Using Desktop Data in Kepler Dan Higgins – NCEAS Prepared for: Ecoinformatics Training for Ecologists LTER (Albuquerque) January 8-12, 2007

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Presentation transcript:

Using Desktop Data in Kepler Dan Higgins – NCEAS Prepared for: Ecoinformatics Training for Ecologists LTER (Albuquerque) January 8-12,

Viewing a Dataset – Text Editor 1999 Sevilleta LTER NPP Quadrat Sampling Data Text Editor view of data from a web page Includes both data and documentation (metadata) In a single text document 727 KB file

Viewing a Dataset - Excel 1999 Sevilleta LTER NPP Quadrat Sampling Data Excel View Data and column header only Can be saved in various formats SevilletaData.xls – 1489 KB SevilletaData.csv – 369 KB SevilletaData.txt – 369 KB SevilletaData.xlm – 5863 KB Only some formats are easily readable by other applications! *.csv - comma separated values ; *.txt - tab separated values (Cutting & Pasting from Excel results in tab separated columns)

Viewing a Dataset – Morpho 1999 Sevilleta LTER NPP Quadrat Sampling Data Morpho view Shows data and eml metadata

Viewing a Dataset – Kepler 1999 Sevilleta LTER NPP Quadrat Sampling Data Kepler view (using KNB Metacat Ecogrid query) Can view formatted EML metadata Default configuration shows a port for each column in the data table

Viewing a Dataset – Kepler 1999 Sevilleta LTER NPP Quadrat Sampling Data Kepler view (using KNB Metacat Ecogrid query) Data source actor can be configured to display the data by running a simple workflow.

Viewing a Dataset - Kepler Kepler view (using local EML2 Dataset actor) Depends on proper format of link from Metadata (eml) to the local data file (not yet working with local Morpho files)

Kepler – ReadTable Actor 1999 Sevilleta LTER NPP Quadrat Sampling Data Kepler view (using the R-based ReadTable actor) Read local file and provide metadata such as separator, file name, header presence, etc.

Kepler – ReadTable Actor 1999 Sevilleta LTER NPP Quadrat Sampling Data Kepler view (using the R-based ReadTable actor) Result of executing workflow

Kepler – ReadTable Actor 1999 Sevilleta LTER NPP Quadrat Sampling Data Kepler view (using the R-based ReadTable actor) Text display from the ReadTable actor after adding ‘dim(df)’ and ‘summary(df)’ commands Row and Column count Data Summary

Kepler – ReadTable Actor 1999 Sevilleta LTER NPP Quadrat Sampling Data Kepler view (using the R-based ReadTable actor) Result of creating a BoxPlot of data in the 9th column (the ‘height’ column)

Kepler – ReadTable Actor Kepler view (using the R-based ReadTable actor) Dataframe created by the ReadTable actor can be passed To another actor for further processing

Kepler – ReadTable Actor Kepler view (using the R-based ReadTable actor) Result of further dataframe processing: Species vs count BoxPlots

Acknowledgements This material is based upon work supported by: The National Science Foundation under Grant Numbers , , , , , and Collaborators: NCEAS (UC Santa Barbara), University of New Mexico (Long Term Ecological Research Network Office), San Diego Supercomputer Center, University of Kansas (Center for Biodiversity Research), University of Vermont, University of North Carolina, Napier University, Arizona State University, UC Davis The National Center for Ecological Analysis and Synthesis, a Center funded by NSF (Grant Number ), the University of California, and the UC Santa Barbara campus. The Andrew W. Mellon Foundation. Kepler contributors: SEEK, Ptolemy II, SDM/SciDAC, GEON