twallema/pySODM issues and pull requests

#125 - Fix printing of diagnostics in running MCMC

Pull Request - State: closed - Opened by twallema 9 days ago

#124 - Dump samples in an xarray while sampling

Pull Request - State: closed - Opened by twallema 10 days ago

#123 - Add type-hinting to all user-focused functions and classes

Pull Request - State: closed - Opened by twallema 11 days ago

#122 - add marginal distribution plot

Pull Request - State: closed - Opened by twallema 12 days ago

#121 - Bugfix validation of calibrated parameters

Pull Request - State: closed - Opened by twallema 20 days ago

#120 - Function to cut out ICF params

Pull Request - State: closed - Opened by twallema about 1 month ago

#119 - Add prior regularization

Pull Request - State: closed - Opened by twallema about 1 month ago

#118 - Overhaul log prior distributions

Pull Request - State: closed - Opened by twallema about 2 months ago

#117 - Resolve no output error when providing expanded prior functions and arguments

Pull Request - State: closed - Opened by twallema about 2 months ago

#116 - Update faulty function flow stochastic models

Pull Request - State: closed - Opened by twallema about 2 months ago

#115 - Harmonize PSO and NM optimizers

Pull Request - State: closed - Opened by twallema about 2 months ago

#114 - Add loc argument to gamma prior

Pull Request - State: closed - Opened by twallema 3 months ago

#113 - Use of unbounded informative prior conflicts with restricting estimated pars within bounds

Pull Request - State: closed - Opened by twallema 3 months ago

#112 - function `perturbate_theta` description of output dimensions is reversed

Pull Request - State: closed - Opened by twallema 3 months ago

#111 - Revert "Function perturbate_theta: description of output dimensions was reversed"

Pull Request - State: closed - Opened by twallema 3 months ago

#110 - Function perturbate_theta: description of output dimensions was reversed

Pull Request - State: closed - Opened by twallema 3 months ago

#109 - Check if simulation contains nans before computing log likelihood

Pull Request - State: closed - Opened by twallema 3 months ago

#108 - Update assign theta

Pull Request - State: closed - Opened by twallema 3 months ago

#107 - Add "upload to 'testpyPItest'" section in docs

Pull Request - State: closed - Opened by twallema 4 months ago

#106 - Version 0.2.5

Pull Request - State: closed - Opened by twallema 4 months ago

#105 - Add documentation on how to publish to pyPI for future reference

Pull Request - State: closed - Opened by twallema 4 months ago

#104 - New github PR template

Pull Request - State: closed - Opened by twallema 4 months ago

#103 - Test the format of states, parameters, stratified_parameters, dimensions defined by user in model class

Pull Request - State: closed - Opened by twallema 4 months ago

#102 - Change 'states' --> 'initial_states' when initializing model

Pull Request - State: closed - Opened by twallema 4 months ago

#101 - Revert draw functions: alter parameters only

Pull Request - State: closed - Opened by twallema 4 months ago

#100 - Deprecation of "warmup"

Pull Request - State: closed - Opened by twallema 4 months ago

#99 - Initial condition functions

Pull Request - State: closed - Opened by twallema 4 months ago

#98 - Verify dataset is not empty

Pull Request - State: closed - Opened by twallema 5 months ago

#97 - Refurbish emcee sampler

Pull Request - State: closed - Opened by twallema 5 months ago

#96 - Change the moves once more

Pull Request - State: closed - Opened by twallema 5 months ago

#95 - Add changes to initial conditions to draw functions

Pull Request - State: closed - Opened by twallema 5 months ago

#94 - Attempting to calibrate to an empty dataset not caught by input checks of `log_posterior_probability`

Issue - State: closed - Opened by twallema 5 months ago - 1 comment

#93 - Mention PR 92 in readme

Pull Request - State: closed - Opened by twallema 5 months ago

#92 - Add the option to manually define the simulation start when calibrating a model

Pull Request - State: closed - Opened by twallema 5 months ago

#91 - Remove hit counter in readme, it returns an internal server error

Pull Request - State: closed - Opened by twallema 5 months ago

#90 - Enable retaining floats in function list_to_dict in log posterior probability function

Pull Request - State: closed - Opened by twallema 5 months ago

#89 - Change to 50% KDE move, 25% DE move, 25% DESnookermove for more mobile chains

Pull Request - State: closed - Opened by twallema 5 months ago

#88 - Implement lognormal log likelihood function

Pull Request - State: closed - Opened by twallema 5 months ago

#87 - Add in a 25% chance of using an emcee.DESnookermove by default

Pull Request - State: closed - Opened by twallema 5 months ago

#86 - Use nplog1p in poisson/negbinom likelihood function

Pull Request - State: closed - Opened by twallema 5 months ago

#85 - Manual seeding randomness in JumpProcess class using "fork" multiprocessing

