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Microsynthesis using quasirandom sampling and/or IPF

Project description

humanleague

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humanleague is a python and an R package for microsynthesising populations from marginal and (optionally) seed data. The core code is implemented in C++, and the current release is version 2.

The package contains algorithms that use a number of different microsynthesis techniques:

The latter provides a bridge between deterministic reweighting and combinatorial optimisation, offering advantages of both techniques:

  • generates high-entropy integral populations
  • can be used to generate multiple populations for sensitivity analysis
  • goes some way to address the 'empty cells' issues that can occur in straight IPF
  • relatively fast compuation time

The algorithms:

  • support arbitrary dimensionality* for both the marginals and the seed.
  • produce statistical data to ascertain the likelihood/degeneracy of the population (where appropriate).

[* excluding the legacy functions retained for backward compatibility with version 1.0.1]

The package also contains the following utility functions:

  • a Sobol sequence generator
  • functionality to convert fractional to nearest-integer marginals (in 1D). This can also be achieved in multiple dimensions by using the QISI algorithm.
  • functionality to 'flatten' a population into a table: this converts a multidimensional array containing the population count for each state into a table listing individuals and their characteristics.

Version 1.0.1 reflects the work described in the Quasirandom Integer Sampling (QIS) paper.

R installation

Official release:

> install.packages("humanleague")

For development version

> devtools::install_github("virgesmith/humanleague")

Or, for the legacy version

> devtools::install_github("virgesmith/humanleague@1.0.1")

python installation

Requires Python 3 and numpy. PyPI package:

python3 -m pip install humanleague

[Conda pacakage is being worked on]

Build and test (from local cloned repo)

$ ./setup.py build
$ python3 tests/test_all.py

Install (from local repo)

$ ./setup.py install

The latter command may require admin rights. On linux, sudo is unnecessary if you have group (e.g. staff) write access to /usr/local/lib.

Examples

Consult the package documentation, e.g.

> library(humanleague)
> ?humanleague

in R, or for python:

>>> import humanleague as hl
>>> help(hl)

Project details


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