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Commit 326ed0c3 authored by pqiao29's avatar pqiao29
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add from E to R: arec.rand, arec.rate, arec.dist.shape, arec.dist.scale

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R/FUN_recovery.R
+ 17
− 1
View file @ 326ed0c3
...@@ -125,7 +125,23 @@ recovery.FUN <- function(dat, at, seed = NULL) { ...@@ -125,7 +125,23 @@ recovery.FUN <- function(dat, at, seed = NULL) {
dat$attr$recovTime[res[[2]]] <- at dat$attr$recovTime[res[[2]]] <- at
status <- res[[3]] status <- res[[3]]
dat$attr$status <- status dat$attr$status <- status
# cat("finished recover \n")
res <- update_status(rate = dat$param$arec.rate,
rand = dat$control$arec.rand,
active,
status = dat$attr$status,
label = c("e"),
state = recovState,
at,
expTime = dat$attr$expTime,
prog.dist.scale = dat$param$arec.dist.scale,
prog.dist.shape = dat$param$arec.dist.shape)
nRecov <- nRecov + res[[1]]
dat$attr$recovTime[res[[2]]] <- at
status <- res[[3]]
dat$attr$status <- status
if (type %in% c("SEIQHRF")) { if (type %in% c("SEIQHRF")) {
# -------------------------------------- case fatality ---------------------------------------- # -------------------------------------- case fatality ----------------------------------------
......
R/set_param.R
+ 79
− 56
View file @ 326ed0c3
### internal function ### internal function
set_param <- function(type = "SEIQHRF", set_param <- function(type = "SEIQHRF",
nsteps = 366, nsteps = 366,
nsims = 8, nsims = 8,
ncores = 4, ncores = 4,
prog.rand = FALSE, prog.rand = FALSE,
rec.rand = FALSE, quar.rand = TRUE,
fat.rand = TRUE, hosp.rand = TRUE,
quar.rand = FALSE, disch.rand = TRUE,
hosp.rand = FALSE, rec.rand = TRUE,
disch.rand = TRUE, arec.rand = TRUE,
infection.FUN = 'infection.FUN', # infection.seiqhrf.icm, fat.rand = TRUE,
recovery.FUN = 'recovery.FUN', # progress.seiqhrf.icm, infection.FUN = 'infection.FUN', # infection.seiqhrf.icm,
departures.FUN = 'departures.FUN', # departures.seiqhrf.icm, recovery.FUN = 'recovery.FUN', # progress.seiqhrf.icm,
arrivals.FUN = 'arrivals.FUN', # arrivals.seiqhrf.icm, departures.FUN = 'departures.FUN', # departures.seiqhrf.icm,
get_prev.FUN = 'get_prev.FUN', # get_prev.seiqhrf.icm, arrivals.FUN = 'arrivals.FUN', # arrivals.seiqhrf.icm,
# init.icm params get_prev.FUN = 'get_prev.FUN', # get_prev.seiqhrf.icm,
s.num = 9997, # init.icm params
e.num=0, s.num = 9997,
i.num = 3, e.num=0,
q.num=0, i.num = 3,
h.num=0, q.num=0,
r.num = 0, h.num=0,
f.num = 0, r.num = 0,
# param.icm params f.num = 0,
inf.prob.e = 0.02, # param.icm params
act.rate.e = 10, inf.prob.e = 0.02,
inf.prob.i = 0.05, act.rate.e = 10,
act.rate.i = 10, inf.prob.i = 0.05,
inf.prob.q = 0.02, act.rate.i = 10,
act.rate.q = 2.5, inf.prob.q = 0.02,
quar.rate = 1/30, act.rate.q = 2.5,
hosp.rate = 1/100, prog.rate = 1/10,
disch.rate = 1/15, quar.rate = 1/30,
prog.rate = 1/10, hosp.rate = 1/100,
prog.dist.scale = 5, disch.rate = 1/15,
