Examples

This page shows some very brief examples for how to use the mrpast command line in certain scenarios.

ARG has too many populations

In this example, we’ll simulate some ARGs with 3 populations and use them in a model with 2 populations.

mkdir ooa3.simdata/
mkdir ooa3_output/
mkdir ooa2_output/

# Simulate our ARGs first (2 ARGs, 10MB length each, 10 individuals per population, 3 population model)
mrpast simulate -r 2 --seq-len 10000000 -n 10 examples/ooa_3g09.yaml ooa3.simdata/ooa3_

# Use them in the same 3-population model
mrpast process --out-dir ooa3_output examples/ooa_3g09.yaml ooa3.simdata/ooa3__

# Now use them in the 2-population model by removing the 3rd population from the ARG
mrpast process --leave-out 2 --out-dir ooa2_output examples/ooa2_2t12.yaml ooa3.simdata/ooa3__

# Same thing, but lets also rearrange the order of the populations that we map. So we'll let the 2nd
# and 3rd population from the ARG be used in our model, and drop the 1st population.
mrpast process --leave-out 0 --map-pops 1:0,2:1 --out-dir ooa2_output examples/ooa2_2t12.yaml ooa3.simdata/ooa3__

ARG has too few populations

In the opposite scenario from above, we’ll use the same simulated ARGs (3 populations) and use them in a model with 4 populations, which means we need to treat one of them as unsampled (we won’t have any coalescences from the ARG to use).

mkdir ooa4_output/

# The model has 4 populations (0, 1, 2, 3) and we choose to map the 3 ARG populations to the first
# 3 populations of that model. For the last mapping, we just need to choose a number that is NOT in
# the ARG's populations and map it to "3" (the 4th population). Any number will do - here we use 100.
mrpast process --map-pops 0:0,1:1,2:2,100:3 --out-dir ooa4_output/ ../examples/ooa_4j17.yaml ooa3.simdata/ooa3__