in your home directory.

Living database

Development version

We will periodically release development versions of the database using github releases. We'll check these automatically using travis-ci. As taxonomy is a moving target, we expect that the lookup to change with time.

Notes for making a release using this living dataset design

  • Update the DESCRIPTION file to increase the version number. Now that we are past version 1.0.0, we will use semantic versioning so be aware of when to change what number.
  • Run remake::make() to rebuild plant_lookup.csv
  • Commit code changes and DESCRIPTION and push to GitHub
  • With R in the package directory, run
taxonlookup:::plant_lookup_release("<description>")

where "<description>" is a brief description of new features of the release.

  • Check that it works by running taxonlookup::plant_lookup(taxonlookup::plant_lookup_version_current(FALSE)) which should pull the data.
  • Update the Zenodo badge on the readme