context("Network extended models (All SOC)")
test_that("edges models", {
skip_on_cran()
nw <- network_initialize(n = 100)
est <- netest(nw, formation = ~edges, target.stats = 25,
coef.diss = dissolution_coefs(~offset(edges), 10, 0),
verbose = FALSE)
expect_is(est, "netest")
## "SI, 1M, CL: 1 sim"
param <- param.net(inf.prob = 0.5)
init <- init.net(i.num = 1)
control <- control.net(type = "SI", nsims = 1, nsteps = 25, verbose = FALSE)
x <- netsim(est, param, init, control)
expect_is(x, "netsim")
expect_is(as.data.frame(x), "data.frame")
expect_true(max(x$epi$i.num) >= 1)
expect_true(max(x$epi$i.num) <= 100)
expect_output(summary(x, at = 25), "EpiModel Summary")
plot(x)
plot(x, y = "si.flow", mean.smooth = TRUE)
plot(x, type = "formation")
plot(x, type = "network")
plot(x, type = "network", sims = "mean", col.status = TRUE)
test_net(x)
rm(x)
## "SI, 1M, CL: 1 sim, inf.prob = 0"
param <- param.net(inf.prob = 0)
init <- init.net(i.num = 1)
control <- control.net(type = "SI", nsims = 1, nsteps = 25, verbose = FALSE)
x <- netsim(est, param, init, control)
expect_is(x, "netsim")
expect_is(as.data.frame(x), "data.frame")
expect_true(max(x$epi$i.num) == 1)
expect_true(max(x$epi$si.flow, na.rm = TRUE) == 0)
expect_output(summary(x, at = 25), "EpiModel Summary")
plot(x)
plot(x, y = "si.flow", mean.smooth = TRUE)
plot(x, type = "formation")
plot(x, type = "network")
plot(x, type = "network", sims = "mean", col.status = TRUE)
test_net(x)
rm(x)
## "SI, 1M, CL: 2 sim"
param <- param.net(inf.prob = 0.5)
init <- init.net(i.num = 1)
control <- control.net(type = "SI", nsims = 2, nsteps = 25, verbose = FALSE,
nwstats.formula = ~edges + meandeg + concurrent)
x <- netsim(est, param, init, control)
expect_is(x, "netsim")
expect_is(as.data.frame(x), "data.frame")
expect_true(max(x$epi$i.num) >= 1)
expect_true(max(x$epi$i.num) <= 100)
expect_output(summary(x, at = 25), "EpiModel Summary")
plot(x)
plot(x, y = "si.flow", mean.smooth = TRUE)
plot(x, type = "formation")
plot(x, type = "formation", plots.joined = FALSE)
plot(x, type = "formation", stats = "edges")
plot(x, type = "formation", stats = c("edges", "meandeg"))
plot(x, type = "formation", sim.lines = TRUE, qnts.smooth = FALSE)
plot(x, type = "network")
plot(x, type = "network", sims = "mean", col.status = TRUE)
test_net(x)
rm(x)
## "SI, 1M, CL: 2 sim, use TEAs"
param <- param.net(inf.prob = 1)
init <- init.net(i.num = 1)
control <- control.net(type = "SI", nsims = 2, nsteps = 25,
verbose = FALSE)
x <- netsim(est, param, init, control)
expect_is(x, "netsim")
expect_is(as.data.frame(x), "data.frame")
expect_true(max(x$epi$i.num) >= 1)
expect_true(max(x$epi$i.num) <= 100)
expect_true(sum(get.vertex.attribute.active(x$network[[1]][[1]],
prefix = "testatus",
at = 1) == "i") >= 0)
expect_output(summary(x, at = 25), "EpiModel Summary")
plot(x)
plot(x, y = "si.flow", mean.smooth = TRUE)
plot(x, type = "formation")
plot(x, type = "network")
