Changelog for epi-sim

0.2.2.0

• Clean up for a release candidate.

0.2.1.0

• Update the stack resolver to lts-16.17 and add bounds on the package versions to use.
• Remove dependency upon epi-types by moving its modules into this package and include the tests from that package.
• Remove unsed Setup.hs file.

0.2.0.1

• Improve documentation in Epidemic.BDSCOD.
• Upgrade to epi-types-0.2.1.2 for the bug fix.

0.2.0.0

• Predicates such as isSampling and isOccurrence have been replaced with clearer named alternatives: isNonReconTreeObservation and isReconTreeLeaf to avoid uncertainty about whether scheduled events are included.
• Upgrade to epi-types-0.2.1.0 which adds substantial amounts of Newick functionality meaning this can be removed.

0.1.9.0

• Upgrade to epi-types-0.2.0.0 which makes a lot of functions redundant so they have been removed.

0.1.8.8

• Upgrade to epi-types-0.1.1.1 and remove joinTimed since it is no longer needed.

0.1.8.7

• Upgrade to epi-types-0.1.1.0 and start using the Timed * class.

0.1.8.6

• Use -j2 to slightly improve compilation time.
• Include a observedEvents function which was missing from the InhomogeneousBDS module.

0.1.8.5

• Start using cabal directly without hpack.
• Move time dependent parameters into a epi-sim package so they are easier to share, and import them here.

0.1.8.4

• Improve documentation of construction of inhomBDSRates and include a test to check this conforms to expectations.
• Implement a birth-death-sampling model with time-dependent birth rates and include an example of what this returns in the README.

0.1.8.3

• Improve error handling in birth-death-lines.R.
• Refactor some of the plotting code in birth-death-lines.R to make it easier to maintain.
• Use the future and furrr packages in R to generate the visualisation of a simulation in parallel since the serial version is frustratingly slow. Both packages are on CRAN so it does not seem unreasonable.

0.1.8.2

• Include an additional parameter in the simulation and simulationWithSystemRandom to determine whether the simulation should be conditioned on having at least two sampled leaves in the reconstructed tree. It does this by repeatedly simulating until such a tree is acheved.

0.1.8.1

• Implement an example of the inhomogeneous birth-death process and include it in the README.
• Fix broken example using the BDSCOD model and organise examples in examples/ rather than just the single one in app/.

0.1.8.0

• Define an inhomogeneous birth-death process in InhomogeneousBD.
• Define an inhomogeneous exponential random sampler using Timed Rates.
• Extend the ModelParameters class to have a birthProb function.
• Include a Timed type for time varying values.
• Include a test that the final size of a birth-death simulation is approximately correct.
• Format the changelog to make it easier to read outside of a browser.
• Fix naming convention and exports in the BirthDeath, BirthDeathSampling and BirthDeathSamplingOccurrencemodules to conform to the pattern used in the BDSCOD module and move simulation into the Utility module since it is common between all models
• Adjust the type of the ModelParameters interface to include potential time dependence.

0.1.7.2

• Make Event an instance of FromRecord to match with ToRecord.

0.1.7.1

• Provide vis/birth-death-lines.R which visualises a simulation.

0.1.7.0

• Provide vis/ott.R to visualise observations through time and make vis/ltt.R ignore disasters.
• Replace some Catastrophe specific functions with equivalents for handling scheduled events more generally
  • noCatastrophe becomes noScheduledEvent
  • firstCatastrophe becomes firstScheduled
• Change the naming of the BDSCO model to be consistent with the new BDSCOD model.
• Implement a birth-death-sampling-catastrophe-occurrence-disaster model in Epidemic.BDSCOD.

0.1.6.2

• Update the visualisation code in vis/ltt.R such that it parses the catastrophe events to draw the LTT.
• BUG FIX: In the observed events catastrophes are replicated when they should not be.

0.1.6.1

• Include a visualisation script for the LTT of reconstructed trees: vis/ltt.R which is described in the README.

0.1.6.0

• Move the ToField declarations into the Epidemic module to avoid orphaned instance and select a representation for multiple people in the CSV output.
• Implement a birth-death-sampling-catastrophe-occurrence model in Epidemic.BirthDeathSamplingCatastropheOccurrence; it's a shame about the length of the name.
• Include a contructor for catastrophe events in which multiple people can be sampled simultaneously.

0.1.5.1

• Include a .gitignore.
• Improved documentation with haddock.

0.1.5.0

• Include some testing with hspec.
• The Epidemic.BirthDeathSamplingOccurrence module now has a function to extract the observable events.
• Change the simulation functions to return events in the order they occurred.
• Change the configuration functions to take tuples of model parameters.

0.1.4.0

• Make Event an instance of the Ord typeclass.
• Implement types and conversion functions for a TransmissionTree and a SampleTree.
• Implement a parser and printer for Newick in Epidemic.Utility.

0.1.3.0

• Implement a birth-death-sampling-occurrence model in Epidemic.BirthDeathSamplingOccurrence.
• Implement a visualisation of the birth-death-sampling LTT in vis/birthDeathSamplingVisualisation.R.
• Implement a birth-death-sampling model in Epidemic.BirthDeathSampling.

0.1.2.0

• Implement a visualisation of the infection network in vis/infection-tree.vg.json.
• Implement Epidemic.Utility.eventsAsJsonTree.
• Move the Epidemic.Simulation module to Epidemic.Utility.

0.1.1.0

• Write the output to CSV using cassava

0.1.0.0

• Basic prototype to simulate a constant rate birth-death process.