prog.dist.shape = 1.5, rec.rate = 0.071,
rec.rate = 0.071, # Based on assumption that disease course is 14 days arec.rate = 0.05,
rec.dist.scale = 35, prog.dist.scale = 5,
rec.dist.shape = 1.5, prog.dist.shape = 1.5,
fat.rate.base = 1/50, quar.dist.scale = 1,
hosp.cap = 40, quar.dist.shape = 1,
fat.rate.overcap = 1/25, hosp.dist.scale = 1,
fat.tcoeff = 0.5, hosp.dist.shape = 1,
vital = TRUE, disch.dist.scale = 1,
a.rate = (10.5/365)/1000, disch.dist.shape = 1,
a.prop.e = 0.01, rec.dist.scale = 35,
a.prop.i = 0.001, rec.dist.shape = 1.5,
a.prop.q = 0.01, arec.dist.scale = 35,
ds.rate = (7/365)/1000, arec.dist.shape = 1.5,
de.rate = (7/365)/1000, fat.rate.base = 1/50,
di.rate = (7/365)/1000, hosp.cap = 40,
dq.rate = (7/365)/1000, fat.rate.overcap = 1/25,
dh.rate = (20/365)/1000, fat.tcoeff = 0.5,
dr.rate = (7/365)/1000, vital = TRUE,
out="mean" a.rate = (10.5/365)/1000,
a.prop.e = 0.01,
a.prop.i = 0.001,
a.prop.q = 0.01,
ds.rate = (7/365)/1000,
de.rate = (7/365)/1000,
di.rate = (7/365)/1000,
dq.rate = (7/365)/1000,
dh.rate = (20/365)/1000,
dr.rate = (7/365)/1000,
out="mean"
) { ) {
control <- control.icm(type = type, control <- control.icm(type = type,
...@@ -62,7 +72,11 @@ set_param <- function(type = "SEIQHRF", ...@@ -62,7 +72,11 @@ set_param <- function(type = "SEIQHRF",
nsims = nsims, nsims = nsims,
ncores = ncores, ncores = ncores,
prog.rand = prog.rand, prog.rand = prog.rand,
quar.rand = quar.rand,
hosp.ramd = hosp.rand,
disch.rand = disch.rand,
rec.rand = rec.rand, rec.rand = rec.rand,
arec.rand = arec.rand,
infection.FUN = infection.FUN, infection.FUN = infection.FUN,
recovery.FUN = recovery.FUN, recovery.FUN = recovery.FUN,
arrivals.FUN = arrivals.FUN, arrivals.FUN = arrivals.FUN,
...@@ -83,15 +97,24 @@ set_param <- function(type = "SEIQHRF", ...@@ -83,15 +97,24 @@ set_param <- function(type = "SEIQHRF",
act.rate.i = act.rate.i, act.rate.i = act.rate.i,
inf.prob.q = inf.prob.q, inf.prob.q = inf.prob.q,
act.rate.q = act.rate.q, act.rate.q = act.rate.q,
prog.rate = prog.rate,
quar.rate = quar.rate, quar.rate = quar.rate,
hosp.rate = hosp.rate, hosp.rate = hosp.rate,
disch.rate = disch.rate, disch.rate = disch.rate,
prog.rate = prog.rate, rec.rate = rec.rate,
arec.rate = arec.rate,
prog.dist.scale = prog.dist.scale, prog.dist.scale = prog.dist.scale,
prog.dist.shape = prog.dist.shape, prog.dist.shape = prog.dist.shape,
rec.rate = rec.rate, quar.dist.scale = quar.dist.scale,
quar.dist.shape = quar.dist.shape,
hosp.dist.scale = hosp.dist.scale,
hosp.dist.shape = hosp.dist.shape,
disch.dist.scale = disch.dist.scale,
disch.dist.shape = disch.dist.shape,
rec.dist.scale = rec.dist.scale, rec.dist.scale = rec.dist.scale,
rec.dist.shape = rec.dist.shape, rec.dist.shape = rec.dist.shape,
arec.dist.scale = arec.dist.scale,
arec.dist.shape = arec.dist.shape,
fat.rate.base = fat.rate.base, fat.rate.base = fat.rate.base,
hosp.cap = hosp.cap, hosp.cap = hosp.cap,
fat.rate.overcap = fat.rate.overcap, fat.rate.overcap = fat.rate.overcap,
......
