Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(cache = FALSE,
collapse = TRUE,
comment = "#>"
)
options()
## ----fig.show='hold'----------------------------------------------------------
library(nph)
## ----001, fig.show='hold', fig.width=12.5, warning=FALSE, out.width='100%'----
times <- c(0, 5 * 365) # Time interval boundaries, in days
# Treatment group
t_resp <- 1 # There are no subgroups
B5 <- pop_pchaz(
T = times,
lambdaMat1 = m2r(matrix(18,nrow = 1)),
lambdaMat2 = m2r(matrix(11,nrow = 1)),
lambdaProgMat = m2r(matrix(9, nrow = 1)),
p = t_resp,
timezero = FALSE, discrete_approximation = TRUE
)
# Control group
c_resp <- 1 # There are no subgroups
K5 <- pop_pchaz(
T = times,
lambdaMat1 = m2r(matrix(11,nrow = 1)),
lambdaMat2 = m2r(matrix(9, nrow = 1)),
lambdaProgMat = m2r(matrix(5, nrow = 1)),
p = c_resp,
timezero = TRUE, discrete_approximation = TRUE
)
pp = plot_diagram(B5, K5)
pp
## ----fig.show='hold', fig.height=3.5, fig.width=10, warning=FALSE, out.width='100%'----
plot_shhr(K5, B5)
## ----002, fig.show='hold', fig.width=12.5, fig.height=10.5, warning=FALSE, out.width='100%'----
times <- c(0, 5 * 365) # Time interval boundaries, in days
# Treatment group
t_resp <- c(.2, .8)
B5 <- pop_pchaz(
T = times,
lambdaMat1 = m2r(matrix(c(30,
18),nrow = 2)),
lambdaMat2 = m2r(matrix(c(20,
11),nrow = 2)),
lambdaProgMat = m2r(matrix(c(15,
9), nrow = 2)),
p = t_resp,
timezero = FALSE, discrete_approximation = TRUE
)
# Control group
c_resp <- 1
K5 <- pop_pchaz(
T = times,
lambdaMat1 = m2r(matrix(11,nrow = 1)),
lambdaMat2 = m2r(matrix(9, nrow = 1)),
lambdaProgMat = m2r(matrix(5, nrow = 1)),
p = c_resp,
timezero = TRUE, discrete_approximation = TRUE
)
pp = plot_diagram(B5, K5, A_subgr_labels = c("S1", "S2"))
pp
## ----fig.show='hold', fig.height=3.5, fig.width=10, warning=FALSE, out.width='100%'----
plot_shhr(K5, B5)
## ----003, fig.show='hold', fig.width=11, warning=FALSE, out.width='100%'-----
times <- c(0, 5 * 365) # Time interval boundaries, in days
# Treatment group
t_resp <- c(.5, .5)
B5 <- pop_pchaz(
T = times,
lambdaMat1 = m2r(matrix(c(30,
18),nrow = 2)),
lambdaMat2 = m2r(matrix(c(20,
11),nrow = 2)),
lambdaProgMat = m2r(matrix(c(15,
9), nrow = 2)),
p = t_resp,
timezero = FALSE, discrete_approximation = TRUE
)
# Control group
c_resp <- 1
K5 <- pop_pchaz(
T = times,
lambdaMat1 = m2r(matrix(11,nrow = 1)),
lambdaMat2 = m2r(matrix(9, nrow = 1)),
lambdaProgMat = m2r(matrix(5, nrow = 1)),
p = c_resp,
timezero = TRUE, discrete_approximation = TRUE
)
## ----fig.show='hold', fig.height=3.5, fig.width=10, warning=FALSE, out.width='100%'----
plot_shhr(K5, B5)
## ----004, fig.show='hold', fig.width=12.5, fig.height=10.5, warning=FALSE, out.width='100%'----
times <- c(0, 5 * 365) # Time interval boundaries, in days
# Treatment group
t_resp <- c(.5, .5)
B5 <- pop_pchaz(
T = times,
lambdaMat1 = m2r(matrix(c(30,
18), nrow = 2)),
lambdaMat2 = m2r(matrix(c(30,
11), nrow = 2)),
lambdaProgMat = m2r(matrix(c(15,
9), nrow = 2)),
p = t_resp,
timezero = FALSE, discrete_approximation = TRUE
)
# Control group
c_resp <- 1
K5 <- pop_pchaz(
T = times,
lambdaMat1 = m2r(matrix(11, nrow = 1)),
lambdaMat2 = m2r(matrix( 9, nrow = 1)),
lambdaProgMat = m2r(matrix( 5, nrow = 1)),
p = c_resp,