plot(x, type = "network", sims = "mean", col.status = TRUE)
test_net(x)
rm(x)
## "SI, 1M, CL: 2 sim, set status.vector"
param <- param.net(inf.prob = 0.5)
init <- init.net(status.vector = c(rep("i", 10),
rep("s", 90)))
control <- control.net(type = "SI", nsims = 2, nsteps = 25,
verbose = FALSE)
x <- netsim(est, param, init, control)
expect_is(x, "netsim")
expect_is(as.data.frame(x), "data.frame")
# this tests that starting infected is same across sims
expect_true(all(x$epi$i.num[1, ] == 10))
expect_true(max(x$epi$i.num) <= 100)
expect_output(summary(x, at = 25), "EpiModel Summary")
plot(x)
plot(x, y = "si.flow", mean.smooth = TRUE)
plot(x, type = "formation")
plot(x, type = "network", col.status = TRUE)
test_net(x)
rm(x)
## "SIR, 1M, CL: 1 sim"
param <- param.net(inf.prob = 0.5, rec.rate = 0.01)
init <- init.net(i.num = 10, r.num = 0)
control <- control.net(type = "SIR", nsims = 1, nsteps = 25,
verbose = FALSE)
x <- netsim(est, param, init, control)
expect_is(x, "netsim")
expect_is(as.data.frame(x), "data.frame")
expect_true(max(x$epi$i.num) >= 1)
expect_true(max(x$epi$i.num) <= 100)
expect_output(summary(x, at = 25), "EpiModel Summary")
plot(x)
plot(x, y = "si.flow", mean.smooth = TRUE)
plot(x, type = "formation")
plot(x, type = "network")
plot(x, type = "network", sims = "mean", col.status = TRUE)
test_net(x)
rm(x)
## "SIR, 1M, CL: 1 sim, inf.prob=0"
param <- param.net(inf.prob = 0, rec.rate = 0.01)
init <- init.net(i.num = 10, r.num = 0)
control <- control.net(type = "SIR", nsims = 1,
nsteps = 25, verbose = FALSE)
x <- netsim(est, param, init, control)
expect_is(x, "netsim")
expect_is(as.data.frame(x), "data.frame")
expect_true(max(x$epi$i.num) == 10)
expect_true(max(x$epi$si.flow, na.rm = TRUE) == 0)
expect_output(summary(x, at = 25), "EpiModel Summary")
plot(x)
plot(x, y = "si.flow", mean.smooth = TRUE)
plot(x, type = "formation")
plot(x, type = "network")
plot(x, type = "network", sims = "mean", col.status = TRUE)
test_net(x)
rm(x)
## "SIR, 1M, CL: 2 sim"
param <- param.net(inf.prob = 0.5, rec.rate = 0.1)
init <- init.net(i.num = 1, r.num = 0)
control <- control.net(type = "SIR", nsims = 2, nsteps = 25,
verbose = FALSE)
x <- netsim(est, param, init, control)
expect_is(x, "netsim")
expect_is(as.data.frame(x), "data.frame")
expect_true(max(x$epi$i.num) >= 1)
expect_true(max(x$epi$i.num) <= 100)
expect_output(summary(x, at = 25), "EpiModel Summary")
plot(x)
plot(x, y = "si.flow", mean.smooth = TRUE)
plot(x, type = "formation")
plot(x, type = "network")
plot(x, type = "network", sims = "mean", col.status = TRUE)
test_net(x)
rm(x)
## "SIR, 1M, CL: 2 sim, set status.vector"
param <- param.net(inf.prob = 0.5, rec.rate = 0.1)
init <- init.net(status.vector = rep(c("s", "i"), each = 50))
control <- control.net(type = "SIR", nsims = 2, nsteps = 25,
verbose = FALSE)
x <- netsim(est, param, init, control)
expect_is(x, "netsim")
expect_is(as.data.frame(x), "data.frame")
