RcppTskitTestLinking

This is a demo package that shows how to link to and import from RcppTskit package, which provides R access to tskit C API.

Key files

The key files you should study are:

• DESCRIPTION

• R/RcppTskitTestLinking-package.R

• src/test.cpp

• src/Makevars.in and src/Makevars.win.in

• tools/configure.R

• configure and configure.win

• cleanup and cleanup.win

Install and test

You can install and test this package by running:

# Install from GitHub
remotes::install_github("HighlanderLab/RcppTskitTestLinking")

# Load the package
library(RcppTskitTestLinking)

# Check the help page for one implemented function
?ts_num_individuals_ptr2

Now run the example from the help page. Below we mark it up to explain what is what.

# Find an example tree sequence file in RcppTskit package
> ts_file <- system.file("examples", "test.trees", package = "RcppTskit")
> ts_file
[1] "/Users/ggorjanc/Library/R/arm64/4.5/library/RcppTskit/examples/test.trees"

# Load tree sequence into R workspace
> ts <- RcppTskit::ts_load(ts_file)

# Check summary of the tree sequence
> ts
Object of class 'TreeSequence'
$ts
         property            value
1     num_samples              160
2 sequence_length            10000
3       num_trees               26
4      time_units      generations
5        min_time                0
6        max_time 7.47028168974859
7    has_metadata            FALSE

$tables
        table number has_metadata
1 provenances      2           NA
2 populations      1         TRUE
3  migrations      0        FALSE
4 individuals     80        FALSE
5       nodes    344        FALSE
6       edges    414        FALSE
7       sites   2376        FALSE
8   mutations   2700        FALSE

# Note that we have 80 individuals in ts

# We can obtain the same number by running
> ts$num_individuals()
[1] 80

# This demo package implemented the same function
# that is available in RcppTskit, but since we here
# focus just on C++ code, we have to work with the
# pointer object (externalptr) `ts$pointer` and
# not with the tree sequence object (TreeSequence) `ts`
> ts_num_individuals_ptr2(ts$pointer)
[1] 80

Wrap up

Hopefully this demo package shows you sufficiently well on how to leverage RcppTskit for your package.

If we develop any methods that should work on the tree sequence object (TreeSequence), then the methods could go into RcppTskit::TreeSequence or new packages could inherit from this class and add their methods.