ldpop | Two locus likelihoods and ARGs under changing population

by popgenmethods Python Version: Current License: MIT

X-Ray Key Features Code Snippets Community Discussions Vulnerabilities Install Support

kandi X-RAY | ldpop Summary

ldpop is a Python library. ldpop has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can download it from GitHub.

Two locus likelihoods and ARGs under changing population size

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Quality

Security

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Support

ldpop has a low active ecosystem.

It has 11 star(s) with 3 fork(s). There are 4 watchers for this library.

It had no major release in the last 6 months.

There are 0 open issues and 1 have been closed. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of ldpop is current.

Quality

ldpop has 0 bugs and 0 code smells.

Security

ldpop has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

ldpop code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

ldpop is licensed under the MIT License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

ldpop releases are not available. You will need to build from source code and install.

Build file is available. You can build the component from source.

Installation instructions, examples and code snippets are available.

It has 997 lines of code, 48 functions and 11 files.

It has high code complexity. Code complexity directly impacts maintainability of the code.

Top functions reviewed by kandi - BETA

kandi has reviewed ldpop and discovered the below as its top functions. This is intended to give you an instant insight into ldpop implemented functionality, and help decide if they suit your requirements.

Compute likelihoods for a population
Generate a stochastic stochastic matrix
Return a MoranStatesAugmented by n
Gets the joint unlinked stationary
Wrapper function for ordered - likelihoods
Calculate the probability density for a population
Check that the given likelihoods are valid
Calculate folded likelihoods
Build a sparse matrix for copy rates
Subtract the rowsum of a matrix
Calculate the hash of a configuration array
Calculate the rates for the given states
Return a list of rows corresponding to the given index
Get a key from a number
Builds the symmetrized configurations
Get the indices of the folded configs
Build all configurations
Make all configurations in a list
Calculates the rates for each state
Calculate the crosscoal rates
Calculate the mutation rates for a given state
Return a list of rhos from a string

Get all kandi verified functions for this library.

ldpop Key Features

No Key Features are available at this moment for ldpop.

ldpop Examples and Code Snippets

No Code Snippets are available at this moment for ldpop.

Community Discussions

No Community Discussions are available at this moment for ldpop.Refer to stack overflow page for discussions.

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install ldpop

To install, in the top-level directory of LDpop (where "setup.py" lives), type.
Python 2.7, 3.5, or 3.6
Optional: Java 8 Not required for computing lookup tables. Required for posterior sampling of 2-locus ARGs.
Use run/ldtable.py to create a lookup table. See. By default run/ldtable.py uses an exact algorithm to compute the likelihoods. To use a reasonable approximation that is much faster and scales to larger sample sizes, use the flag --approx. run/ldproposal.py and run/ImportanceSampler.jar are for importance sampling from the posterior distribution of 2-locus ARGs. run/ldproposal.py creates a proposal distribution, that run/ImportanceSampler.jar uses to sample the ARGs. See their --help for instructions. Also, see the examples.

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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