# this tests that starting infected is same across sims
expect_true(all(x$epi$i.num[1, ] == 50))
expect_true(max(x$epi$i.num) <= 100)
expect_output(summary(x, at = 25), "EpiModel Summary")
plot(x)
plot(x, y = "si.flow", mean.smooth = TRUE)
plot(x, type = "formation")
plot(x, type = "network")
plot(x, type = "network", sims = "mean", col.status = TRUE)
test_net(x)
rm(x)
## "SIS, 1M, CL: 1 sim"
param <- param.net(inf.prob = 0.9, rec.rate = 0.01)
init <- init.net(i.num = 1)
control <- control.net(type = "SIS", nsims = 1, nsteps = 25,
verbose = FALSE)
x <- netsim(est, param, init, control)
expect_is(x, "netsim")
expect_is(as.data.frame(x), "data.frame")
expect_true(max(x$epi$i.num) >= 1)
expect_true(max(x$epi$i.num) <= 100)
expect_output(summary(x, at = 25), "EpiModel Summary")
plot(x)
plot(x, y = "si.flow", mean.smooth = TRUE)
plot(x, type = "formation")
plot(x, type = "network")
plot(x, type = "network", sims = "mean", col.status = TRUE)
test_net(x)
rm(x)
## "SIS, 1M, CL: 1 sim, inf.prob=0"
param <- param.net(inf.prob = 0, rec.rate = 0.01)
init <- init.net(i.num = 1)
control <- control.net(type = "SIS", nsims = 1, nsteps = 25,
verbose = FALSE)
x <- netsim(est, param, init, control)
expect_is(x, "netsim")
expect_is(as.data.frame(x), "data.frame")
expect_true(max(x$epi$i.num) == 1)
expect_true(max(x$epi$si.flow, na.rm = TRUE) == 0)
expect_output(summary(x, at = 25), "EpiModel Summary")
plot(x)
plot(x, y = "si.flow", mean.smooth = TRUE)
plot(x, type = "formation")
plot(x, type = "network")
plot(x, type = "network", sims = "mean", col.status = TRUE)
test_net(x)
rm(x)
## "SIS, 1M, CL: 2 sim"
param <- param.net(inf.prob = 0.5, rec.rate = 0.01)
init <- init.net(i.num = 1)
control <- control.net(type = "SIS", nsims = 2, nsteps = 25,
verbose = FALSE)
x <- netsim(est, param, init, control)
expect_is(x, "netsim")
expect_is(as.data.frame(x), "data.frame")
expect_true(max(x$epi$i.num) >= 1)
expect_true(max(x$epi$i.num) <= 100)
expect_output(summary(x, at = 25), "EpiModel Summary")
plot(x)
plot(x, y = "si.flow", mean.smooth = TRUE)
plot(x, type = "formation")
test_net(x)
rm(x)
## "SIS, 1M, CL: 2 sim, test TEAs"
param <- param.net(inf.prob = 1, rec.rate = 0.01)
init <- init.net(i.num = 1)
control <- control.net(type = "SIS", nsims = 2, nsteps = 25,
verbose = FALSE)
x <- netsim(est, param, init, control)
expect_is(x, "netsim")
expect_is(as.data.frame(x), "data.frame")
expect_true(max(x$epi$i.num) <= 100)
expect_true(sum(get.vertex.attribute.active(x$network[[1]][[1]],
prefix = "testatus",
at = 1) == "i") >= 0)
expect_output(summary(x, at = 25), "EpiModel Summary")
plot(x)
plot(x, y = "si.flow", mean.smooth = TRUE)
plot(x, type = "formation")
plot(x, type = "network")
plot(x, type = "network", sims = "mean", col.status = TRUE)
test_net(x)
rm(x)
## "SIS, 1M, CL: 2 sim, set status.vector"
param <- param.net(inf.prob = 0.5, rec.rate = 0.01)
init <- init.net(status.vector = c(rep("i", 10), rep("s", 90)))
control <- control.net(type = "SIS", nsims = 2, nsteps = 25,
