POPdemog

POPdemog is a R package to visualize demographic history from coalescent simulation script. Currently, this POPdemog package does not check the simulation program input for correctness, but assumes the simulation program input has been validated by the simulation program.

We have verified the POPdemog package can be installed on R of version 2.15.0, 2.15.1, 3.0.0, 3.0.2, 3.1.0, 3.1.2, 3.2.0, 3.2.2, 3.3.0, 3.3.2, 3.4.1, and 3.4.3; but not all examples in the tutorial file can run on all these versions. We suggest user to use R (>= 3.3.0) to install and run this package.

Citation

Zhou, Y., Tian, X., Browning, B.L. and Browning, S.R., 2018. POPdemog: visualizing population demographic history from simulation scripts. Bioinformatics, 34(16), pp.2854-2855.

Installation

Now user can install this package directly from the CRAN as:

    install.packages("POPdemog")

User can also download and then install it as

    install.package("POPdemog_1.0.3.tar.gz", repos=NULL, source=TRUE)

For R version >= 3.3.0, package POPdemog can be installed from the source file

    install.packages("https://github.com/YingZhou001/POPdemog/raw/master/POPdemog_1.0.3.tar.gz", repos=NULL)

then loaded it with

    library(POPdemog)

Note: Safari may automatically unzip the gz file when download the package source. Please see this page for how to download files with Safari without unzipping files.

Docs and materials: doc/

User can start with the tutorial, and check function details with the manual

Tools: tools/

msprime2ms.py

Convert the demographic model specified in msprime to the ms-compatible format.

Usage:

python msprime2ms.py [demofile] [population_configurations] [migration_matrix] [demographic_events]

[demofile] = input python file which specified the demographic model in msprime format
[population_configurations] = name of the variable for population_configurations in msprime
[migration_matrix] = name of the variable for migration_matrix in msprime
[demographic_events] = name of the variable for demographic_events in msprime

Notes:

• The python version should be the same as you use to install msprime.
• The reference effective population size is set as Ne=10,000, for the followed plot, N4=4*Ne=40,000.
• The sample size for each subpopulation is set as 1 since it is irrelevant here.

An example:

python tools/msprime2ms.py doc/demo1.py population_configurations migration_matrix demographic_events > msprime.demo.cmd

Who to blame: Ying Zhou (yz001(at)uw(dot)edu)