cystiSim (version 0.1.0)

cystiSim: 'cystiSim' object

Description

Functions to initiate and explore 'cystiSim' objects. A 'cystiSim' object corresponds to multiple runs of a cystiSim model.

Usage

cystiSim(n = 100, mod, main = NULL)
report(x, ...)
"print"(x, ...)
"summary"(object, round = 3, ...)
"plot"(x, y, annotate = TRUE, ...)
"report"(x, name = "cystiSim", ...)
"elim"(x, show = c("m", "y"), ...)

Arguments

n

Number of iterations (months).

mod

cystiSim model.

main

cystiSim model label.

x

Object of class 'cystiSim'.

object

Object of class 'cystiSim'.

y

Currently ignored.

round

Number of decimal digits to be printed.

annotate

Should plot be annotated with summary information?

name

Report name.

show

Show time till elimination in terms of months or years?

...

Other arguments to be passed to generics.

Value

cystiSim returns an object of S3 class 'cystiSim'.

See Also

cystiRun

Examples

## Not run: 
# 
# ## we will use the built-in Mbeya dataset
# prevalence(pig_mbeya$cysti)
# prevalence(man_mbeya$taenia)
# 
# ## define transmission probabilities
# ph2m <- 0.000174918
# pl2m <- 0.000149501
# m2p  <- 6.85E-05
# e2p  <- 0.00022611
# 
# ## set seed for reproducibility
# set.seed(264)
# 
# ## need to define coverage and efficacy of all interventions
# cov_man_mda <- 0.80
# cov_pig_mda <- 0.90
# cov_pig_vac <- NULL
# eff_man_mda <- 0.70
# eff_pig_mda <- 0.90
# eff_pig_vac <- NULL
# 
# ## run the simulations
# sim <-
# cystiSim(
#   n = 10,
#   main = "example",
#   mod = {
# initiate(man_mbeya, pig_mbeya, ph2m, pl2m, m2p, e2p) %>%
#   update(240) %>%
#   do_man_mda(coverage = cov_man_mda, efficacy = eff_man_mda) %>%
#   do_pig_mda(coverage = cov_pig_mda, efficacy = eff_pig_mda) %>%
#   update(120)
#   }
# )
# 
# ## summarize results
# summary(sim)
# 
# ## plot simulations (mean and uncertainty interval)
# plot(sim)
# 
# ## create PDF report and plot
# report(sim)
# ## End(Not run)