verbose = FALSE)
x <- netsim(est, param, init, control)
expect_is(x, "netsim")
expect_is(as.data.frame(x), "data.frame")
# this tests that starting infected is same across sims
expect_true(all(x$epi$i.num[1, ] == 10))
expect_true(max(x$epi$i.num) <= 100)
expect_output(summary(x, at = 25), "EpiModel Summary")
plot(x)
plot(x, y = "si.flow", mean.smooth = TRUE)
plot(x, type = "formation")
plot(x, type = "network")
plot(x, type = "network", sims = "mean", col.status = TRUE)
test_net(x)
})
################################################################################
test_that("High departure rate models", {
skip_on_cran()
## "netsim: 1M, ds.rate = 0.5"
nw <- network_initialize(n = 25)
est <- netest(nw, formation = ~edges, target.stats = 12,
coef.diss = dissolution_coefs(~offset(edges), 10, 0.01),
edapprox = TRUE, verbose = FALSE)
param <- param.net(inf.prob = 0.5, act.rate = 2,
a.rate = 0.01, ds.rate = 0.25,
di.rate = 0.1)
init <- init.net(i.num = 10)
control <- control.net(type = "SI", nsteps = 25, nsims = 1,
resimulate.network = TRUE, verbose = FALSE)
x <- netsim(est, param, init, control)
expect_equal(unique(sapply(x$epi, nrow)), 25)
expect_output(summary(x, at = 25), "EpiModel Summary")
capture_output(
get_nwstats(x)
)
plot(x)
plot(x, y = "si.flow", mean.smooth = TRUE)
plot(x, type = "formation")
test_net(x)
rm(x)
## "netsim: 1M, di.rate = 0.5"
param <- param.net(inf.prob = 0.1, act.rate = 2, a.rate = 0.01,
ds.rate = 0.01, di.rate = 0.25)
init <- init.net(i.num = 10)
control <- control.net(type = "SI", nsteps = 25, nsims = 1,
resimulate.network = TRUE, verbose = FALSE)
x <- netsim(est, param, init, control)
expect_equal(unique(sapply(x$epi, nrow)), 25)
expect_output(summary(x, at = 25), "EpiModel Summary")
plot(x)
plot(x, y = "si.flow", mean.smooth = TRUE)
plot(x, type = "formation")
test_net(x)
})
################################################################################
test_that("erroneous two-group models", {
skip_on_cran()
nw <- network_initialize(n = 100)
nw <- set_vertex_attribute(nw, "group", rep(0:1, each = 50))
est <- netest(nw, formation = ~edges, target.stats = 25,
coef.diss = dissolution_coefs(~offset(edges), 10, 0),
edapprox = TRUE, verbose = FALSE)
param <- param.net(inf.prob = 0.5, inf.prob.g2 = 0.1)
init <- init.net(i.num = 10, i.num.g2 = 0)
control <- control.net(type = "SI", nsims = 2, nsteps = 25, verbose = FALSE)
expect_error(netsim(est, param, init, control))
})
################################################################################
test_that("edges two-group models", {
skip_on_cran()
nw <- network_initialize(n = 100)
nw <- set_vertex_attribute(nw, "group", rep(1:2, each = 50))
est5 <- netest(nw, formation = ~edges, target.stats = 25,
coef.diss = dissolution_coefs(~offset(edges), 10, 0),
edapprox = TRUE, verbose = FALSE)
expect_is(est5, "netest")
## "SI, 2M, CL: 2 sim"
param <- param.net(inf.prob = 0.5, inf.prob.g2 = 0.1)