R/simulation.R
+ 58
− 9
View file @ 326ed0c3
...@@ -15,9 +15,13 @@ ...@@ -15,9 +15,13 @@
#' distribution but it makes little difference and speed of computation #' distribution but it makes little difference and speed of computation
#' matters), with parameters prog.dist.scale and prog.dist.shape #' matters), with parameters prog.dist.scale and prog.dist.shape
#' @param rec.rand Method for recovery transition from I, Q or H to R. If TRUE, #' @param rec.rand Method for recovery transition from I, Q or H to R. If TRUE,
#' random binomial draws at prog.rate, if FALSE, random draws from a #' random binomial draws at rec.rate, if FALSE, random draws from a
#' random draws from a Weibull distribution, with parameters #' random draws from a Weibull distribution, with parameters
#' rec.dist.scale and rec.dist.shape. #' rec.dist.scale and rec.dist.shape.
#' @param arec.rand Method for recovery transition from E to R. If TRUE,
#' random binomial draws at arec.rate, if FALSE, random draws from a
#' random draws from a Weibull distribution, with parameters
#' arec.dist.scale and raec.dist.shape.
#' @param fat.rand Method for case fatality transition from H to F. If TRUE, #' @param fat.rand Method for case fatality transition from H to F. If TRUE,
#' random binomial draws at fat.rate.base, if FALSE, random sample with #' random binomial draws at fat.rate.base, if FALSE, random sample with
#' a sample fraction also given by fat.rate.base. However, if the #' a sample fraction also given by fat.rate.base. However, if the
...@@ -117,6 +121,11 @@ ...@@ -117,6 +121,11 @@
#' a low rate reflecting low community awareness or compliance with #' a low rate reflecting low community awareness or compliance with
#' self-isolation requirements or practices, but this can be tweaked when #' self-isolation requirements or practices, but this can be tweaked when
#' exploring scenarios. #' exploring scenarios.
#' @param quar.dist.scale Scale parameter for Weibull distribution for
#' recovery, see quar.rand for details.
#' @param quar.dist.shape Shape parameter for Weibull distribution for
#' recovery, see quar.rand for details. Read up on the Weibull distribution
#' before changing the default.
#' @param hosp.rate Rate per day at which symptomatic (or tested #' @param hosp.rate Rate per day at which symptomatic (or tested
#' positive), infected I compartment people or self-isolated Q compartment #' positive), infected I compartment people or self-isolated Q compartment
#' people enter the state of requiring hospital care -- that is, become #' people enter the state of requiring hospital care -- that is, become
...@@ -124,8 +133,18 @@ ...@@ -124,8 +133,18 @@
#' duration of about 10 days means a bit less than 10% of cases will #' duration of about 10 days means a bit less than 10% of cases will
#' require hospitalisation, which seems about right (but can be tweaked, #' require hospitalisation, which seems about right (but can be tweaked,
#' of course). #' of course).
#' @param hosp.dist.scale Scale parameter for Weibull distribution for
#' recovery, see hosp.rand for details.
#' @param hosp.dist.shape Shape parameter for Weibull distribution for
#' recovery, see hosp.rand for details. Read up on the Weibull distribution
#' before changing the default.
#' @param disch.rate Rate per day at which people needing #' @param disch.rate Rate per day at which people needing
#' hospitalisation recover. #' hospitalisation recover.
#' @param disch.dist.scale Scale parameter for Weibull distribution for
#' recovery, see disch.rand for details.
#' @param disch.dist.shape Shape parameter for Weibull distribution for
#' recovery, see disch.rand for details. Read up on the Weibull distribution
#' before changing the default.
#' @param prog.rate Rate per day at which people who are infected #' @param prog.rate Rate per day at which people who are infected
#' but asymptomatic (E compartment) progress to becoming symptomatic (or #' but asymptomatic (E compartment) progress to becoming symptomatic (or
#' test-positive), the I compartment. See prog.rand above for more details. #' test-positive), the I compartment. See prog.rand above for more details.
...@@ -142,6 +161,13 @@ ...@@ -142,6 +161,13 @@
#' @param rec.dist.shape Shape parameter for Weibull distribution for #' @param rec.dist.shape Shape parameter for Weibull distribution for
#' recovery, see rec.rand for details. Read up on the Weibull distribution #' recovery, see rec.rand for details. Read up on the Weibull distribution
#' before changing the default. #' before changing the default.
