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Smithsonian / ETERnity

R package for Evolution of Terrestrial Ecosystems (ETE) Program
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ETERnity

The goal of ete is to provide an interface to the Evolution of Terrestrial Ecosystems (ETE) Program database.

Installation

You can install the released version of ete from GitHub with:

devtools::install_github("smithsonian/ETERnity")

Examples

Loading ETE Data

The first step to using ETERnity is to load the library, and then use the load_ete_data function to donwload the latest verion of ETE data from Figshare, and load it into 6 tables.

library(ETERnity)

data_tables <- load_ete_data(download_if_missing = TRUE)
#> Downloading version 1 of the data...
#> trying URL 'https://ndownloader.figshare.com/articles/[...]'
#> Content type 'application/zip' length 53537971 bytes (51.1 MB)
#> ==================================================
#> downloaded 51.1 MB
#> Unzipping file to /Users/[username]/.ete...

names(data_tables)
#> [1] "dataset_table"      "occurrence_table"   "sites_table"       
#> [4] "sitetrait_table"    "species_table"      "speciestrait_table"

User Functions

We have created a suite of user functions that allow you to pull data out of the ETE tables by provider. You can pull out yours or anyone else’s.

geteteoccur(provider): Get your occurrence table in long format.

amatangelo_occur <- geteteoccur(data_tables, 'Amatangelo')
head(amatangelo_occur)
#>   occurid        sitekey  sitename speciesid observed  sid timeybp
#> 1  849237 Amatan_3034_10 3034_2000    ABIBAL        1 3034      10
#> 2  849238 Amatan_3034_10 3034_2000    ACERUB        0 3034      10
#> 3  849239 Amatan_3034_10 3034_2000    ACESAC       28 3034      10
#> 4  849240 Amatan_3034_10 3034_2000    BETALL        0 3034      10
#> 5  849241 Amatan_3034_10 3034_2000    BETPAP        1 3034      10
#> 6  849242 Amatan_3034_10 3034_2000    CARCAR        0 3034      10
#>         datasetname latitude longitude duration spaceextent   provider
#> 1 Amatan_WI_Pla_Mod 44.96245 -87.19103        1       5e-04 Amatangelo
#> 2 Amatan_WI_Pla_Mod 44.96245 -87.19103        1       5e-04 Amatangelo
#> 3 Amatan_WI_Pla_Mod 44.96245 -87.19103        1       5e-04 Amatangelo
#> 4 Amatan_WI_Pla_Mod 44.96245 -87.19103        1       5e-04 Amatangelo
#> 5 Amatan_WI_Pla_Mod 44.96245 -87.19103        1       5e-04 Amatangelo
#> 6 Amatan_WI_Pla_Mod 44.96245 -87.19103        1       5e-04 Amatangelo

geteteoccurDataset(dataset): Get your occurrence table in long format for one timebin

amatan_wi_occur <- geteteoccurDataset(data_tables, 'Amatan_WI_Pla_Hist')
head(amatan_wi_occur)
#>   occurid        sitekey  sitename speciesid observed  sid timeybp
#> 1  851577 Amatan_3034_60 3034_1950    ABIBAL        1 3034      60
#> 2  851578 Amatan_3034_60 3034_1950    ACERUB        1 3034      60
#> 3  851579 Amatan_3034_60 3034_1950    ACESAC       31 3034      60
#> 4  851580 Amatan_3034_60 3034_1950    ACESPI        0 3034      60
#> 5  851581 Amatan_3034_60 3034_1950    BETALL        2 3034      60
#> 6  851582 Amatan_3034_60 3034_1950    BETPAP        8 3034      60
#>          datasetname latitude longitude duration spaceextent
#> 1 Amatan_WI_Pla_Hist 44.96245 -87.19103        1       5e-04
#> 2 Amatan_WI_Pla_Hist 44.96245 -87.19103        1       5e-04
#> 3 Amatan_WI_Pla_Hist 44.96245 -87.19103        1       5e-04
#> 4 Amatan_WI_Pla_Hist 44.96245 -87.19103        1       5e-04
#> 5 Amatan_WI_Pla_Hist 44.96245 -87.19103        1       5e-04
#> 6 Amatan_WI_Pla_Hist 44.96245 -87.19103        1       5e-04

unmelt2specXsite(table): Put your occurrence table in P/A matrix format

PAtable <- unmelt2specXsite(amatan_wi_occur)
PAtable[1:5,1:5]
#>        Amatan_1_60 Amatan_10_60 Amatan_1000_60 Amatan_1002_60
#> ABIBAL         NaN          NaN            NaN            NaN
#> ACENEG           0            0              0              0
#> ACERUB           0            0              0              1
#> ACESAC          11           11             37              0
#> ACESPI         NaN          NaN            NaN            NaN
#>        Amatan_1003_60
#> ABIBAL            NaN
#> ACENEG              0
#> ACERUB              0
#> ACESAC              0
#> ACESPI            NaN

getlatlon(provider): Get a list of your sites and their coordinates

wing_sites <- getlatlon(data_tables, 'Wing')
head(wing_sites)
#>         sitekey sitename latitude longitude
#> 1 Wing_16-4_73m    BCR15  43.8527  -107.536
#> 2 Wing_17-0_73m    BCR16  43.8527  -107.536
#> 3 Wing_17-9_73m    BCR17  43.8524  -107.535
#> 4 Wing_18-0_73m    BCR18  43.8524  -107.535
#> 5 Wing_18-1_73m    BCR19  43.8523  -107.536
#> 6 Wing_18-2_73m    BCR20  43.8523  -107.535

getages(provider): Get a list of your sites and their ages

ages <- getages(data_tables, "Behrensmeyer1")
head(ages)
#>                sitekey  timeybp
#> 1 Behren_D0025_10.474m 10474000
#> 2 Behren_D0027_10.474m 10474000
#> 3 Behren_D0062_10.066m 10066000
#> 4 Behren_GB001_10.768m 10768000
#> 5 Behren_GB002_10.876m 10876000
#> 6 Behren_KL017_10.568m 10568000

getsitetraits(provider): Get your site traits matrix

sitetraits <- getsitetraits(data_tables, "Blois")
head(sitetraits)
#>      sitekey  variablename   numvar discvar
#> 1 Blois_1_1k ANN_PRECIP_MM 283.7258        
#> 2 Blois_1_2k ANN_PRECIP_MM 283.2045        
#> 3 Blois_1_3k ANN_PRECIP_MM 282.3187        
#> 4 Blois_1_4k ANN_PRECIP_MM 282.2152        
#> 5 Blois_1_5k ANN_PRECIP_MM 275.3530        
#> 6 Blois_1_6k ANN_PRECIP_MM 275.3668

getspptraits(provider): Get your species trait matrix

spptraits <- getspptraits(data_tables,"Lyons")
head(spptraits)
#>   speciesid traitname numvalue discvalue
#> 1   Ago_pac    AFR_MO     10.5          
#> 2   Ago_pac    AFR_MO     10.5          
#> 3   Ago_pac    AFR_MO     10.5          
#> 4   Ago_pac    AFR_MO     10.5          
#> 5   Ago_pac    AFR_MO     10.5          
#> 6   Ago_pac    AFR_MO     10.5

Citation

If you use the ETERnity package, please cite accordingly:

Attribution

The dataset download and load functions all borrowed heavily from portalr.