init <- init.net(i.num = 10, i.num.g2 = 0)
control <- control.net(type = "SI", nsims = 2, nsteps = 25,
verbose = FALSE)
x <- netsim(est5, param, init, control)
expect_is(x, "netsim")
expect_is(as.data.frame(x), "data.frame")
expect_equal(x$param$groups, 2)
expect_output(summary(x, at = 25), "EpiModel Summary")
plot(x)
plot(x, y = "si.flow", mean.smooth = TRUE)
plot(x, type = "formation")
plot(x, type = "network")
plot(x, type = "network", shp.g2 = "triangle")
#FLAG: Adding "two-group" attribute to network type
expect_error(plot(x, type = "network", shp.g2 = TRUE))
test_net(x)
rm(x)
## "SIR, 2M, CL: 2 sim"
param <- param.net(inf.prob = 0.5, inf.prob.g2 = 0.1,
rec.rate = 0.1, rec.rate.g2 = 0.1)
init <- init.net(i.num = 10, i.num.g2 = 10,
r.num = 0, r.num.g2 = 0)
control <- control.net(type = "SIR", nsims = 2, nsteps = 25,
verbose = FALSE)
x <- netsim(est5, param, init, control)
expect_is(x, "netsim")
expect_is(as.data.frame(x), "data.frame")
expect_equal(x$param$groups, 2)
expect_output(summary(x, at = 25), "EpiModel Summary")
plot(x)
plot(x, y = "si.flow", mean.smooth = TRUE)
plot(x, type = "formation")
test_net(x)
rm(x)
## "SIR, 2M, CL: rec.rate = 0"
param <- param.net(inf.prob = 0.5, inf.prob.g2 = 0.25,
rec.rate = 0, rec.rate.g2 = 0, act.rate = 2)
init <- init.net(i.num = 10, i.num.g2 = 10,
r.num = 0, r.num.g2 = 0)
control <- control.net(type = "SIR", nsteps = 10, nsims = 2,
verbose = FALSE)
x <- netsim(est5, param, init, control)
expect_equal(max(x$epi$ir.flow, na.rm = TRUE), 0)
expect_equal(max(x$epi$ir.flow.g2, na.rm = TRUE), 0)
expect_output(summary(x, at = 10), "EpiModel Summary")
plot(x)
plot(x, y = "si.flow", mean.smooth = TRUE)
plot(x, type = "formation")
test_net(x)
rm(x)
## "SIS, 2M, CL: 2 sim"
param <- param.net(inf.prob = 0.5, inf.prob.g2 = 0.25,
rec.rate = 0.01, rec.rate.g2 = 0.01)
init <- init.net(i.num = 10, i.num.g2 = 10)
control <- control.net(type = "SIS", nsims = 2, nsteps = 25,
verbose = FALSE)
x <- netsim(est5, param, init, control)
expect_is(x, "netsim")
expect_is(as.data.frame(x), "data.frame")
expect_equal(x$param$groups, 2)
expect_output(summary(x, at = 25), "EpiModel Summary")
plot(x)
plot(x, y = "si.flow", mean.smooth = TRUE)
plot(x, type = "formation")
test_net(x)
rm(x)
## "SIS, 2M, CL: rec.rate = 0"
param <- param.net(inf.prob = 0.5, inf.prob.g2 = 0.25,
rec.rate = 0, rec.rate.g2 = 0, act.rate = 2)
init <- init.net(i.num = 10, i.num.g2 = 10)
control <- control.net(type = "SIS", nsteps = 10, nsims = 2,
verbose = FALSE)
x <- netsim(est5, param, init, control)
expect_equal(max(x$epi$is.flow, na.rm = TRUE), 0)
expect_equal(max(x$epi$is.flow.g2, na.rm = TRUE), 0)
expect_output(summary(x, at = 10), "EpiModel Summary")
plot(x)
plot(x, y = "si.flow", mean.smooth = TRUE)
plot(x, type = "formation")
test_net(x)
rm(x)
})
################################################################################
test_that("Open population 1 group models", {
skip_on_cran()
