You can install traitdata from Github with:
# Install devtools if not available
if(!"remotes" %in% installed.packages()[,"Package"]) install.packages("remotes")
# Install traitdata package from Github
remotes::install_github("RS-eco/traitdata", build_vignettes = T, force=T)After installation, simply load the traitdata package:
library(traitdata)If you encounter a bug or if you have any problems, please file an issue on Github.
There are 32 different data sets, which are included in this package:
| datasetName | basisOfRecord | rightsHolder | DOI |
|---|---|---|---|
| amniota | traitDatabase | Myrhvold et al. 2016 | 10.1890/15-0846R.1 |
| amphi_lifehist | traitDatabase | Trochet et al. 2014 | 10.3897/BDJ.2.e4123 |
| amphibio | traitDatabase | Oliveira et al. 2017 | 10.1038/sdata.2017.123 |
| an_age | traitDatabase | Tacutu et al. 2018 | 10.1093/nar/gkx1042 |
| anuran_morpho | traitDatabase | Mendoza-Henao et al. 2019 | 10.1002/ecy.2685 |
| arthropods | traitDatabase | Gossner et al. 2015 | 10.1038/sdata.2015.13 |
| atlantic_birds | traitDatabase | Rodrigues et al. 2019 | 10.1002/ecy.2647 |
| australian_birds | traitDatabase | Garnett et al. 2015 | 10.1038/sdata.2015.61 |
| AvianBodySize | traitDatabase | Lislevand et al. 2007 | 10.1890/06-2054 |
| bird_behav | traitDatabase | Tobias & Pigot 2019 | 10.1098/rstb.2019.0012 |
| carabids | traitDatabase | van der Plas et al. 2017 | 10.5061/dryad.53ds2 |
| climber | traitDatabase | Schweiger et al. 2014 | 10.3897/zookeys.367.6185 |
| disperse | traitDatabase | Sarremejane et al. 2020 | 10.1038/s41597-020-00732-7 |
| elton_birds | traitDatabase | Wilman et al. 2014 | 10.1890/13-1917.1 |
| elton_mammals | traitDatabase | Wilman et al. 2014 | 10.1890/13-1917.1 |
| epiphytes | traitDatabase | Hietz et al. 2021 | 10.1111/1365-2745.13802 |
| eubirds | traitDatabase | Storchová & Hořák 2017 | 10.1111/geb.12709 |
| fishmorph | traitDatabase | Brosse et al. 2021 | 10.1111/geb.13395 |
| globalHWI | traitDatabase | Sheard et al. 2020 | 10.1038/s41467-020-16313-6 |
| globTherm | traitDatabase | Bennett et al. 2018 | 10.1038/sdata.2018.22 |
| heteroptera | traitDatabase | Gossner et al. 2016 | 10.6084/m9.figshare.c.3307611.v1 |
| heteropteraRaw | traitDatabase | Gossner et al. 2016 | 10.6084/m9.figshare.c.3307611.v1 |
| lizard_traits | traitDatabase | Meiri 2018 | 10.1111/geb.12773 |
| mammal_diet | traitDatabase | Kissling et al. 2014 | 10.1002/ece3.1136 |
| mammal_diet2 | traitDatabase | Gainsbury et al. 2018 | 10.1111/mam.12119 |
| marsupials | traitDatabase | Fisher et al. 2001 | 10.1890/0012-9658(2001)082[3531:TEBOLH]2.0.CO;2 |
| migbehav_birds | literatureData | Eyres & Fritz | 10.12761/SGN.2017.10058 |
| pantheria | traitDatabase | Jones et al. 2009 | 10.1890/08-1494.1 |
| passerines | traitDatabase | Ricklefs 2017 | 10.1002/ecy.1783 |
| primates | traitDatabase | Galán-Acedo et al. 2020 | 10.1038/s41597-019-0059-9 |
| reptile_lifehist | traitDatabase | Grimm et al. 2014 | 10.3897/natureconservation.9.8908 |
| tetra_density | traitDatabase | Santini et al. 2018 | 10.1111/geb.12756 |
Note: The code for how these datatsets were downloaded and processed can be found in the data-raw folder.