#' @param arec.rate Rate per day at which people who are exposed but asymptotic
#' (E compartment) recover, thus entering the R compartment.
#' See arec.rand above for more details.
#' @param arec.dist.scale Scale parameter for Weibull distribution for
#' recovery, see raec.rand for details.
#' @param arec.dist.shape Shape parameter for Weibull distribution for
#' recovery, see arec.rand for details.
#' @param fat.rate.base Baseline mortality rate per day for people #' @param fat.rate.base Baseline mortality rate per day for people
#' needing hospitalisation (deaths due to the virus). See fat.rand for more #' needing hospitalisation (deaths due to the virus). See fat.rand for more
#' details. #' details.
...@@ -193,11 +219,12 @@ simulate_seiqhrf <- function(type = "SEIQHRF", ...@@ -193,11 +219,12 @@ simulate_seiqhrf <- function(type = "SEIQHRF",
nsims = 8, nsims = 8,
ncores = 4, ncores = 4,
prog.rand = FALSE, prog.rand = FALSE,
rec.rand = FALSE, quar.rand = TRUE,
fat.rand = TRUE, hosp.rand = TRUE,
quar.rand = FALSE,
hosp.rand = FALSE,
disch.rand = TRUE, disch.rand = TRUE,
rec.rand = TRUE,
arec.rand = TRUE,
fat.rand = TRUE,
infection.FUN = 'infection.FUN', # infection.seiqhrf.icm, infection.FUN = 'infection.FUN', # infection.seiqhrf.icm,
recovery.FUN = 'recovery.FUN', # progress.seiqhrf.icm, recovery.FUN = 'recovery.FUN', # progress.seiqhrf.icm,
departures.FUN = 'departures.FUN', # departures.seiqhrf.icm, departures.FUN = 'departures.FUN', # departures.seiqhrf.icm,
...@@ -218,15 +245,24 @@ simulate_seiqhrf <- function(type = "SEIQHRF", ...@@ -218,15 +245,24 @@ simulate_seiqhrf <- function(type = "SEIQHRF",
act.rate.i = 10, act.rate.i = 10,
inf.prob.q = 0.02, inf.prob.q = 0.02,
act.rate.q = 2.5, act.rate.q = 2.5,
prog.rate = 1/10,
quar.rate = 1/30, quar.rate = 1/30,
hosp.rate = 1/100, hosp.rate = 1/100,
disch.rate = 1/15, disch.rate = 1/15,
prog.rate = 1/10, rec.rate = 0.071,
arec.rate = 0.05,
prog.dist.scale = 5, prog.dist.scale = 5,
prog.dist.shape = 1.5, prog.dist.shape = 1.5,
rec.rate = 0.071, # Based on assumption that disease course is 14 days quar.dist.scale = 1,
quar.dist.shape = 1,
hosp.dist.scale = 1,
hosp.dist.shape = 1,
disch.dist.scale = 1,
disch.dist.shape = 1,
rec.dist.scale = 35, rec.dist.scale = 35,
rec.dist.shape = 1.5, rec.dist.shape = 1.5,
arec.dist.scale = 35,
arec.dist.shape = 1.5,
fat.rate.base = 1/50, fat.rate.base = 1/50,
hosp.cap = 40, hosp.cap = 40,
fat.rate.overcap = 1/25, fat.rate.overcap = 1/25,
...@@ -250,7 +286,11 @@ simulate_seiqhrf <- function(type = "SEIQHRF", ...@@ -250,7 +286,11 @@ simulate_seiqhrf <- function(type = "SEIQHRF",
nsims = nsims, nsims = nsims,
ncores = ncores, ncores = ncores,
prog.rand = prog.rand, prog.rand = prog.rand,
quar.rand = quar.rand,
hosp.ramd = hosp.rand,
disch.rand = disch.rand,
rec.rand = rec.rand, rec.rand = rec.rand,
arec.rand = arec.rand,
infection.FUN = infection.FUN, infection.FUN = infection.FUN,
recovery.FUN = recovery.FUN, recovery.FUN = recovery.FUN,
arrivals.FUN = arrivals.FUN, arrivals.FUN = arrivals.FUN,
...@@ -271,15 +311,24 @@ simulate_seiqhrf <- function(type = "SEIQHRF", ...@@ -271,15 +311,24 @@ simulate_seiqhrf <- function(type = "SEIQHRF",
act.rate.i = act.rate.i, act.rate.i = act.rate.i,
inf.prob.q = inf.prob.q, inf.prob.q = inf.prob.q,
act.rate.q = act.rate.q, act.rate.q = act.rate.q,