timezero = TRUE, discrete_approximation = TRUE
)
pp = plot_diagram(B5, K5, A_subgr_labels = c("S1", "S2"))
pp
## ----fig.show='hold', fig.height=3.5, fig.width=10, warning=FALSE, out.width='100%'----
plot_shhr(K5, B5)
## ----005, fig.show='hold', fig.width=12.5, warning=FALSE, out.width='100%'----
times <- c(0, 100, 5 * 365) # Time interval boundaries, in days
# Treatment group
t_resp <- 1 # There are no subgroups
B5 <- pop_pchaz(
T = times,
lambdaMat1 = m2r(matrix(c(11, 18), nrow = 1)),
lambdaMat2 = m2r(matrix(c( 9, 11), nrow = 1)),
lambdaProgMat = m2r(matrix(c( 5, 9), nrow = 1)),
p = t_resp,
timezero = FALSE, discrete_approximation = TRUE
)
# Control group
c_resp <- 1
K5 <- pop_pchaz(
T = times,
lambdaMat1 = m2r(matrix(c(11, 11), nrow = 1)),
lambdaMat2 = m2r(matrix(c( 9, 9), nrow = 1)),
lambdaProgMat = m2r(matrix(c( 5, 5), nrow = 1)),
p = c_resp,
timezero = TRUE, discrete_approximation = TRUE
)
pp = plot_diagram(B5, K5)
pp
## ----fig.show='hold', fig.height=3.5, fig.width=10, warning=FALSE, out.width='100%'----
plot_shhr(K5, B5)
## ----006, fig.show='hold', fig.width=12.5, fig.height=10.5, warning=FALSE, out.width='100%'----
times <- c(0, 100, 5 * 365) # Time interval boundaries, in days
# Treatment group
t_resp <- c(0.5, 0.5) #Proportion of subgroups
B5 <- pop_pchaz(
T = times,
lambdaMat1 = m2r(matrix(c(11, 30,
11, 18), byrow = TRUE, nrow = 2)),
lambdaMat2 = m2r(matrix(c( 9, 20,
9, 11), byrow = TRUE, nrow = 2)),
lambdaProgMat = m2r(matrix(c( 5, 15,
5, 9), byrow = TRUE, nrow = 2)),
p = t_resp,
timezero = FALSE, discrete_approximation = TRUE
)
# Control group
c_resp <- 1
K5 <- pop_pchaz(
T = times,
lambdaMat1 = m2r(matrix(c(11, 11), nrow = 1, ncol = 2)),
lambdaMat2 = m2r(matrix(c( 9, 9), nrow = 1, ncol = 2)),
lambdaProgMat = m2r(matrix(c( 5, 5), nrow = 1, ncol = 2)),
p = c_resp,
timezero = TRUE, discrete_approximation = TRUE
)
pp = plot_diagram(B5, K5, A_subgr_labels = c("S1", "S2"))
pp
## ----fig.show='hold', fig.height=3.5, fig.width=10, warning=FALSE, out.width='100%'----
plot_shhr(K5, B5)
## ----007, fig.show='hold', fig.width=12.5, fig.height=10.5, warning=FALSE, out.width='100%'----
times <- c(0, 5 * 365) # Time interval boundaries, in days
# Treatment group
t_resp <- 1 # There are no subgroups
B5 <- pop_pchaz(
T = times,
lambdaMat1 = m2r(matrix(18, nrow = 1)),
lambdaMat2 = m2r(matrix(11, nrow = 1)),
lambdaProgMat = m2r(matrix( 9, nrow = 1)),
p = t_resp,
timezero = FALSE, discrete_approximation = TRUE
)
# Control group
c_resp <- c(1/3, 2/3) #non-switcher, switcher reponse
K5 <- pop_pchaz(
T = times,
lambdaMat1 = m2r(matrix(c(11,
11), nrow = 2, ncol = 1)),
lambdaMat2 = m2r(matrix(c( 9,
11), nrow = 2, ncol = 1)),
lambdaProgMat = m2r(matrix(c( 5,
5), nrow = 2, ncol = 1)),
p = c_resp,
timezero = TRUE, discrete_approximation = TRUE
)
pp = plot_diagram(B5, K5, B_subgr_labels = c("Non-switcher","Switcher"))
pp
## ----fig.show='hold', fig.height=3.5, fig.width=10, warning=FALSE, out.width='100%'----
plot_shhr(K5, B5)
## ----007b, fig.show='hold', fig.width=12.5, fig.height=10.5, warning=FALSE, out.width='100%'----
times <- c(0, 5 * 365) # Time interval boundaries, in days
# Treatment group
t_resp <- 1 # There are no subgroups
B5 <- pop_pchaz(
T = times,