Pull Request - State: closed - Opened by twallema 6 months ago

#84 - change the behavior of retain_floats to False because it does not wor…

Pull Request - State: closed - Opened by twallema 6 months ago - 1 comment

#83 - Prohibit automatic multithreading in Numpy, Tensorflow & Torch for large matrices

Pull Request - State: closed - Opened by twallema 6 months ago

#82 - Allow uniform priors to handle infinite bounds --> equivalent to having "no prior"

Pull Request - State: closed - Opened by twallema 6 months ago

#81 - remove if: github.event_name == 'push' from deploy docs workflow file

Pull Request - State: closed - Opened by twallema 7 months ago

#80 - something tiny

Pull Request - State: closed - Opened by twallema 7 months ago

#79 - Update local docs build commands

Pull Request - State: closed - Opened by twallema 7 months ago

#78 - Make documentation intro and readme more succinct

Pull Request - State: closed - Opened by twallema 7 months ago

#77 - Split base.py in ODE and JumpProcess

Issue - State: open - Opened by twallema 7 months ago

#76 - Change name of tutorial conda environment

Pull Request - State: closed - Opened by twallema 7 months ago

#75 - Draw functions with flexible number of parameters

Pull Request - State: closed - Opened by twallema 7 months ago

#74 - Test if a draw function is a function in `validate_draw_function`

Pull Request - State: closed - Opened by twallema 7 months ago

#73 - Close issue 62, change names input parameters 'draw_functions' to 'parameters' and 'samples' instead of 'param_dict' and 'samples_dict'

Pull Request - State: closed - Opened by twallema 7 months ago

#72 - Simplify influenza data conversion script

Pull Request - State: closed - Opened by twallema 8 months ago

#71 - Change BE demographics to Jan 1, 2018 for influenza case study

Pull Request - State: closed - Opened by twallema 8 months ago

#70 - Tryout on MacBook pro 14

Pull Request - State: closed - Opened by twallema 8 months ago

#69 - Address warnings + remove warning suppression

Pull Request - State: closed - Opened by twallema 9 months ago

#68 - Change license from MIT to CC-BY-NC-SA.

Pull Request - State: closed - Opened by twallema 9 months ago

#67 - Validate use of Python 3.12

Pull Request - State: closed - Opened by twallema 9 months ago

#66 - Bugs in documentation reported by Rita

Pull Request - State: closed - Opened by twallema 11 months ago

#65 - test of docs

Pull Request - State: closed - Opened by twallema about 1 year ago

#64 - Bugs in installation + Bump to version 0.2.4

Pull Request - State: closed - Opened by twallema about 1 year ago

#63 - Error performing `df.values` in `call()` method of class `log_posterior_probability()` when optimising a model with a timeseries of length 1

Issue - State: open - Opened by twallema over 1 year ago
Labels: bug

#62 - 'samples_dict' in a draw function, 'samples' in simulation function

Issue - State: closed - Opened by twallema over 1 year ago - 2 comments
Labels: enhancement

#61 - `ODEModel` class --> `ODE`

Pull Request - State: closed - Opened by twallema over 1 year ago

#60 - Rename `state_dimensions` --> `dimensions_per_state` in model declaration

Pull Request - State: closed - Opened by twallema over 1 year ago

#59 - rename SDEModel JumpProcess and update docs

Pull Request - State: closed - Opened by twallema over 1 year ago

#58 - Drop suffix names in model declaration

Pull Request - State: closed - Opened by twallema over 1 year ago

#57 - Improve scaleability of multinomial sampling in `_tau_leap()`

Pull Request - State: closed - Opened by twallema over 1 year ago

#56 - Omit dependency on numba in base.py

Pull Request - State: closed - Opened by twallema over 1 year ago

#55 - Validate the use of python 3.11

Pull Request - State: closed - Opened by twallema over 1 year ago

#54 - pass-date-as-timestamp-to-integration-functions

Pull Request - State: closed - Opened by twallema over 1 year ago

#53 - Avoiding the use of enumerate in _draw_transitionings seems to result in a small speedup

Pull Request - State: closed - Opened by twallema over 1 year ago

#52 - Omit use of pd.Timestamp/pd.to_datetime/pd.Timedelta in favor of datetime alternative

Pull Request - State: closed - Opened by twallema over 1 year ago

#51 - Peer review R1

Pull Request - State: closed - Opened by twallema over 1 year ago

#50 - The suffix '_names' in the model declaration seems redundant

Issue - State: closed - Opened by twallema over 1 year ago - 1 comment
Labels: enhancement