Tuesday, September 10, 2013

ANDS User Acceptance Testing of ePiSaT Version 1.0

The user acceptance testing was conducted once the ePiSaT Software was released to the public via github. Each tester was selected for their specialist expertise, thus representing a range of potential users. Firstly, Associate Professor Lindsay Hutley from Charles Darwin University was selected because he provided flux tower data to the project and he understands the ‘flux data’. Secondly, Dr Siddeswara Guru from Queensland University was selected because he understands data processing and software. The reviewers were provided the github repository URL, and the documentation and asked to test if the system was capable of perform as described.

The key outcome is that both reviewers concluded that the package performs as expected and commended it as a positive contribution to the community.  Following are the 2 reviewers complete responses;

Reviewer # 1

Dear Brad,

Thank you for allowing me to review your ePiSaT system.

I have followed simple instructions as provided and looked at your blog that hosts the system.

As novice user to this system, I was able, with no major problems to download and use the test flux data and run the these data through the R scripts.

The system / model appears to be robust and uses the latest gridded climate data and fPAR/GPP products for Australia. Functions as detailed are all standard versions as described in the literature.

I was able to generate 30 minute partitioned GPP and Re that appeared to me to be reasonable and in-line with previous efforts to partition flux data in savanna at a plot scale – your product we have the capability at biome and continental scales.

I could see some savanna specific improvements that could be made (e.g. see the LUE and GPP models of Kannihar et al) but this system is focused on partitioning fluxes but in my view it is relatively user-friendly, well documented and has provided credible outputs. Key variables outputted from the model (Amax, quantum efficiency, respiration etc) are in line with previous efforts to partition this data.

Congratulations on a very useful tool, there are numerous methods to partition flux data and this is a product pitched at integrating current OzFlux data and spatially extrapolate this over space and time, a hugely useful outcome. For a ‘flux ecologist’ like myself GPP and respiration data can now be compared with site values, compared to other models, integrated with maps of fire, soil types, climate envelopes to further unpack spatial and temporal patterns of carbon cycling in savanna.

Regards
Assoc Prof Lindsay Hutley
Principal Research Fellow
Research Institute for the Environment and Livelihoods
Charles Darwin University

http://riel.cdu.edu.au/people/profile/lindsay-hutley



Reviewer # 2


A selected quote from S.M.Guru;

"I was able to conduct the user acceptance testing on the ePiSaT product ... The plotting functionality is also impressive. Good luck with the software release and there is a huge potential for the product."


S.M.Guru




Dr. Siddeswara Guru

Data Synthesis and Integration Coordinator

Terrestrial Ecosystem Research Network (TERN) and Australian Centre for Ecological Analysis and Synthesis (ACEAS)



This project is supported by the Australian National Data Service (ANDS). ANDS is supported by the Australian Government through the National Collaborative Research Infrastructure Strategy Program and the Education Investment Fund (EIF) Super Science Initiative.

For more information visit the ANDS website ands.org.au and Research Data Australia services.ands.org.au.

Sunday, September 1, 2013

ePiSaT software version 1.0 released !

The ePiSaT software has been released. The code and sample OzFlux data can be downloaded from:

https://github.com/belgaroo/ePiSaT-ecosystem-Production-in-Space-and-Time

The package and code is self explanatory, enabling the user to partition flux data to generate an estimate of GPP. ePiSaT users wanting to replicate the project can download more OzFlux data directly:

http://www.ozflux.org.au/

Please note that there have been some subtle changes to previously-posted details on how and where the ePiSaT software will be released. This post details the first official release of the ePiSaT software.

Background


Ecosystem Production in Space and Time (ePiSaT) models Gross Primary Production (GPP) across the Australian continent from OzFlux flux tower data, gridded climate and satellite (MODIS) data. ePiSaT can be used to estimate ecosystem variables by partitioning OzFlux eddy covariance data to estimate GPP, light use efficiency (LUE), the maximum rate of carboxylation (Amax) etc. Once determined, the ePiSaT-modelled variables can be used in the well-founded and tested LUE approach to estimate GPP. Sample OzFlux data from Howard Springs is provided; ePiSaT requires the user to provide fAPAR, observed radiation, temperature and humidity data.


Australian National Data Service (ANDS)


This project is supported by the Australian National Data Service (ANDS). ANDS is supported by the Australian Government through the National Collaborative Research Infrastructure Strategy Program and the Education Investment Fund (EIF) Super Science Initiative. For more information visit the ANDS website ands.org.au and Research Data Australia services.ands.org.au


Installation Instructions

Once downloaded, you can install episat using the following terminal command.R CMD INSTALL episat_1.0.tar.gzAlternatively, from an R GUI go the package manager and follow the prompts to install a package from source.


Running the software in R

Once installed, from an R command prompt, run the following code:
library(episat) 

?episat # <-- for help and how to use the package.


About the license

This work is licensed under a Creative Commons Attribution 3.0 Attribution-NonCommercial- CC BY-NC 

http://creativecommons.org/licenses/by-nc/3.0/legalcode 

This license lets others remix, tweak, and build upon your work non-commercially, and although their new works must also acknowledge you and be non-commercial, they don't have to license their derivative works on the same terms.

REQUIRED ATTRIBUTION : DOI XXX.XXX.XXXX.XXX


AUTHORS: Bradley Evans, Colin Prentice, Tyler W. Davis, Xavier Gilbert 

ORGANISATION: Macquarie University, Sydney Australia

REFERENCE: Evans, B.J., Prentice, I.C., Davis, T.W., Gilbert, X., 2013, Ecosystem Production in Space and Time, http://episat-software.blogspot.com.au

EXAMPLE: You wish to use this code or data in your own work, a peer reviewed journal article, then you need to attribute the work by referencing published article listed above and/ or the DOI (i.e. for output data only).

Contact the author and maintainer if you have any questions.

MAINTAINER: bradley.evans << at >> mq.edu.au