nw <- network_initialize(n = 100)
est.vit <- netest(nw, formation = ~edges, target.stats = 25,
coef.diss = dissolution_coefs(~offset(edges), 10, 0.01),
verbose = FALSE)
## "SI, 1M, OP: 1 sim"
param <- param.net(inf.prob = 0.5, act.rate = 2, a.rate = 0.01,
ds.rate = 0.01, di.rate = 0.01)
init <- init.net(i.num = 10)
control <- control.net(type = "SI", nsteps = 10, nsims = 1,
resimulate.network = TRUE, verbose = FALSE)
x <- netsim(est.vit, param, init, control)
expect_is(x, "netsim")
expect_is(as.data.frame(x), "data.frame")
expect_equal(x$param$vital, TRUE)
expect_output(summary(x, at = 10), "EpiModel Summary")
plot(x)
plot(x, y = "si.flow", mean.smooth = TRUE)
plot(x, type = "formation")
test_net(x)
rm(x)
## "SI, 1M, OP: 2 sim"
param <- param.net(inf.prob = 0.5, act.rate = 2, a.rate = 0.01,
ds.rate = 0.01, di.rate = 0.01)
init <- init.net(i.num = 10)
control <- control.net(type = "SI", nsteps = 10, nsims = 2,
resimulate.network = TRUE, verbose = FALSE)
x <- netsim(est.vit, param, init, control)
expect_is(x, "netsim")
expect_is(as.data.frame(x), "data.frame")
expect_equal(x$param$vital, TRUE)
expect_output(summary(x, at = 10), "EpiModel Summary")
plot(x)
plot(x, y = "si.flow", mean.smooth = TRUE)
plot(x, type = "formation")
test_net(x)
rm(x)
## "SIR, 1M OP: 1 sim"
param <- param.net(inf.prob = 0.5, rec.rate = 0.1, act.rate = 2,
a.rate = 0.01, ds.rate = 0.01, di.rate = 0.01,
dr.rate = 0.01)
init <- init.net(i.num = 10, r.num = 0)
control <- control.net(type = "SIR", nsteps = 10, nsims = 1,
resimulate.network = TRUE, verbose = FALSE)
x <- netsim(est.vit, param, init, control)
expect_is(x, "netsim")
expect_is(as.data.frame(x), "data.frame")
expect_equal(x$param$vital, TRUE)
expect_output(summary(x, at = 10), "EpiModel Summary")
plot(x)
plot(x, y = "si.flow", mean.smooth = TRUE)
plot(x, type = "formation")
test_net(x)
rm(x)
## "SIR, 1M, OP: 2 sim"
param <- param.net(inf.prob = 0.5, rec.rate = 0.1, act.rate = 2,
a.rate = 0.01, ds.rate = 0.01, di.rate = 0.01,
dr.rate = 0.01)
init <- init.net(i.num = 10, r.num = 0)
control <- control.net(type = "SIR", nsteps = 10, nsims = 2,
resimulate.network = TRUE, verbose = FALSE)
x <- netsim(est.vit, param, init, control)
expect_is(x, "netsim")
expect_is(as.data.frame(x), "data.frame")
expect_equal(x$param$vital, TRUE)
expect_output(summary(x, at = 10), "EpiModel Summary")
plot(x)
plot(x, y = "si.flow", mean.smooth = TRUE)
plot(x, type = "formation")
test_net(x)
rm(x)
## "SIS, 1M, OP: 1 sim"
param <- param.net(inf.prob = 0.5, rec.rate = 0.01, act.rate = 2,
a.rate = 0.01, ds.rate = 0.01, di.rate = 0.01)
init <- init.net(i.num = 10)
control <- control.net(type = "SIS", nsteps = 10, nsims = 1,
resimulate.network = TRUE, verbose = FALSE)
x <- netsim(est.vit, param, init, control)
expect_is(x, "netsim")
expect_is(as.data.frame(x), "data.frame")
expect_equal(x$param$vital, TRUE)
expect_output(summary(x, at = 10), "EpiModel Summary")
plot(x)
plot(x, y = "si.flow", mean.smooth = TRUE)
