Title:	Estimate Transmission Assortativity Coefficients
Version:	0.1.0
Description:	Estimates group transmission assortativity coefficients from transmission trees. Group transmission assortativity coefficients measure the tendency for individuals to transmit within their own group (e.g. age group, vaccination status, or location) compared to other groups. The package requires information on who infected whom, group membership for all individuals, and the relative sizes of each group in the population. For more details see Geismar et al. (2024) <doi:10.1371/journal.pone.0313037>.
License:	CC BY 4.0
Encoding:	UTF-8
RoxygenNote:	7.3.3
Suggests:	knitr, rmarkdown, testthat (≥ 3.0.0), pak, epicontacts, visNetwork
Config/testthat/edition:	3
Depends:	R (≥ 3.5)
LazyData:	true
VignetteBuilder:	knitr
URL:	https://github.com/CyGei/linktree, https://cygei.github.io/linktree/
BugReports:	https://github.com/CyGei/linktree/issues
NeedsCompilation:	no
Packaged:	2025-12-09 19:18:40 UTC; cy
Author:	Cyril Geismar [aut, cre, cph]
Maintainer:	Cyril Geismar <c.geismar21@imperial.ac.uk>
Repository:	CRAN
Date/Publication:	2025-12-15 18:30:02 UTC

Check 'alpha' value

Description

Check 'alpha' value

Usage

check_alpha(alpha)

Arguments

Check 'delta' value

Description

Check 'delta' value

Usage

check_delta(delta)

Arguments

Check 'f' levels

Description

Check 'f' levels

Usage

check_flevels(f, levels)

Arguments

Check 'from' and 'to' vectors

Description

Check 'from' and 'to' vectors

Usage

check_fromto(from, to)

Arguments

Check 'gamma' value

Description

Check 'gamma' value

Usage

check_gamma(gamma)

Arguments

Check 'x' and 'n' values

Description

Check 'x' and 'n' values

Usage

check_xn(x, n)

Arguments

Convert delta to gamma

Description

Convert delta to gamma

Usage

delta2gamma(delta)

Arguments

Value

A numeric vector of the corresponding gamma coefficients.

Examples

delta2gamma(delta = c(-1,0,1))

Convert gamma to delta

Description

Convert gamma to delta

Usage

gamma2delta(gamma)

Arguments

Value

A numeric vector delta coefficients.

Examples

gamma2delta(gamma = c(0,1,10, Inf))

Calculate delta

Description

Computes the scaled tansmission assortativity coefficient, see function gamma2delta.

Usage

get_delta(from, to, f, alpha = 0.05)

Arguments

Value

A data frame with the estimated delta, lower and upper confidence limits for each group.

Examples

from <- c("A", "A", NA, "C", "C", "C")
to <- c("A", "B", "B", "C", "C", "C")
f <- c(A = 0.3, B = 0.2, C = 0.5)
get_delta(from, to, f, alpha = 0.05)

Calculate gamma

Description

Computes the tansmission assortativity coefficient defined as the excess probability of a secondary infection taking place within-group compared to random expectations.

Usage

get_gamma(from, to, f, alpha = 0.05)

Arguments

Value

A data frame with the estimated gamma, lower and upper confidence limits for each group.

Examples

from <- c("A", "A", NA, "C", "C", "C")
to <- c("A", "B", "B", "C", "C", "C")
f <- c(A = 0.3, B = 0.2, C = 0.5)
get_gamma(from, to, f, alpha = 0.05)

Calculate Pi Values

Description

Calculates the within-group transmission proportion 'pi' for each group in the data.

Usage

get_pi(from, to, alpha = 0.05)

Arguments

Value

A data frame with the group names and the corresponding 'pi' values and confidence intervals.

Examples

from <- c("A", "A", "NA", "C", "C", "C")
to <- c("A", "B", "B", "C", "C", "C")
get_pi(from, to, alpha = 0.05)

Plot linktree objects

Description

Plots error bars for objects of class linktree (with subclasses gamma, delta, or pi). The method displays point estimates with confidence intervals for each group. A horizontal dotted line is added at the neutral value: y = 1 for subclass gamma and y = 0 for subclass delta.

Usage

## S3 method for class 'linktree'
plot(x, ...)

Arguments

Value

No return value, called for side effects (produces a plot).

Examples

from <- c("A", "A", NA, "C", "C", "C")
to <- c("A", "B", "B", "C", "C", "C")
f <- c(A = 0.3, B = 0.2, C = 0.5)
plot(get_delta(from, to, f))
plot(get_gamma(from, to, f))

Simulated transmission tree

Description

This dataset represents a simulated transmission tree. This simulation was generated using the R package o2groups (see https://github.com/CyGei/o2groups for more information). Group HCW is assortative with a gamma coefficient of 2 and group patient is disassortative with a gamma coefficient of 1/1.25. Suceptible group sizes were 100 and 350, respectively. Code to reproduce the data below:

pak::pak("CyGei/o2groups")
set.seed(123)
sim_tree <- o2groups::simulate_groups(
  duration = 100,
  group_n = 2,
  size = c(100, 350), # susceptible group sizes
  name = c("HCW", "patient"),
  gamma = c(2, 0.8), # assortativity coefficients
  intro_n = c(1, 3),
  r0 = c(2, 2),
  generation_time = c(0, 0.1, 0.2, 0.4, 0.2, 0.1, 0),
  incubation_period = sample(1:14, 1000, replace = TRUE)
)

Usage

sim_tree

Format

A data frame with 373 rows and 6 columns:

group

Character. The group to which the individual belongs.

id

Character. Unique identifier for each individual in the study.

source

Character. The ID of the individual who was the source of infection, if known. NA indicates an unknown source.

source_group

Character. The group of the source individual. NA for unknown sources.

date_infection

Numeric. The date of infection. Represented as the number of days since the start of the study.

date_onset

Numeric. The date of onset of symptoms. Represented as the number of days since the start of the study.

Source

This dataset is simulated (see R package o2groups) and does not correspond to real-world data.