lambdaMat1 = m2r(matrix(18, nrow = 1)),
lambdaMat2 = m2r(matrix(11, nrow = 1)),
lambdaProgMat = m2r(matrix( 9, nrow = 1)),
p = t_resp,
timezero = FALSE, discrete_approximation = TRUE
)
# Control group
c_resp <- c(1/3, 2/3) #non-switcher, switcher reponse
K5 <- pop_pchaz(
T = times,
lambdaMat1 = m2r(matrix(c(11,
11), nrow = 2, ncol = 1)),
lambdaMat2 = m2r(matrix(c( 9,
14), nrow = 2, ncol = 1)),
lambdaProgMat = m2r(matrix(c( 5,
5), nrow = 2, ncol = 1)),
p = c_resp,
timezero = TRUE, discrete_approximation = TRUE
)
pp = plot_diagram(B5, K5, B_subgr_labels = c("Non-switcher","Switcher"))
pp
## ----fig.show='hold', fig.height=3.5, fig.width=10, warning=FALSE, out.width='100%'----
plot_shhr(K5, B5)
## ----008, fig.show='hold', fig.width=12.5, fig.height=10.5, warning=FALSE, out.width='100%'----
times <- c(0, 5 * 365) # Time interval boundaries, in days
# Treatment group
t_resp <- 1 # There are no subgroups
B5 <- pop_pchaz(
T = times,
lambdaMat1 = m2r(matrix(18,nrow = 1)),
lambdaMat2 = m2r(matrix(11,nrow = 1)),
lambdaProgMat = m2r(matrix(9, nrow = 1)),
p = t_resp,
timezero = FALSE, discrete_approximation = TRUE
)
# Control group
c_resp <- c(2/3, 1/3) #non-switcher, switcher reponse
K5 <- pop_pchaz(
T = times,
lambdaMat1 = m2r(matrix(c(11,
11), nrow = 2, ncol = 1)),
lambdaMat2 = m2r(matrix(c(9,
11), nrow = 2, ncol = 1)),
lambdaProgMat = m2r(matrix(c(5,
5), nrow = 2, ncol = 1)),
p = c_resp,
timezero = TRUE, discrete_approximation = TRUE
)
pp = plot_diagram(B5, K5, B_subgr_labels = c("Non-switcher","Switcher"))
pp
## ----fig.show='hold', fig.height=3.5, fig.width=10, warning=FALSE, out.width='100%'----
plot_shhr(K5, B5)
## ----008b, fig.show='hold', fig.width=12.5, fig.height=10.5, warning=FALSE, out.width='100%'----
times <- c(0, 5 * 365) # Time interval boundaries, in days
# Treatment group
t_resp <- 1 # There are no subgroups
B5 <- pop_pchaz(
T = times,
lambdaMat1 = m2r(matrix(18, nrow = 1)),
lambdaMat2 = m2r(matrix(11, nrow = 1)),
lambdaProgMat = m2r(matrix( 9, nrow = 1)),
p = t_resp,
timezero = FALSE, discrete_approximation = TRUE
)
# Control group
c_resp <- c(2/3, 1/3) #non-switcher, switcher reponse
K5 <- pop_pchaz(
T = times,
lambdaMat1 = m2r(matrix(c(11,
11), nrow = 2, ncol = 1)),
lambdaMat2 = m2r(matrix(c( 9,
14), nrow = 2, ncol = 1)),
lambdaProgMat = m2r(matrix(c( 5,
5), nrow = 2, ncol = 1)),
p = c_resp,
timezero = TRUE, discrete_approximation = TRUE
)
pp = plot_diagram(B5, K5, B_subgr_labels = c("Non-switcher","Switcher"))
pp
## ----fig.show='hold', fig.height=3.5, fig.width=10, warning=FALSE, out.width='100%'----
plot_shhr(K5, B5)
## ----009, fig.show='hold', fig.width=12.5, fig.height=13, warning=FALSE, out.width='100%'----
times <- c(0, 5 * 365) # Time interval boundaries, in days
# Treatment group
t_resp <- c(.5, .5)
B5 <- pop_pchaz(
T = times,
lambdaMat1 = m2r(matrix(c( 2,
18), nrow = 2)),
lambdaMat2 = m2r(matrix(c( 2,
18), nrow = 2)),
lambdaProgMat = m2r(matrix(c(19,
19), nrow = 2)),
p = t_resp,
timezero = FALSE, discrete_approximation = TRUE
)
# Control group
c_resp <- c(1)
K5 <- pop_pchaz(
T = times,
lambdaMat1 = m2r(matrix(c(11), nrow = 1, ncol = 1)),
lambdaMat2 = m2r(matrix(c( 9), nrow = 1, ncol = 1)),
lambdaProgMat = m2r(matrix(c( 5), nrow = 1, ncol = 1)),
