utils

Numerical utilities for running Covasim.

These include the viral load, transmissibility, and infection calculations at the heart of the integration loop.

Functions

sample	Draw a sample from the distribution specified by the input.
get_pdf	Return a probability density function for the specified distribution.
set_seed	Reset the random seed -- complicated because of Numba, which requires special syntax to reset the seed.
n_binomial	Perform multiple binomial (Bernolli) trials
binomial_filter	Binomial "filter" -- the same as n_binomial, except return the elements of arr that succeeded.
binomial_arr	Binomial (Bernoulli) trials each with different probabilities.
n_multinomial	An array of multinomial trials.
poisson	A Poisson trial.
n_poisson	An array of Poisson trials.
n_neg_binomial	An array of negative binomial trials.
choose	Choose a subset of items (e.g., people) without replacement.
choose_r	Choose a subset of items (e.g., people), with replacement.
choose_w	Choose n items (e.g. people), each with a probability from the distribution probs.
true	Returns the indices of the values of the array that are true: just an alias for arr.nonzero()[0].
false	Returns the indices of the values of the array that are false.
defined	Returns the indices of the values of the array that are not-nan.
undefined	Returns the indices of the values of the array that are not-nan.
itrue	Returns the indices that are true in the array -- name is short for indices[true]
ifalse	Returns the indices that are true in the array -- name is short for indices[false]
idefined	Returns the indices that are defined in the array -- name is short for indices[defined]
iundefined	Returns the indices that are undefined in the array -- name is short for indices[undefined]
itruei	Returns the indices that are true in the array -- name is short for indices[true[indices]]
ifalsei	Returns the indices that are false in the array -- name is short for indices[false[indices]]
idefinedi	Returns the indices that are defined in the array -- name is short for indices[defined[indices]]
iundefinedi	Returns the indices that are undefined in the array -- name is short for indices[defined[indices]]