conf_ints_virulence {anovir} R Documentation

## Approximate 95% confidence intervals for virulence

### Description

Function calculating the 95% confidence intervals for a hazard function based on the variance and covariance of its location and scale parameters.

### Usage

conf_ints_virulence(
a2 = a2,
b2 = b2,
var_a2 = var_a2,
var_b2 = var_b2,
cov_a2b2 = cov_a2b2,
d2 = "",
tmax = 21
)


### Arguments

 a2 numeric. Estimated value of location parameter describing mortality due to infection b2 numeric. Estimated value of scale parameter describing mortality due to infection var_a2 numeric. Estimated variance of location parameter describing mortality due to infection var_b2 numeric. Estimated variance of scale parameter describing mortality due to infection cov_a2b2 numeric. Estimated covariance of location and scale parameters above d2 character. Probability distribution assumed to describe virulence; Weibull, Gumbel or Fréchet tmax maximum time virulence will be calculated for. Default value; tmax = 21

### Details

The approach is based on the interval being estimated as a complementary log-log function of the hazard function, h(t), with the variance of virulence being estimated by the Delta method applied to log(h[t]).

### Value

matrix containing estimates of virulence over time ± approx. 95% confidence intervals

### Examples


# the values, variance and covariance of the location and scale parameters
# [a2,a2] describing mortality due to infection were estimated as;
# a2 = 2.5807642
# b2 = 0.1831328
# var_a2 = 0.0008196927
# var_b2 = 0.0010007282
# cov_a2b2 = -0.0003119921

ci_matrix01 <- conf_ints_virulence(
a2 = 2.5807642,
b2 = 0.1831328,
var_a2 = 0.0008196927,
var_b2 = 0.0010007282,
cov_a2b2 = -0.0003119921,
d2 = "Weibull",
tmax = 15)

tail(ci_matrix01)

plot(ci_matrix01[, 't'], ci_matrix01[, 'h2'],
type = 'l', col = 'red',
xlab = 'time', ylab = 'virulence (± 95% ci)')
lines(ci_matrix01[, 'lower_ci'], col = 'grey')
lines(ci_matrix01[, 'upper_ci'], col = 'grey')



[Package anovir version 0.1.0 Index]