prog.rate = prog.rate,
quar.rate = quar.rate, quar.rate = quar.rate,
hosp.rate = hosp.rate, hosp.rate = hosp.rate,
disch.rate = disch.rate, disch.rate = disch.rate,
prog.rate = prog.rate, rec.rate = rec.rate,
arec.rate = arec.rate,
prog.dist.scale = prog.dist.scale, prog.dist.scale = prog.dist.scale,
prog.dist.shape = prog.dist.shape, prog.dist.shape = prog.dist.shape,
rec.rate = rec.rate, quar.dist.scale = quar.dist.scale,
quar.dist.shape = quar.dist.shape,
hosp.dist.scale = hosp.dist.scale,
hosp.dist.shape = hosp.dist.shape,
disch.dist.scale = disch.dist.scale,
disch.dist.shape = disch.dist.shape,
rec.dist.scale = rec.dist.scale, rec.dist.scale = rec.dist.scale,
rec.dist.shape = rec.dist.shape, rec.dist.shape = rec.dist.shape,
arec.dist.scale = arec.dist.scale,
arec.dist.shape = arec.dist.shape,
fat.rate.base = fat.rate.base, fat.rate.base = fat.rate.base,
hosp.cap = hosp.cap, hosp.cap = hosp.cap,
fat.rate.overcap = fat.rate.overcap, fat.rate.overcap = fat.rate.overcap,
......
man/simulate_seiqhrf.Rd
+ 74
− 28
View file @ 326ed0c3
...@@ -10,11 +10,12 @@ simulate_seiqhrf( ...@@ -10,11 +10,12 @@ simulate_seiqhrf(
nsims = 8, nsims = 8,
ncores = 4, ncores = 4,
prog.rand = FALSE, prog.rand = FALSE,
rec.rand = FALSE, quar.rand = TRUE,
fat.rand = TRUE, hosp.rand = TRUE,
quar.rand = FALSE,
hosp.rand = FALSE,
disch.rand = TRUE, disch.rand = TRUE,
rec.rand = TRUE,
arec.rand = TRUE,
fat.rand = TRUE,
infection.FUN = "infection.FUN", infection.FUN = "infection.FUN",
recovery.FUN = "recovery.FUN", recovery.FUN = "recovery.FUN",
departures.FUN = "departures.FUN", departures.FUN = "departures.FUN",
...@@ -33,15 +34,24 @@ simulate_seiqhrf( ...@@ -33,15 +34,24 @@ simulate_seiqhrf(
act.rate.i = 10, act.rate.i = 10,
inf.prob.q = 0.02, inf.prob.q = 0.02,
act.rate.q = 2.5, act.rate.q = 2.5,
prog.rate = 1/10,
quar.rate = 1/30, quar.rate = 1/30,
hosp.rate = 1/100, hosp.rate = 1/100,
disch.rate = 1/15, disch.rate = 1/15,
prog.rate = 1/10, rec.rate = 0.071,
arec.rate = 0.05,
prog.dist.scale = 5, prog.dist.scale = 5,
prog.dist.shape = 1.5, prog.dist.shape = 1.5,
rec.rate = 0.071, quar.dist.scale = 1,
quar.dist.shape = 1,
hosp.dist.scale = 1,
hosp.dist.shape = 1,
disch.dist.scale = 1,
disch.dist.shape = 1,
rec.dist.scale = 35, rec.dist.scale = 35,
rec.dist.shape = 1.5, rec.dist.shape = 1.5,
arec.dist.scale = 35,
arec.dist.shape = 1.5,
fat.rate.base = 1/50, fat.rate.base = 1/50,
hosp.cap = 40, hosp.cap = 40,
fat.rate.overcap = 1/25, fat.rate.overcap = 1/25,
...@@ -78,11 +88,31 @@ Weibull distribution (yes, I know it should be a discrete Weibull ...@@ -78,11 +88,31 @@ Weibull distribution (yes, I know it should be a discrete Weibull
distribution but it makes little difference and speed of computation distribution but it makes little difference and speed of computation
matters), with parameters prog.dist.scale and prog.dist.shape} matters), with parameters prog.dist.scale and prog.dist.shape}
\item{quar.rand}{Method for self-isolation transition from I to Q. If TRUE,
random binomial draws at quar.rate, if FALSE, random sample with a
sample fraction also given by `quar.rate.}
\item{hosp.rand}{Method for transition from I or Q to H -- that is, from
infectious or from self-isolated to requiring hospitalisation. If
TRUE, random binomial draws at hosp.rate, if FALSE, random sample