See also https://opentraits.org/datasets.html for an extensive list of Trait datasets.
An overview of the different datasets can also be found here:
vignette("data_info").
- All published datasets contain their original variables and species names. Species names were split into 2 columns (Genus and Species) and where applicable into a 3rd column with Subspecies names.
- All datasets also have a scientificNameStd column, which is a standardised scientific name, in order to be able to merge the different datasets by species.
Note: Not all species names could be standardised, therefore some
data entries might not contain a scientificNameStd value, please then
refer to the Genus and Species column. In case you are interested in
which species could not be standardised have a look at the
names_nonStd file. Please also check out the synonyms data file, for
species where an alternative name has been used for standardising the
scientific name.
An overview of all variables with a description of each variable can be
found in the trait_glossary data file:
data(trait_glossary)or in the glossary vignette:
vignette("trait_glossary")To connect to one or more datasets, we simply use the data() function.
# Load Elton Traits
data("elton_birds")Now we can use standard R calls to have a look at the data.
First, we look at the column names of our dataset.
# Look at the variable names
colnames(elton_birds)## [1] "SpecID" "PassNonPass" "Order"
## [4] "Family" "BLFamilyEnglish" "BLFamSequID"
## [7] "Taxo" "Genus" "Species"
## [10] "English" "Diet.Inv" "Diet.Vend"
## [13] "Diet.Vect" "Diet.Vfish" "Diet.Vunk"
## [16] "Diet.Scav" "Diet.Fruit" "Diet.Nect"
## [19] "Diet.Seed" "Diet.PlantO" "Diet.5Cat"
## [22] "Diet.Source" "Diet.Certainty" "Diet.EnteredBy"
## [25] "ForStrat.watbelowsurf" "ForStrat.wataroundsurf" "ForStrat.ground"
## [28] "ForStrat.understory" "ForStrat.midhigh" "ForStrat.canopy"
## [31] "ForStrat.aerial" "PelagicSpecialist" "ForStrat.Source"
## [34] "ForStrat.SpecLevel" "ForStrat.EnteredBy" "Nocturnal"
## [37] "BodyMass.Value" "BodyMass.Source" "BodyMass.SpecLevel"
## [40] "BodyMass.Comment" "Record.Comment" "Full.Reference"
## [43] "scientificNameStd"
Then, we check the class and first 6 rows of the first 10 columns of the
elton_traits dataset:
class(elton_birds)## [1] "data.frame"
head(elton_birds[,1:10])## SpecID PassNonPass Order Family BLFamilyEnglish
## 1 28 Nonpasseriformes Struthioniformes Struthionidae Ostriches
## 2 37 Nonpasseriformes Rheiformes Rheidae Rheas
## 3 38 Nonpasseriformes Rheiformes Rheidae Rheas
## 4 45 Nonpasseriformes Casuariiformes Casuariidae Cassowaries
## 5 46 Nonpasseriformes Casuariiformes Casuariidae Cassowaries
## 6 47 Nonpasseriformes Casuariiformes Casuariidae Cassowaries
## BLFamSequID Taxo Genus Species English
## 1 2 BL3 Struthio camelus Ostrich
## 2 3 BL3 Rhea americana Greater Rhea
## 3 3 BL3 Rhea pennata Lesser Rhea
## 4 4 BL3 Casuarius casuarius Southern Cassowary
## 5 4 BL3 Casuarius bennetti Dwarf Cassowary
## 6 4 BL3 Casuarius unappendiculatus Northern Cassowary
For more information on how to use the data within the package, check
out the access-data and all the other vignettes.
vignette("access-data")Additional examples of how to use the different trait datasets can be found in the following vignettes:
vignette("island-birds")
vignette("migbehav_birds")
vignette("morpho-indices")
vignette("pantheria")
vignette("passerines")