Little fixes #31
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Little fixes #31
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jcblemai
commented
Apr 18, 2023
jcblemai
commented
- Argument to set inference_job time limit
- fix ground truth env variable
saraloo
previously approved these changes
Apr 19, 2023
…into little-fixes
Updated some likelihood functions and added lognormal - updated sqrtnorm to have a constant standard deviation not constant coefficient of variation. Created new distribution sqrtnorm_cov - for norm_cov and sqrtnorm_cov, standard deviation is scaled by the SIMULATION, not the observation, since the simulated value is the mean of the distribution -added the lognormal distribution. The MLE/mode of this distribution is the simulated value. All zeros in the data must be converted into "1" first to avoid infinite values for the log
Before if add_one was one we always added one to all zero simulation values. The problem with this is that if the data was also zero, this is artificially moving the model away from the data and lowering the likelihood. In addition, having data values of zero is also a problem for some likelihood functions. Now, we do something slightly more nuanced. * If the model and data are both zero at a timepoint, we assign a likelihood of 1. * If only the model is zero but data is non-zero, if add_one is TRUE we add one to model value and calculate likelihood. * If the model is non-zero, then the likelihood is evaluated as normal UNLESS the function is lognormal, and then we add one to the observed data
Updated tests to include lognormal and to include check that when data and simulation are both zero, log likelihood is zero (the highest likelihood possible)
saraloo
approved these changes
Apr 24, 2023
shauntruelove
approved these changes
Apr 24, 2023
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