with a sample fraction also given by `hosp.rate.}
\item{disch.rand}{Method for transition from H to R -- that is, from
requiring hospitalisation to recovered. If TRUE, random binomial
draws at disch.rate, if FALSE, random sample with a sample fraction
also given by disch.rate. Note that the only way out of the H
compartment is recovery or death.}
\item{rec.rand}{Method for recovery transition from I, Q or H to R. If TRUE, \item{rec.rand}{Method for recovery transition from I, Q or H to R. If TRUE,
random binomial draws at prog.rate, if FALSE, random draws from a random binomial draws at rec.rate, if FALSE, random draws from a
random draws from a Weibull distribution, with parameters random draws from a Weibull distribution, with parameters
rec.dist.scale and rec.dist.shape.} rec.dist.scale and rec.dist.shape.}
\item{arec.rand}{Method for recovery transition from E to R. If TRUE,
random binomial draws at arec.rate, if FALSE, random draws from a
random draws from a Weibull distribution, with parameters
arec.dist.scale and raec.dist.shape.}
\item{fat.rand}{Method for case fatality transition from H to F. If TRUE, \item{fat.rand}{Method for case fatality transition from H to F. If TRUE,
random binomial draws at fat.rate.base, if FALSE, random sample with random binomial draws at fat.rate.base, if FALSE, random sample with
a sample fraction also given by fat.rate.base. However, if the a sample fraction also given by fat.rate.base. However, if the
...@@ -99,21 +129,6 @@ as a linear function of the number of days the individual has been ...@@ -99,21 +129,6 @@ as a linear function of the number of days the individual has been
in the H compartment. Use of the co-efficient better approximates in the H compartment. Use of the co-efficient better approximates
the trapezoid survival time distribution typical of ICU patients.} the trapezoid survival time distribution typical of ICU patients.}
\item{quar.rand}{Method for self-isolation transition from I to Q. If TRUE,
random binomial draws at quar.rate, if FALSE, random sample with a
sample fraction also given by `quar.rate.}
\item{hosp.rand}{Method for transition from I or Q to H -- that is, from
infectious or from self-isolated to requiring hospitalisation. If
TRUE, random binomial draws at hosp.rate, if FALSE, random sample
with a sample fraction also given by `hosp.rate.}
\item{disch.rand}{Method for transition from H to R -- that is, from
requiring hospitalisation to recovered. If TRUE, random binomial
draws at disch.rate, if FALSE, random sample with a sample fraction
also given by disch.rate. Note that the only way out of the H
compartment is recovery or death.}
\item{infection.FUN}{No, being infected with SARS-CoV2 is not fun. Rather \item{infection.FUN}{No, being infected with SARS-CoV2 is not fun. Rather
this is the the name of the function to implement infection this is the the name of the function to implement infection
processes. Use the default.} processes. Use the default.}
...@@ -197,6 +212,10 @@ greater degree of social isolation for someone in (self-)isolation. The ...@@ -197,6 +212,10 @@ greater degree of social isolation for someone in (self-)isolation. The
exposure event rate is not zero for this group, just much less. exposure event rate is not zero for this group, just much less.
