In nickmckay/lipdR: LiPD utilities for R

knitr::opts_chunk$set(echo = TRUE)
devtools::load_all()

Load Data

First we grab the ISO2k data and the standardization tables

library(lipdR)
iso2k <- readLipd("https://lipdverse.org/iso2k/current_version/iso2k1_0_1.zip")

And now we'll convert that to a LiPD TS object

TS <- as.lipdTs(iso2k)

First, update the metadata

TS1 <- updateMetaDataFromStandardTables(TS, "paleoData_units")

This function produces an updated TS object as well as a data frame showing the changes

standardizeValue() looks for synonyms and replaces them with valid lipd names

TS2 <- standardizeValue(lipdTS=TS1$TS, key="paleoData_units")

This function also produces a data frame showing any changes

A quick sanity check

isValidValue(TS2$TS, "paleoData_units")
TS[[2]]$paleoData_units
TS2$TS[[2]]$paleoData_units

Looks good

Finally we can update either paleoData_notes or notes with the changes made

TS1 <- lipdR:::updateNotes(lipdTS=TS2$TS,
                           key = "paleoData_units",
                           metadataChangesDF=TS1$ChangesDF,
                           standardizeSynonymDF=TS2$synonymDF$synonymDF)

Let's have a look at some examples

unchanged

TS[[1]]$paleoData_notes
TS1[[1]]$paleoData_notes

Changed a peice of metadata

TS[[2]]$paleoData_notes
TS1[[2]]$paleoData_notes

Changed metadata and standardized value

TS[[240]]$paleoData_notes
TS1[[240]]$paleoData_notes

Now let's try this for a more complicated key

TS1 <- updateMetaDataFromStandardTables(TS, "interpretation_seasonality")
TS1

There is no metadata to update this time

Let's try standardizing

TS2 <- standardizeValue(TS, "interpretation_seasonality")

We see a long string of output here, reflecting the 7 unique interpretation_seasonality keys

Let's have a look now

a2 <- isValidValue(lipdTS=TS2$TS, key="interpretation_seasonality")

Cool, that took care of all of them

An example of values changed

TS[[1851]]$interpretation5_seasonality
TS2$TS[[1851]]$interpretation5_seasonality

Finally, the notes

This is set up to be run once per interpretation, although the automation could be added

TS1 <- lipdR:::updateNotes(lipdTS=TS2$TS,
                           standardizeSynonymDF=TS2$synonymDF[[1]]$synonymDF)

before and after

TS[[328]]$notes
TS1[[328]]$notes

for interp 5

TS1 <- lipdR:::updateNotes(lipdTS=TS2$TS,
                           standardizeSynonymDF=TS2$synonymDF[[5]]$synonymDF)

before and after

TS[[1851]]$notes
TS1[[1851]]$notes

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