plot(x, type = "formation")
test_net(x)
rm(x)
## "SIS, 1M, OP: 2 sim"
control <- control.net(type = "SIS", nsteps = 10, nsims = 2,
resimulate.network = TRUE, verbose = FALSE)
x <- netsim(est.vit, param, init, control)
expect_is(x, "netsim")
expect_is(as.data.frame(x), "data.frame")
expect_equal(x$param$vital, TRUE)
expect_output(summary(x, at = 10), "EpiModel Summary")
plot(x)
plot(x, y = "si.flow", mean.smooth = TRUE)
plot(x, type = "formation")
test_net(x)
rm(x)
})
################################################################################
test_that("Open-population two-group models", {
skip_on_cran()
nw <- network_initialize(n = 100)
nw <- set_vertex_attribute(nw, "group", rep(1:2, each = 50))
est5.vit <- netest(nw, formation = ~edges + nodematch("group"),
target.stats = c(25, 0),
coef.diss = dissolution_coefs(~offset(edges), 10, 0.01),
edapprox = TRUE, verbose = FALSE)
## "SI, 2M, OP: 1 sim"
param <- param.net(inf.prob = 0.5, inf.prob.g2 = 0.1, act.rate = 2,
a.rate = 0.01, ds.rate = 0.01, di.rate = 0.01,
a.rate.g2 = 0.01, ds.rate.g2 = 0.01, di.rate.g2 = 0.01)
init <- init.net(i.num = 10, i.num.g2 = 10)
control <- control.net(type = "SI", nsteps = 10, nsims = 1,
resimulate.network = TRUE, verbose = FALSE)
x <- netsim(est5.vit, param, init, control)
expect_is(x, "netsim")
expect_is(as.data.frame(x), "data.frame")
expect_equal(x$param$vital, TRUE)
expect_output(summary(x, at = 10), "EpiModel Summary")
plot(x)
plot(x, y = "si.flow", mean.smooth = TRUE)
plot(x, type = "formation")
test_net(x)
rm(x)
## "SI, 2M, OP: 2 sim"
param <- param.net(inf.prob = 0.5, inf.prob.g2 = 0.1, act.rate = 2,
a.rate = 0.01, ds.rate = 0.01, di.rate = 0.01,
a.rate.g2 = 0.01, ds.rate.g2 = 0.01, di.rate.g2 = 0.01)
init <- init.net(i.num = 10, i.num.g2 = 10)
control <- control.net(type = "SI", nsteps = 10, nsims = 2,
resimulate.network = TRUE, verbose = FALSE)
x <- netsim(est5.vit, param, init, control)
expect_is(x, "netsim")
expect_is(as.data.frame(x), "data.frame")
expect_equal(x$param$vital, TRUE)
expect_output(summary(x, at = 10), "EpiModel Summary")
plot(x)
plot(x, y = "si.flow", mean.smooth = TRUE)
plot(x, type = "formation")
test_net(x)
rm(x)
## "SIR, 2M, OP: 1 sim"
param <- param.net(inf.prob = 0.5, inf.prob.g2 = 0.1, rec.rate = 0.1,
rec.rate.g2 = 0.1, act.rate = 2, a.rate = 0.01,
a.rate.g2 = NA, ds.rate = 0.01, ds.rate.g2 = 0.01,
di.rate = 0.01, di.rate.g2 = 0.01, dr.rate = 0.01,
dr.rate.g2 = 0.01)
init <- init.net(i.num = 10, i.num.g2 = 0,
r.num = 0, r.num.g2 = 10)
control <- control.net(type = "SIR", nsteps = 10, nsims = 1,
resimulate.network = TRUE, verbose = FALSE)
x <- netsim(est5.vit, param, init, control)
expect_is(x, "netsim")
expect_is(as.data.frame(x), "data.frame")
expect_equal(x$param$vital, TRUE)
expect_output(summary(x, at = 10), "EpiModel Summary")
plot(x)
plot(x, y = "si.flow", mean.smooth = TRUE)
plot(x, type = "formation")
test_net(x)
rm(x)