Otherwise as for act.rate.i.} Otherwise as for act.rate.i.}
\item{prog.rate}{Rate per day at which people who are infected
but asymptomatic (E compartment) progress to becoming symptomatic (or
test-positive), the I compartment. See prog.rand above for more details.}
\item{quar.rate}{Rate per day at which symptomatic (or tested \item{quar.rate}{Rate per day at which symptomatic (or tested
positive), infected I compartment people enter self-isolation (Q positive), infected I compartment people enter self-isolation (Q
compartment). Asymptomatic E compartment people can't enter compartment). Asymptomatic E compartment people can't enter
...@@ -216,9 +235,13 @@ of course).} ...@@ -216,9 +235,13 @@ of course).}
\item{disch.rate}{Rate per day at which people needing \item{disch.rate}{Rate per day at which people needing
hospitalisation recover.} hospitalisation recover.}
\item{prog.rate}{Rate per day at which people who are infected \item{rec.rate}{Rate per day at which people who are infected and
but asymptomatic (E compartment) progress to becoming symptomatic (or symptomatic (I compartment) recover, thus entering the R compartment.
test-positive), the I compartment. See prog.rand above for more details.} See rec.rand above for more details.}
\item{arec.rate}{Rate per day at which people who are exposed but asymptotic
(E compartment) recover, thus entering the R compartment.
See arec.rand above for more details.}
\item{prog.dist.scale}{Scale parameter for Weibull distribution \item{prog.dist.scale}{Scale parameter for Weibull distribution
for progression, see prog.rand for details.} for progression, see prog.rand for details.}
...@@ -227,9 +250,26 @@ for progression, see prog.rand for details.} ...@@ -227,9 +250,26 @@ for progression, see prog.rand for details.}
for progression, see prog.rand for details. Read up on the Weibull for progression, see prog.rand for details. Read up on the Weibull
distribution before changing the default.} distribution before changing the default.}
\item{rec.rate}{Rate per day at which people who are infected and \item{quar.dist.scale}{Scale parameter for Weibull distribution for
symptomatic (I compartment) recover, thus entering the R compartment. recovery, see quar.rand for details.}
See rec.rand above for more details.}
\item{quar.dist.shape}{Shape parameter for Weibull distribution for
recovery, see quar.rand for details. Read up on the Weibull distribution
before changing the default.}
\item{hosp.dist.scale}{Scale parameter for Weibull distribution for
recovery, see hosp.rand for details.}
\item{hosp.dist.shape}{Shape parameter for Weibull distribution for
recovery, see hosp.rand for details. Read up on the Weibull distribution
before changing the default.}
\item{disch.dist.scale}{Scale parameter for Weibull distribution for
recovery, see disch.rand for details.}
\item{disch.dist.shape}{Shape parameter for Weibull distribution for
recovery, see disch.rand for details. Read up on the Weibull distribution
before changing the default.}
\item{rec.dist.scale}{Scale parameter for Weibull distribution for \item{rec.dist.scale}{Scale parameter for Weibull distribution for
recovery, see rec.rand for details.} recovery, see rec.rand for details.}
...@@ -238,6 +278,12 @@ recovery, see rec.rand for details.} ...@@ -238,6 +278,12 @@ recovery, see rec.rand for details.}
recovery, see rec.rand for details. Read up on the Weibull distribution recovery, see rec.rand for details. Read up on the Weibull distribution
before changing the default.} before changing the default.}
\item{arec.dist.scale}{Scale parameter for Weibull distribution for
recovery, see raec.rand for details.}
\item{arec.dist.shape}{Shape parameter for Weibull distribution for
recovery, see arec.rand for details.}
\item{fat.rate.base}{Baseline mortality rate per day for people \item{fat.rate.base}{Baseline mortality rate per day for people
needing hospitalisation (deaths due to the virus). See fat.rand for more needing hospitalisation (deaths due to the virus). See fat.rand for more
details.} details.}
......
tests/testthat/test-icm-seiqhrf.R
+ 1
− 1
View file @ 326ed0c3
test_that("Identical output as Churches' original function: icm_seiqhrf", { test_that("Identical output as Churches' original function: icm_seiqhrf", {
full_params <- set_param(s.num = 1000, nsteps = 10) full_params <- set_param(s.num = 1000, nsteps = 10, arec.rate = 0)
param <- full_params$param param <- full_params$param
init <- full_params$init init <- full_params$init
......
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