fpaircase: Expected distributions of distances (functions)

In thibautjombart/vimes: VIsualisation and Monitoring of EpidemicS

Description

The function fpaircase returns functions which compute the expected distributions of distances between pairs of cases given a case reporting probability 'pi'. See dpaircase for details on different types of distances between cases for which distributions can be computed.

Usage

fpaircase(type = c("temporal", "genetic", "spatial", "empiric"), gamma_shape,
  gamma_rate = 1, gamma_scale = 1/gamma_rate, poisson_rate, sd_spatial, p,
  alpha = 0.001)

## S3 method for class 'fpaircase'
print(x, ...)

## S3 method for class 'fpaircase'
plot(x, y = NULL, pi = 1, xlim = c(0, 10),
  lines_args = list(), ...)

Arguments

type	type of distance to be considered (one of "temporal","genetic", "spatial" or "empiric").
gamma_shape	shape of the gamma distribution used for the serial interval
gamma_rate	an alternative way to specify the scale of the gamma distribution used for the serial interval
gamma_scale	scale of the gamma distribution used for the serial interval
poisson_rate	rate (i.e. mean) of the poisson distribution used for the per time unit genetic mutation rate
sd_spatial	standard deviation of the Normal spatial kernel.
p	A numeric vector providing the probability mass function, or empirical frequencies, of pairwise distances.
alpha	The probability threshold to be used to determine the maximum value of generations between two successive cases to consider; this value ('max_kappa') will be the smallest k so that p(k > max_kappa) < alpha. Defaults to 0.001.
x	vector of quantiles.
...	further arguments passed to methods (print, plot, etc.)
y	An optional vector of probabilities used for adding quantiles to the plot.
pi	The reporting probability, i.e. the proportion of cases of the outbreak that have been reported.
xlim	A vector of 2 numbers indicating the limits of the x-axis.
lines_args	A list of named arguments to be passed to abline for plotting quantiles.

Author(s)

Thibaut Jombart [e-mail].

Examples

## spatial distribution

f <- fpaircase("spatial", sd_spatial=10)
plot(f)
plot(f, xlim = c(0, 100))
plot(f, xlim = c(0, 100), pi = 0.4)


## adding quantiles, 50% sampling and customisation

plot(f, seq(0.5, .99, le=10), pi = 0.5, xlim = c(0,50),
     lines_args = list(lty = 2, col = rev(heat.colors(10))))


## genetic distribution

f <- fpaircase("genetic", gamma_shape = 1, gamma_scale = 2,
               poisson_rate = 0.5)

plot(f)
plot(f, xlim = c(0, 20), pi = 0.4)

thibautjombart/vimes documentation built on May 31, 2019, 10:38 a.m.