tsdate | Infer the age of ancestral nodes in a tree sequence | Genomics library

by tskit-dev Python Version: 0.2.0 License: MIT

X-Ray Key Features Code Snippets Community Discussions(6)Vulnerabilities Install Support

kandi X-RAY | tsdate Summary

tsdate is a Python library typically used in Artificial Intelligence, Genomics applications. tsdate has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can install using 'pip install tsdate' or download it from GitHub, PyPI.

tsdate is a scalable method for estimating the age of ancestral nodes in a tree sequence. The method uses a coalescent prior and updates node times on the basis of the number of mutations along each edge of the tree sequence (i.e. using the "molecular clock"). The method is designed to operate on the output of tsinfer, which efficiently infers tree sequence topologies from large genetic datasets. Please refer to the documentation for information on installing and using the software. The algorithm is described in this BioRxiv preprint. We also provide evaluations of the accuracy and computational requirements of the method using both simulated and real data. The code to reproduce these results can be found in another repository. Anthony Wilder Wohns, Yan Wong, Ben Jeffery, Ali Akbari, Swapan Mallick, Ron Pinhasi, Nick Patterson, David Reich, Jerome Kelleher, and Gil McVean (2021) A unified genealogy of modern and ancient genomes. bioRxiv 2021.02.16.431497; doi: Please cite this preprint if you use tsdate in published work.

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Support

tsdate has a low active ecosystem.

It has 14 star(s) with 6 fork(s). There are 10 watchers for this library.

There were 1 major release(s) in the last 12 months.

There are 44 open issues and 66 have been closed. On average issues are closed in 94 days. There are 5 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of tsdate is 0.2.0

Quality

tsdate has 0 bugs and 0 code smells.

Security

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

tsdate code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

tsdate 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

tsdate releases are available to install and integrate.

Deployable package is available in PyPI.

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

It has 5567 lines of code, 316 functions and 18 files.

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

Top functions reviewed by kandi - BETA

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

Perform the analysis on the tree
Add a prior to the ConditionalCoalescentTimes object
Compute tau expectation of i
Return a single root node
Evaluate posterior distribution
Evaluate node accuracy
Compute the mixture prior parameter for a list of spans_by_samples
Calculate prior confidence intervals for each node
Calculate the outside of an edge
Calculate the fixed - likelihood
Returns the values inside the given edge
Wrapper around _liklihoods
Concatenate sparse matrices
Preprocess a tskit tree
Get the outside of an edge
Get elements inside an edge
Wrapper function for _liklihoods
Create a date from a tskit file
Calculate the tau variance of the tree
Calculate the covariance matrix for the posterior distribution
Calculate the sites time of a tree sequence
Preprocess a tree sequence
Function to update the priors with new priors
Finalize the tree
Compute the priors for the given trees
Calculate the precalculated prior lookup table

Get all kandi verified functions for this library.

tsdate Key Features

No Key Features are available at this moment for tsdate.

tsdate Examples and Code Snippets

No Code Snippets are available at this moment for tsdate.

Community Discussions

Trending Discussions on tsdate

VBScript moved and new created file with same date-time

Query Update For MAX ID and LNUM

Create a timeseries from start and end dates

Oracle query to find previous 2 entries

Why does JavaScript runtime error: Object doesn't support property or method 'getTime' happen?(getTime is not a function)

Why does JavaScript runtime error: Object doesn't support property or method 'datepicker' happen?(datepicker is not a function)

QUESTION

VBScript moved and new created file with same date-time

Asked 2022-Mar-11 at 06:00

I'm using the following code to rotate log files. If the Log.txt file is different than the current date-time (based on file property .DateCreated), the file is moved using the .DateCreated value to rename it and then a new Log.txt file is created but the new file date created value is the same as the moved (archived) file.

If the script is run again a few seconds later it fails to move the Log.txt file as an archived version already exist.

...

ANSWER

Answered 2022-Mar-11 at 05:55

Based on LesFerch comment I have tested adding a delay of 16 seconds to overcome the default Tunneling cache time and that resolved the issue using the C drive.

Source https://stackoverflow.com/questions/71433113

QUESTION

Query Update For MAX ID and LNUM

Asked 2022-Jan-26 at 02:06

i have 1 table for Update MAX(TID) and TEDATE = TSDATE - 1

...

ANSWER

Answered 2022-Jan-25 at 06:03

What is MAX(TID)? There's only one row.

Did you mean something like this?

Source https://stackoverflow.com/questions/70844030

QUESTION

Create a timeseries from start and end dates

Asked 2021-Mar-24 at 09:47

I want to create a time-series from a table that contains Start and End dates for subscriptions. The input table contains account names for subscriptions and their respective start and end dates.

...

ANSWER

Answered 2021-Mar-24 at 09:47

I think you need first convert values to datetimes and then use concat in list comprehension, last use Index.value_counts:

Source https://stackoverflow.com/questions/66778266

QUESTION

Oracle query to find previous 2 entries

Asked 2020-Oct-12 at 15:33

EMP     Code      Date
123     'ESL'     '10-12-2020'
123     'ASU'     '10-09-2020'
123     'PTO'     '10-07-2020'


EMP     Code      Date
567     'ESL'     '10-12-2020'
567     'PTO'     '10-09-2020'
567     'PTO'     '10-07-2020'

...

ANSWER

Answered 2020-Oct-12 at 15:33

Use the COUNT analytic function with a window of the 2 preceding rows:

Source https://stackoverflow.com/questions/64320247

QUESTION

Why does JavaScript runtime error: Object doesn't support property or method 'getTime' happen?(getTime is not a function)

Asked 2020-Aug-19 at 01:31

The following code is MVC C# cshtml document.

...

ANSWER

Answered 2020-Aug-19 at 01:31

In your code,

Source https://stackoverflow.com/questions/63478740

QUESTION

Why does JavaScript runtime error: Object doesn't support property or method 'datepicker' happen?(datepicker is not a function)

Asked 2020-Aug-18 at 07:39

The following code is MVC C# cshtml document.

...

ANSWER

Answered 2020-Aug-18 at 05:42

Using cdn links to .js and .css

Source https://stackoverflow.com/questions/63461767

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

Vulnerabilities

No vulnerabilities reported

Install tsdate

You can install using 'pip install tsdate' or download it from GitHub, PyPI.
You can use tsdate like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.

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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