tests/egf_examples_fixed.R

In davidearn/epigrowthfit: Nonlinear Mixed Effects Models of Epidemic Growth

library(epigrowthfit)
options(warn = 2L, error = if (interactive()) recover)


## exponential #########################################################

r <- log(2) / 20
c0 <- 100

zz <- simulate(egf_model(curve = "exponential", family = "pois"),
               nsim = 1L,
               seed = 412575L,
               mu = log(c(r, c0)),
               cstart = 10)
mm <- egf(zz)

stopifnot(all.equal(coef(zz), coef(mm), tolerance = 5e-02))


## subexponential ######################################################

alpha <- log(2) / 20
c0 <- 100
p <- 0.95

zz <- simulate(egf_model(curve = "subexponential", family = "pois"),
               nsim = 1L,
               seed = 696182L,
               mu = c(log(alpha), log(c0), qlogis(p)),
               cstart = 10)
mm <- egf(zz,
          formula_priors = list(logit(p) ~ Normal(mu = qlogis(p), sigma = 0.5)))

stopifnot(all.equal(coef(zz), coef(mm), tolerance = 5e-02))


## gompertz ############################################################

alpha <- log(2) / 20
tinfl <- 100
K <- 25000

zz <- simulate(egf_model(curve = "gompertz", family = "pois"),
               nsim = 1L,
               seed = 720748L,
               mu = log(c(alpha, tinfl, K)),
               cstart = 10)
mm <- egf(zz)

stopifnot(all.equal(coef(zz), coef(mm), tolerance = 5e-02))


## logistic ############################################################

r <- log(2) / 20
tinfl <- 100
K <- 25000

zz <- simulate(egf_model(curve = "logistic", family = "pois"),
               nsim = 1L,
               seed = 366465L,
               mu = log(c(r, tinfl, K)),
               cstart = 10)
mm <- egf(zz)

stopifnot(all.equal(coef(zz), coef(mm), tolerance = 5e-02))


## richards ############################################################

r <- log(2) / 20
tinfl <- 100
K <- 25000
a <- 1.005

zz <- simulate(egf_model(curve = "richards", family = "pois"),
               nsim = 1L,
               seed = 51520L,
               mu = log(c(r, tinfl, K, a)),
               cstart = 10)
mm <- egf(zz,
          formula_priors = list(log(a) ~ Normal(mu = log(a), sigma = 0.05)))

stopifnot(all.equal(coef(zz), coef(mm), tolerance = 5e-02))