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spIBDerverse

The goal of spIBDerverse is to give a series of function to apply ERGMs to IBD networks.

Installation

You can install the development version of spIBDerverse from GitHub with:

# install.packages("pak")
pak::pak("jonotuke/spIBDerverse")

Example

Data

The fundemental object for the spIBDerverse package is the IBD network. You are create this using two TSV files.

IBD dataset (edge info)

The first file is the IBD file. It should have the following headers.

#> -  iid1 
#> -  iid2 
#> -  max_IBD 
#> -  sum_IBD>8 
#> -  n_IBD>8 
#> -  sum_IBD>12 
#> -  n_IBD>12 
#> -  sum_IBD>16 
#> -  n_IBD>16 
#> -  sum_IBD>20 
#> -  n_IBD>20

Meta dataset (node info)

The next file needed is the meta file. This can contain any meta-data about the samples, but needs two columns:

  1. iid this has the sample IDs and must have an entry for each of the IDs mentioned in the iid1 and iid2 column of the IBD file.
  2. A frac_gp column.

Creating the IBD network.

There are example files within the spIBDerverse package that can be used as an example. These can be obtained with

ibd_file <- fs::path_package(
  "extdata",
  "example-ibd-data.tsv",
  package = "spIBDerverse"
)
meta_file <- fs::path_package(
  "extdata",
  "example-meta-data.tsv",
  package = "spIBDerverse"
)

We convert these to an IBD network with

ibd_network <- load_ibd_network(
  ibd_file,
  meta_file,
  ibd_co = c(0, 2, 1, 0),
  frac_co = 0.49
)
ibd_network
#> IGRAPH e615b11 UN-- 328 2103 -- 
#> + attr: name (v/c), frac_gp (v/n), frac_missing (v/n), frac_het (v/n),
#> | n_cov_snp (v/n), Archaeological_ID (v/c), Master_ID (v/c), Projects
#> | (v/c), Locality (v/c), Province (v/c), Country (v/c), Latitude (v/n),
#> | Longitude (v/n), date (v/c), date_type (v/c), imputation_type (v/c),
#> | degree (v/n), closeness (v/n), betweenness (v/n), eigencentrality
#> | (v/n), frac_gp1 (e/n), frac_gp2 (e/n), max_ibd (e/n), sum_ibd_8
#> | (e/n), n_ibd_8 (e/n), sum_ibd_12 (e/n), n_ibd_12 (e/n), sum_ibd_16
#> | (e/n), n_ibd_16 (e/n), sum_ibd_20 (e/n), n_ibd_20 (e/n), wij (e/n)
#> + edges from e615b11 (vertex names):
#> [1] KUP007--KUP023 RKC013--RKC029 RKC031--RKF238 RKF195--RKF196 RKC020--RKF142
#> + ... omitted several edges