05/11/2018 GitHub - nickmckay/LiPD-utilities: Input/output and manipulation utilities for LiPD files in Matlab, R and Python

DOI 10.5281/zenodo.1256889 python 3.4 matlab R2017a R 3.3.1 license GPL

Input/output and manipulation utilities for LiPD files in Matlab, R and Python.

What is it?
LiPD is short for Linked PaleoData. LiPD files are the data standard for storing and exchanging
data amongst paleoclimate scientists. The package will help you convert your existing paleoclimate
observations into LiPD files that can be shared and analyzed.

Organizing and using your observation data can be time consuming. Our goal is to let you focus on
more important tasks than data wrangling.

Core functions
The functions below are considered the core functions of the LiPD package. These functions are
consistent in Matlab, Python, and R. The function names, parameters and returned data are the
same.

readLipd
Read LiPD files from your computer into your workspace

writeLipd
Write LiPD data from your workspace onto your computer.

extractTs
Extract a time series from one or more datasets in the workspace. Your hierarchical LiPD data
structure is extracted into a flattened time series structure.

collapseTs
Collapse a time series back into LiPD dataset form in the workspace. Your flattened time series
structure is condensed back into a hierarchical LiPD data structure

filterTs
Retrieve time series objects that match a specific criteria. This filters out the data that you don't
want, and returns a new time series of data that you do want.

https://github.com/nickmckay/LiPD-utilities 1/3
05/11/2018 GitHub - nickmckay/LiPD-utilities: Input/output and manipulation utilities for LiPD files in Matlab, R and Python

queryTs
Retrieve the index numbers of time series objects that match a specific criteria. This filters out the
data that you don't want, and returns a list of index numbers of the data that you do want.

Language-specific Documentation
The core functions are consistent across the 3 languages; However, each language has some
nuances that you may be unfamiliar with. For example, in Python you may use lipd.readLipd() ,
whereas in R you use lipd::readLipd() or readLipd() .

Additionally, while the core functions remain the same, we chose to take advantage of the
strengths of each language. The Python utilities have additional functions for converting and
validating data. The R and Matlab utilities are better suited for data analyzation. The language-
specific documentation linked below will go into detail about all the functions included in each
language.

Python Docs

R Docs

Matlab Docs

FAQ

What is a time series?

The LiPD dataset hierarchy is great for organization and giving context to data, but can be more
difficult to sift through to find relevant information since it can often go 10+ levels deep.

A time series is a flattened set of data that makes data more approachable and is used to perform
data analysis. A time series is a collection of time series objects.

1-to-1 ratio 1 time series object = 1 measurement table column

Each object within a time series is made from one column of data in a measurement table. It's
important to note that this only pertains to measurement table data. All model data (ensemble,
distribution, summary) are not included when creating a time series.

Example 1: One dataset

ODP1098B13
1 measurement table
5 columns
depth, depth1, SST, TEX86, age

extractTs creates a time series ( ts ) of 5 objects

Example 2: Multiple datasets

ODP1098B13

https://github.com/nickmckay/LiPD-utilities 2/3
05/11/2018 GitHub - nickmckay/LiPD-utilities: Input/output and manipulation utilities for LiPD files in Matlab, R and Python

1 measurement table
5 columns
depth, depth1, SST, TEX86, age

Ant-CoastalDML.Thamban.2006

1 measurement table
2 columns
d18O, year

CO00COKY

1 measurement table
2 columns
d18O, year

extractTs creates a time series ( ts ) of 9 objects

How to Cite this code

DOI 10.5281/zenodo.1256889

Use this link to visit the Zenodo website. It provides citation information in many popular formats.

https://github.com/nickmckay/LiPD-utilities 3/3