Nothing
## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----setup--------------------------------------------------------------------
library(covidprobability)
## ---- fig.width=8, fig.height=4-----------------------------------------------
plot(0:21, dlnorm(0:21, 1.63, 0.5),
xlab="Days after exposure",
ylab="Probability",
main="Incubation period",
type = "b")
## ---- fig.width=8, fig.height=4-----------------------------------------------
plot(0:21, plnorm(0:21, 1.63, 0.5),
ylab="Proportion",
xlab = "Days since exposure",
main="Infected expected to have developed symptoms",
type="b")
## ---- fig.width=8, fig.height=4-----------------------------------------------
plot(0:14, sapply(0:14, prop_remaining, asympt = 0.279, mu = 1.63, sigma = 0.5),
ylab="Proportion remaining", xlab = "Day", ylim = c(0,1), type = "b")
## ---- fig.width=8, fig.height=4-----------------------------------------------
plot(0:14, c(0.13, adjust_pretest(pre0 = 0.13, asymp = 0.279, days = 14)),
ylab="pretest probability", xlab="Day", type = "b", ylim = c(0, 0.2))
## ---- fig.width=8, fig.height=4-----------------------------------------------
plot(sens$point, ylim=c(0,1),
main="PCR Sensitivity with 95% CI",
xlab="Days since exposure", ylab="Sensitivity",
type="l");
lines(sens$lower, col="grey")
lines(sens$upper, col="grey")
## ---- fig.width=8, fig.height=4-----------------------------------------------
example <- posttest_series(pre0 = 0.13, asympt = 0.279,
sens = sens$point, spec = 1)
example_upper <- posttest_series(pre0 = 0.13, asympt = 0.279, sens = sens$upper,
spec = 1)
example_lower <- posttest_series(pre0 = 0.13, asympt = 0.279, sens = sens$lower,
spec = 1)
plot(example$x, example$y,
xlab="Day of testing",
ylab="Probability of having COVID-19",
main="Red = pretest; Blue = posttest",
ylim=c(0, 0.25), col="blue", type="l")
lines(example$x, example$y,
col="blue", type="l")
lines(example_lower$x, example_lower$y,
col="lightblue", type="l")
lines(example_upper$x, example_upper$y,
col="lightblue", type="l")
lines(1:14, adjust_pretest(0.13, asympt = 0.279),
col="red", type="l")
## ---- fig.width=8, fig.height=4-----------------------------------------------
unit_size <- 4
any_example <- probability_any(unit_size, example$y)
any_example_upper <- probability_any(unit_size, example_upper$y)
any_example_lower <- probability_any(unit_size, example_lower$y)
plot(example$x, any_example,
xlab="Day of testing",
ylab="Probability of any person having COVID-19",
ylim=c(0, 0.50), col="blue", type="l")
lines(example_lower$x, any_example_lower,
col="lightblue", type="l")
lines(example_upper$x, any_example_upper,
col="lightblue", type="l")
abline(v=example$x[example[,2]==min(example$y)])
## ---- fig.width=8, fig.height=4-----------------------------------------------
test <- individual_probability(test_day = 9, pre0 = 0.13, sens = sens, spec = 1,
asymp = 0.279, days = 14, mu = 1.63, sigma = 0.5)
plot(1:14, test$point, type="l", ylim=c(0,0.3),
main = "Individual probabiltiy of undetected COVID-19",
xlab = "Days since exposure",
ylab = "Probability")
lines(test$lower, type="l", col="grey")
lines(test$upper, type="l", col="grey")
## ---- fig.width=8, fig.height=4-----------------------------------------------
test_n <- unit_probability(test_day = 9, pre0 = 0.13, sens = sens, spec = 1,
asympt = 0.279, days = 14, mu = 1.63, sigma = 0.5,
n = 10)
plot(1:14, test_n$point, type="b", ylim=c(0,1),
main = "Unit-wide probabiltiy of undetected COVID-19",
xlab = "Days since exposures",
ylab = "Probability")
lines(test_n$lower, type="l", col="grey")
lines(test_n$upper, type="l", col="grey")
abline(v = 9)
text(1:14, (test_n$point + 0.1), round(test_n$point, 2), cex = 1)
## -----------------------------------------------------------------------------
test_n$point[9]
test_n$point[14]
test_n$lower[9]
test_n$lower[14]
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