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[ Uncertainty And Sensitivity Analysis | Home ]
All content and files © 2007-2018, 2019 - Dr. Denise Kirschner - University of Michigan |
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[ Uncertainty And Sensitivity Analysis | Home ]
All content and files © 2007-2018, 2019 - Dr. Denise Kirschner - University of Michigan |
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An e-mail written by Stephanie Evans:
An R package exists called "Spartan" that was written by one of my colleagues from grad school so if you are going to use any of this please cite his paper to give him due credit (attached). I have re-written parts of his scripts to make it more user friendly though. Here is the link to the original package https://cran.r-project.org/web/packages/spartan/index.html and I have attached my version of the scripts. I have tried to annotate it as best as I can but if you want to chat about it I am always happy to skype and answer any questions you may have. My "user friendly version" requires a series of scripts that need to be called to allow the function: lhc_generatePRCoEffs_from_workspace_over_time(FILENAME, PARAMETERS, MEASURES, CORCOEFFSOUTPUTFILENAME, TIMEPOINTS) to work. In this function the definitions are: FILENAME: name of file in r workspace to use for LHS, PARAMETERS: List of column names of varied columns, MEASURES: what to do PRCCs on e.g. Collagen etc., CORCOEFFSOUTPUTFILENAME: what to call output when it adds it to workspace, TIMEPOINTS: time points to do LHS (e.g 144,288 etc). and the result is that in the R workspace another item is created called whatever you put in the CORCOEFFSOUTPUTFILENAME variable of the function (in the example attached I called it prcc_col. I have included the dataset I used as an example too. The file "LHS in R example for HG.r" is going to be the one you want to use as an example, the others are the scripts it depends on to run. | |
Kieran Alden, Mark Read, Jon Timmis, Paul S. Andrews, Henrique Veiga-Fernandes, Mark Coles,
Spartan: A Comprehensive Tool for Understanding
Uncertainty in Simulations of Biological Systems,
PLOS Computational Biology | www.ploscompbiol.org , 1 February 2013 | Volume 9 | Issue 2 | e1002916,
DOI:
10.1371/journal.pcbi.1002916,
PMID: 23468606,
PMCID: 3585389
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PRCC in R research files ... | |
fibro_switch_combo_actuall_switch_july2.csv | |
LHS_in_R_example_for_HG.r.zip | |
prcc_from_workspace_other.r.zip | |
prcc_from_workspace_over_time.r.zip | |
prcc_from_workspace.r.zip |
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- University of Michigan |
