In nickmckay/lipdR: LiPD utilities for R

library(lipdR)
knitr::opts_chunk$set(echo = TRUE)

This is a demonstration of the new lipd2neotoma() function

I will use a neotoma dataset, called Bambili 2, for this demonstration

First, we will load this record and convert into lipd format

B <- neotoma2::get_sites(sitename = "Bambili 2")
D <- neotoma2::get_downloads(B)
L <- neotoma2lipd(D)

LiPD

Let's see a summary of the record in LiPD

summary(L)

Neotoma

Now we will convert back to neotoma and observe the changes

N <- lipd2neotoma(L)

D@sites[[1]]
N

The site printout looks good

Site level metadata

D
D@sites
D@sites[[1]]
N



D@sites[[1]]@siteid
N@siteid


D@sites[[1]]@sitename
N@sitename

D@sites[[1]]$geography
N@geography

D@sites[[1]]$altitude
N@altitude

D@sites[[1]]$geopolitical
N@geopolitical

D@sites[[1]]$area
N@area

D@sites[[1]]$notes
N@notes

D@sites[[1]]$description
N@description

D@sites[[1]]$collunits
N@collunits

We do pretty good here with the exception of "geopolitical", which could be added to the lipd under "geo"

We also see an error in trying to print the "collunit", which is detailed later

Sample datum

D@sites[[1]]@collunits@collunits[[1]]@datasets@datasets[[1]]@samples@samples[[1]]@datum
N@collunits@collunits[[1]]@datasets@datasets[[1]]@samples@samples[[1]]@datum

note that D is the original neotoma dataset and N is the new one N is a site rather than a sites

Aside from some loss in the variablename, these data frames look identical. Improved variablename fidelity is possible with alteration to the neotoma2lipd() function

What's the difference between element and elementtype?

Let's jump to the last datum to see if this fidelity holds

length(D@sites[[1]]@collunits@collunits[[1]]@datasets@datasets[[1]]@samples@samples)
D@sites[[1]]@collunits@collunits[[1]]@datasets@datasets[[1]]@samples@samples[[140]]@datum
N$collunits@collunits[[1]]@datasets@datasets[[1]]@samples@samples[[140]]@datum

again, we see some minor changes to variablename, but otherwise the data frame is identical

Chronologies

Let's have a look at the chronology data

D@sites[[1]]@collunits@collunits[[1]]@chronologies@chronologies[[1]]@chroncontrols
N$collunits@collunits[[1]]@chronologies@chronologies[[1]]@chroncontrols

I could not identify the sorting of the original chronology table to follow

The tables are otherwise identical

Outstanding Issues

Collection unit print doesn't work

D@sites[[1]]@collunits@collunits[[1]]
N$collunits@collunits[[1]]

new("site")
new("collunits")
new("collunit")

creating a new "collunit" is an issue?

Some of the chronology metadata isn't retained, lipd doesn't store metadata at this level

D@sites[[1]]@collunits@collunits[[1]]@chronologies@chronologies[[1]]
N$collunits@collunits[[1]]@chronologies@chronologies[[1]]

Same for "collunit" metadata

D@sites[[1]]@collunits@collunits[[1]]
N$collunits@collunits[[1]]

nickmckay/lipdR documentation built on April 13, 2025, 5:58 p.m.