## "SIR, 2M, OP: 3 sim"
control <- control.net(type = "SIR", nsteps = 10, nsims = 2,
resimulate.network = TRUE, verbose = FALSE)
x <- netsim(est5.vit, param, init, control)
expect_is(x, "netsim")
expect_is(as.data.frame(x), "data.frame")
expect_equal(x$param$vital, TRUE)
expect_output(summary(x, at = 10), "EpiModel Summary")
plot(x)
plot(x, y = "si.flow", mean.smooth = TRUE)
plot(x, type = "formation")
test_net(x)
rm(x)
})
################################################################################
test_that("Extinction open-population models", {
skip_on_cran()
nw <- network_initialize(n = 25)
nw <- set_vertex_attribute(nw, "group", rep(1:2, c(15, 10)))
est <- netest(nw, formation = ~edges + nodematch("group"),
target.stats = c(15, 0),
coef.diss = dissolution_coefs(~offset(edges), 10, 0.01),
edapprox = TRUE, verbose = FALSE)
## "netsim: 2M, ds.rate = 0.5"
param <- param.net(inf.prob = 0.1, inf.prob.g2 = 0.1, act.rate = 2,
a.rate = 0.01, ds.rate = 0.5, di.rate = 0.5,
a.rate.g2 = 0.01, ds.rate.g2 = 0.01, di.rate.g2 = 0.01)
init <- init.net(i.num = 5, i.num.g2 = 0)
control <- control.net(type = "SI", nsteps = 30, nsims = 1,
resimulate.network = TRUE, verbose = FALSE)
x <- netsim(est, param, init, control)
expect_output(summary(x, at = 10), "EpiModel Summary")
plot(x)
plot(x, y = "si.flow", mean.smooth = TRUE)
plot(x, type = "formation")
test_net(x)
rm(x)
## "netsim: 2M, ds.rate.g2 = 0.5"
param <- param.net(inf.prob = 0.1, inf.prob.g2 = 0.1, act.rate = 2,
a.rate = 0.01, ds.rate = 0.01, di.rate = 0.01,
a.rate.g2 = 0.01, ds.rate.g2 = 0.5, di.rate.g2 = 0.5)
init <- init.net(i.num = 5, i.num.g2 = 0)
control <- control.net(type = "SI", nsteps = 30, nsims = 1,
resimulate.network = TRUE, verbose = FALSE)
x <- netsim(est, param, init, control)
expect_output(summary(x, at = 10), "EpiModel Summary")
plot(x)
plot(x, y = "si.flow", mean.smooth = TRUE)
plot(x, type = "formation")
test_net(x)
rm(x)
})
################################################################################
test_that("status.vector and infTime.vector", {
skip_on_cran()
n <- 100
nw <- network_initialize(n = n)
formation <- ~edges
target.stats <- 50
coef.diss <- dissolution_coefs(dissolution = ~offset(edges), duration = 20)
est1 <- netest(nw, formation, target.stats, coef.diss, verbose = FALSE)
# Epidemic model
param <- param.net(inf.prob = 0.3, rec.rate = 0.01)
status <- sample(c("s", "i"), size = n, replace = TRUE, prob = c(0.8, 0.2))
infTime <- rep(NA, n)
infTime[which(status == "i")] <- -rgeom(sum(status == "i"), prob = 0.01) + 2
init <- init.net(status.vector = status, infTime.vector = infTime)
control <- control.net(type = "SIS", nsteps = 100, nsims = 5, verbose = FALSE)
mod1 <- netsim(est1, param, init, control)
expect_is(mod1, "netsim")
control <- control.net(type = "SIR", nsteps = 100, nsims = 5, verbose = FALSE)
mod2 <- netsim(est1, param, init, control)
expect_is(mod2, "netsim")
})
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