p = c_resp,
timezero = TRUE, discrete_approximation = TRUE
)
pp = plot_diagram(B5, K5,
A_subgr_labels = c("S1", "S2"))
pp
## ----fig.show='hold', fig.height=3.5, fig.width=10, warning=FALSE, out.width='100%'----
plot_shhr(K5, B5)
## ----010, fig.show='hold', fig.width=12.5, fig.height=13.5, warning=FALSE, out.width='100%'----
times <- c(0, 5 * 365) # Time interval boundaries, in days
# Treatment group
t_resp <- c(.2, .8)
B5 <- pop_pchaz(
T = times,
lambdaMat1 = m2r(matrix(c(30,
18), nrow = 2)),
lambdaMat2 = m2r(matrix(c(30,
11), nrow = 2)),
lambdaProgMat = m2r(matrix(c(15,
9), nrow = 2)),
p = t_resp,
timezero = FALSE, discrete_approximation = TRUE
)
# Control group
c_resp <- c(2/3, 1/3*t_resp[1], 1/3*t_resp[2])
K5 <- pop_pchaz(
T = times,
lambdaMat1 = m2r(matrix(c(11), nrow = 3, ncol = 1)),
lambdaMat2 = m2r(matrix(c( 9,
25,
14), nrow = 3)),
lambdaProgMat = m2r(matrix(c( 5), nrow = 3,ncol = 1)),
p = c_resp,
timezero = TRUE, discrete_approximation = TRUE
)
pp = plot_diagram(B5, K5,
A_subgr_labels = c("S1", "S2"),
B_subgr_labels = c("Non-switcher","Switcher-S1","Switcher-S2"))
pp
## ----fig.show='hold', fig.height=3.5, fig.width=10, warning=FALSE, out.width='100%'----
plot_shhr(K5, B5)
## ----010b, fig.show='hold', fig.width=12.5, fig.height=13.5, warning=FALSE, out.width='100%'----
times <- c(0, 5 * 365) # Time interval boundaries, in days
# Treatment group
t_resp <- c(.5, .5)
B5 <- pop_pchaz(
T = times,
lambdaMat1 = m2r(matrix(c(30,
18), nrow = 2)),
lambdaMat2 = m2r(matrix(c(30,
11), nrow = 2)),
lambdaProgMat = m2r(matrix(c(15,
9), nrow = 2)),
p = t_resp,
timezero = FALSE, discrete_approximation = TRUE
)
# Control group
c_resp <- c(2/3, 1/3*t_resp[1], 1/3*t_resp[2])
K5 <- pop_pchaz(
T = times,
lambdaMat1 = m2r(matrix(c(11), nrow = 3, ncol = 1)),
lambdaMat2 = m2r(matrix(c( 9,
25,
14), nrow = 3)),
lambdaProgMat = m2r(matrix(c( 5), nrow = 3,ncol = 1)),
p = c_resp,
timezero = TRUE, discrete_approximation = TRUE
)
pp = plot_diagram(B5, K5,
A_subgr_labels = c("S1", "S2"),
B_subgr_labels = c("Non-switcher","Switcher-S1","Switcher-S2"))
pp
## ----fig.show='hold', fig.height=3.5, fig.width=10, warning=FALSE, out.width='100%'----
plot_shhr(K5, B5)
## ----010c, fig.show='hold', fig.width=12.5, fig.height=13.5, warning=FALSE, out.width='100%'----
times <- c(0, 5 * 365) # Time interval boundaries, in days
# Treatment group
t_resp <- c(.5, .5)
B5 <- pop_pchaz(
T = times,
lambdaMat1 = m2r(matrix(c(30,
18), nrow = 2)),
lambdaMat2 = m2r(matrix(c(20,
11), nrow = 2)),
lambdaProgMat = m2r(matrix(c(15,
9), nrow = 2)),
p = t_resp,
timezero = FALSE, discrete_approximation = TRUE
)
# Control group
c_resp <- c(1/3, 2/3*t_resp[1], 2/3*t_resp[2])
K5 <- pop_pchaz(
T = times,
lambdaMat1 = m2r(matrix(c(11), nrow = 3, ncol = 1)),
lambdaMat2 = m2r(matrix(c( 9,
25,
14), nrow = 3)),
lambdaProgMat = m2r(matrix(c( 5), nrow = 3,ncol = 1)),
p = c_resp,
timezero = TRUE, discrete_approximation = TRUE
)
pp = plot_diagram(B5, K5,
A_subgr_labels = c("S1", "S2"),
B_subgr_labels = c("Non-switcher","Switcher-S1","Switcher-S2"))
pp
## ----fig.show='hold', fig.height=3.5, fig.width=10, warning=FALSE, out.width='100%'----
plot_shhr(K5, B5)
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