Add evaluateKinetics.py script to testing folder#117
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Raise errors if depository isn't found. Remove averaging and adding of training reactions in the family, assumes you have done it outside the function. Compares reverse kinetics if the NIST reaction is in the reverse direction from the family template
retrieves data involving the family Now shows the top node names, and also the number of rules csv file has headers now. Does not average the families or add training data. Assumes any type of manipulation has been done outside the folder. Also, don't load any kineticsLibraries or thermoLibraries by default except the primaryThermoLibrary. But do load all the depositories
Add NIST folder to ketoenol. Fix atom labeling for several reactions
Is not quite the original leaveOneOut test as it was done before. The original test takes extremely long to run because it must average up the family after each exact rate rule. In this method, we remove the original rate rule, and see if using an average that (should incorporate the original) does a good job of estimating that rate rule. The option to use the original version of the algorithm can still be used by setting averaging=True Write data to csv file after each family rather than after entire set of families so that they are in alphabetical order
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| The original family should not contained averaged nodes when starting out. The | ||
| leave one out test should be performed only for original exact matches. | ||
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Need to update comment here explaining about the averaging boolean
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Maybe |
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I think |
This used to excise parity data, it's better to keep them for complete statistical analysis
…MG kinetics in parityData User gets to choose whether it wants all kinetics in the parity Data (both exact and non-exact), or only the exact ones
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This is a revised and updated script of Nathan's old kinetics evaluation script containing 3 main functionalities:
obtainKineticsFamilyStatistics: gathers and saves data about families into a .csv files containing info on the number of exact rate rules, number of groups per tree in the groupsleaveOneOut: performs a leave one out test by deleting an exact node (excludes averaged ones), averaging the tree and then trying to estimate that tree. Creates parity plots for each family and creates a .csv of the root mean square error.compareNIST: compares the family estimated kinetics against the exact kinetics from the NIST depository within each family. Also creates parity plots and .csv of error data.