- 06 Feb, 2018 2 commits
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Nathaniel Osgood (ndo885) authored
Fixed other formulas for CompletingLatentPeriod to not scale by dt, given that resulting net flows are multiplied by dt
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Nathaniel Osgood (ndo885) authored
Fixed formula for CompletingLatentPeriod to not scale by dt, given that resulting net flows are multiplied by dt
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- 21 Jan, 2018 9 commits
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Nathaniel Osgood (ndo885) authored
Added comments at the top of the .c file to clarify that there is only one currently active model and that it must be run from a corresponding R harness, and to note the need to use ulimit -c
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Nathaniel Osgood (ndo885) authored
Added comments in the .c file to clarify that currently active model must be run from a corresponding R harness
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Nathaniel Osgood (ndo885) authored
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Nathaniel Osgood (ndo885) authored
Added support for the SEIRWithLogCParameter scenario, so as to use stochastic evolution and a more generous/accomodating r dispersion parameter (100 vs. 1000, thereby allowing a broader likelihood function
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Nathaniel Osgood (ndo885) authored
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Nathaniel Osgood (ndo885) authored
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Nathaniel Osgood (ndo885) authored
Added support for the SEIRWithLogCParameter scenario, improved indication of how to use the C interface from different models (for now, until separate modules supported), improved logging
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Nathaniel Osgood (ndo885) authored
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Nathaniel Osgood (ndo885) authored
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- 20 Jan, 2018 13 commits
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Nathaniel Osgood (ndo885) authored
Cleaned up logging to revert to more reasonable levels for debugging-related logging messages still of interest for genreal logging
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Nathaniel Osgood (ndo885) authored
Broadened the conditions of resampling to be done conceptually before the model is advanced (at the end of the previous observation, even for the initial timeepoint), as appears to be consistent with step 2b in Andrieu et al. p272
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Nathaniel Osgood (ndo885) authored
Added code to include the initial values of parameters and latent stated within the recorded values; it had previously been omitted -- something which further impeded interpretability, as initial values were uninitialized
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Nathaniel Osgood (ndo885) authored
Fixed key bug within copy3DDoubleArray whereby one of the indexes was iterating over the count of elements for the other index
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Nathaniel Osgood (ndo885) authored
Fixed key bug within copy3DDoubleArrayLooselyTyped whereby one of the indexes was iterating over the count of elements for the other index
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Nathaniel Osgood (ndo885) authored
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Nathaniel Osgood (ndo885) authored
Updated R code so that arrays of ints for timepoints and observations that should be arrays of double are now properly arrays of double
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Nathaniel Osgood (ndo885) authored
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Nathaniel Osgood (ndo885) authored
Modified limited span/scope of stateVariableByParticleTimeStateVariable by confining it to performSMCAndSampleParticularStateVariableTrajectory (the function that performs SMC and samples the trajectory). This can be done because -- per Juxin Derivation of Calculation of p sub Theta of y1.pdf and equation 9 -- values of state variables are not required to compute p sub Theta of y1 through yT; rather, just the value of weights are.
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Nathaniel Osgood (ndo885) authored
For greater clarity, changed function name stateVariablesSampledByTimepointAndStateVariable to sampledStateVariablesByTimepointAndStateVariable
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Nathaniel Osgood (ndo885) authored
Modified to account for the fact that computeProbOfAllObservablesPSubThetaOfY1ThroughT does not require knowledge of state variable values, only values of weights
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Nathaniel Osgood (ndo885) authored
Modified to account for the fact that only unnormalized weights are used in Juxin Derivation of Calculation of p sub Theta of y1.pdf; had to pass around both unnormalized weights more broadly for this reason, and normalized weights when performing resampling and picking a trajectory
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Nathaniel Osgood (ndo885) authored
Modified to account for Juxin Derivation of Calculation of p sub Theta of y1.pdf, as of Juxin's not of January 15, 2018
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- 07 Jan, 2018 6 commits
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Nathaniel Osgood (ndo885) authored
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Nathaniel Osgood (ndo885) authored
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Nathaniel Osgood (ndo885) authored
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Nathaniel Osgood (ndo885) authored
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Nathaniel Osgood (ndo885) authored
Improved and more consistent logging levels, allowing meaningful high-level output even for levels 0 and 1
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Nathaniel Osgood (ndo885) authored
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- 06 Jan, 2018 10 commits
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Nathaniel Osgood (ndo885) authored
Misc debugging bug fixes and changes to constants, as well as additions of many diagnostic test points
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Nathaniel Osgood (ndo885) authored
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Nathaniel Osgood (ndo885) authored
Per Andrieu p272, fix to ensure that no resampling or ancestor array accumulation takes place for initial timepoint
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Nathaniel Osgood (ndo885) authored
Updated to use regular weights and probabilities rather than log versions thereof, removed Mohammad Obeidat code
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Nathaniel Osgood (ndo885) authored
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Nathaniel Osgood (ndo885) authored
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Nathaniel Osgood (ndo885) authored
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Nathaniel Osgood (ndo885) authored
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Nathaniel Osgood (ndo885) authored
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Nathaniel Osgood (ndo885) authored
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