Manuscript # 2016GC006307R 
Current Revision #1
Other Version2016GC006307
Submission Date2016-04-18 17:43:39
Current StageManuscript Sent to Production
TitlePmagPy: Software package for paleomagnetic data analysis and a bridge to the Magnetics Information Consortium (MagIC) Database
Running TitlePMAGPY: BRIDGE TO MAGIC
Manuscript TypeTechnical Reports: Methods
Special SectionsMagnetism From Atomic to Planetary Scales: Physical Principles and Interdisciplinary Applications in Geo- and Planetary Sciences
Authors
1Lisa Tauxe (University of California, San Diego) (corr-auth)
2Ron Shaar (Hebrew University of Jerusalem)
3Lori Jonestrask (University of California, San Diego)
4Nicholas Swanson-Hysell (University of California, Berkeley)
5Rupert Minnett (Cogense, Inc.)
6Anthony Koppers (Oregon State University)
7Catherine Constable (UCSD)
8Nicholas Jarboe (University of California, San Diego)
9Kevin Gaastra (University of California, Berkeley)
10Luke Fairchild (University of California, Berkeley)
Abstract The Magnetics Information Consortium (MagIC) database provides an archive with a flexible data model for paleomagnetic and rock magnetic data. The PmagPy software package is a cross-platform and open-source set of tools written in Python for the analysis of paleomagnetic data that serves as one interface to MagIC, accommodating various levels of user expertise. PmagPy facilitates thorough documentation of sampling, measurements, datasets, visualization, and interpretation of paleomagnetic and rock magnetic experimental data. Although not the only route into the MagIC database, PmagPy makes preparation of newly published datasets for contribution to MagIC as a byproduct of normal data analysis and allows manipulation as well as reanalysis of datasets downloaded from MagIC with a single software package. The graphical user interface (GUI), Pmag GUI enables use of much of PmagPy's functionality, but the full capabilities of PmagPy extend well beyond that. Over 400 programs and functions can be called from the command line interface mode, or from within the interactive Jupyter notebooks. Use of PmagPy within a notebook allows for documentation of the workflow from the laboratory to the production of each published figure or data table, making research results fully reproducible. The PmagPy design and its development using GitHub accommodates extensions to its capabilities through development of new tools by the user community. Here we describe the PmagPy software package and illustrate the power of data discovery and re-use through a re-analysis of published paleointensity data which illustrates how the effectiveness of selection criteria can be tested.
Associate EditorNot Assigned
Keyword(s)Magnetics Information Consortium, MagIC database, PmagPy software package, Paleomagnetic and rock magnetic database
Index Terms1599, 1594, 0530, 0525, 0520
Funding Body Archiving Mandates National Science Foundation (NSF): Catherine Constable EAR-1225520; National Science Foundation (NSF): Catherine Constable EAR-1347297; National Science Foundation (NSF): Lisa Tauxe EAR-1141840; National Science Foundation (NSF): Anthony A.P. Koppers EAR-1419894
Data Policy The authors comply with AGU's data policy, and a statement is included in the acknowledgements identifying where readers can access the data.
Supporting Information (SI) Yes
Key Points Please state the three main points of the article.
Main point #1: (140 character limit including spaces)

PmagPy software provides an interface to interact with Magnetics Information Consortium (MagIC) data


Main point #2: (140 character limit including spaces)
Tools support visualization and interpretation across a range of rock and paleomagnetic data types


Main point #3: (140 character limit including spaces)
Novice and expert programmers can use PmagPy for data analysis and preparation for MagIC database
File Permissions Have you reproduced or modified any part of an article that has been previously published or submitted to another journal? Yes

Figure 1 slightly modified, Figure 3 eliminated.

Embargo

Manuscript Items

  1. "Response to Reviewer" PDF (55KB) 
  2. Merged File containing manuscript text and 6 Figure files. PDF (1592KB) 
    1. Article File PDF (114KB) 
    2. Figure 1 PDF (181KB) 
      Figure
    3. Figure 2 PDF (253KB) 
      Figure
    4. Figure 3 PDF (167KB) 
      Figure
    5. Figure 4 PDF (379KB) 
      Figure
    6. Figure 5 PDF (85KB) 
      Figure
    7. Figure 6 PDF (466KB) 
      Figure
  3. Supporting Information SI - Jupyter notebooks illustrating use of PmagPy for analysis of paleomagnetic data. PDF (2874KB) 
    Supporting Information (SI)
  4. 785877_1_1461621528_jats.xml - XML  


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