tests/testthat/test-cmt-order.R
In nlmixr2/rxode2: Facilities for Simulating from ODE-Based Models
rxTest({
warfarin <- nlmixr2data::warfarin
test_that("cmt() syntax makes sense", {
mod <- rxode2({
a <- 6
b <- 0.6
cmt(blood) # cmt = 1 now
d / dt(intestine) <- -a * intestine
d / dt(blood) <- a * intestine - b * blood
})
expect_equal(c("blood", "intestine"), rxState(mod))
mod <- rxode2({
a <- 6
b <- 0.6
d / dt(intestine) <- -a * intestine
d / dt(blood) <- a * intestine - b * blood
})
expect_equal(c("intestine", "blood"), rxState(mod))
expect_output(
expect_error(expect_message(rxode2({
a <- 6
b <- 0.6
cmt(matt) # cmt = 1 now
d/dt(intestine) <- -a * intestine
d/dt(blood) <- a * intestine - b * blood
}))),
regexp = "compartment 'matt' needs differential equations defined"
)
tmp <- rxode2({
a <- 6
b <- 0.6
cmt(blood) # cmt = 1 now
cmt(intestine) # cmt = 2 now
cmt(matt)
d / dt(intestine) <- -a * intestine
d / dt(blood) <- a * intestine - b * blood
})
expect_equal(tmp$stateExtra, "matt")
})
test_that("Compartment melding with dvid", {
w <- rxode2({
ktr <- exp(tktr + eta.ktr)
ka <- exp(tka + eta.ka)
cl <- exp(tcl + eta.cl)
##
logit <- exp(poplogit + eta.emax)
emax <- logit / (1 + logit)
ec50 <- exp(tec50 + eta.ec50)
kout <- exp(tkout + eta.kout)
e0 <- exp(te0 + eta.e0)
##
DCP <- center / v
PD <- 1 - emax * DCP / (ec50 + DCP)
##
pca(0) <- e0
kin <- e0 * kout
##
d / dt(depot) <- -ktr * depot
d / dt(gut) <- ktr * depot - ka * gut
d / dt(center) <- ka * gut - cl / v * center
d / dt(pca) <- kin * PD - kout * pca
##
cp <- center / v
cmt(cp)
## These dvid w/ negative values are counted backward from the last
dvid(-1, 4)
})
w2 <- warfarin
tmp <- etTrans(w2, w, addCmt = TRUE)
expect_equal(
tmp$CMT[tmp$ID == 1],
c(
1L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 4L, 5L, 4L, 5L, 4L, 5L,
4L, 4L, 4L, 4L
)
)
w <- rxode2({
ktr <- exp(tktr + eta.ktr)
ka <- exp(tka + eta.ka)
cl <- exp(tcl + eta.cl)
##
logit <- exp(poplogit + eta.emax)
emax <- logit / (1 + logit)
ec50 <- exp(tec50 + eta.ec50)
kout <- exp(tkout + eta.kout)
e0 <- exp(te0 + eta.e0)
##
DCP <- center / v
PD <- 1 - emax * DCP / (ec50 + DCP)
##
pca(0) <- e0
kin <- e0 * kout
##
d / dt(depot) <- -ktr * depot
d / dt(gut) <- ktr * depot - ka * gut
d / dt(center) <- ka * gut - cl / v * center
d / dt(pca) <- kin * PD - kout * pca
##
cp <- center / v
cmt(cp)
dvid(5, 4)
})
w2 <- warfarin
tmp <- etTrans(w2, w, addCmt = TRUE)
expect_equal(
tmp$CMT[tmp$ID == 1],
c(
1L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 4L, 5L, 4L, 5L, 4L, 5L,
4L, 4L, 4L, 4L
)
)
w2$dvid <- paste(w2$dvid)
tmp <- etTrans(w2, w, addCmt = TRUE)
expect_equal(
tmp$CMT[tmp$ID == 1],
c(
1L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 4L, 5L, 4L, 5L, 4L, 5L,
4L, 4L, 4L, 4L
)
)
w2 <- warfarin
w2$dvid <- as.integer(w2$dvid)
tmp <- etTrans(w2, w, addCmt = TRUE)
expect_equal(
tmp$CMT[tmp$ID == 1],
c(
1L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 4L, 5L, 4L, 5L, 4L, 5L,
4L, 4L, 4L, 4L
)
)
w2 <- warfarin
w2$dvid <- as.integer(w2$dvid) * 10
expect_warning(tmp <- etTrans(w2, w, addCmt = TRUE))
expect_equal(
tmp$CMT[tmp$ID == 1],
c(
1L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 4L, 5L, 4L, 5L, 4L, 5L,
4L, 4L, 4L, 4L
)
)
w <- rxode2({
ktr <- exp(tktr + eta.ktr)
ka <- exp(tka + eta.ka)
cl <- exp(tcl + eta.cl)
##
logit <- exp(poplogit + eta.emax)
emax <- logit / (1 + logit)
ec50 <- exp(tec50 + eta.ec50)
kout <- exp(tkout + eta.kout)
e0 <- exp(te0 + eta.e0)
##
DCP <- center / v
PD <- 1 - emax * DCP / (ec50 + DCP)
##
pca(0) <- e0
kin <- e0 * kout
##
d / dt(depot) <- -ktr * depot
d / dt(gut) <- ktr * depot - ka * gut
d / dt(center) <- ka * gut - cl / v * center
d / dt(pca) <- kin * PD - kout * pca
##
cp <- center / v
cmt(cp)
dvid(5)
})
w2 <- warfarin
w2$dvid <- as.integer(w2$dvid) * 10
expect_warning(tmp <- etTrans(w2, w, addCmt = TRUE))
expect_equal(
tmp$CMT[tmp$ID == 1],
c(
1L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 1L, 5L, 1L, 5L, 1L, 5L,
1L, 1L, 1L, 1L
)
)
w <- rxode2({
ktr <- exp(tktr + eta.ktr)
ka <- exp(tka + eta.ka)
cl <- exp(tcl + eta.cl)
##
logit <- exp(poplogit + eta.emax)
emax <- logit / (1 + logit)
ec50 <- exp(tec50 + eta.ec50)
kout <- exp(tkout + eta.kout)
e0 <- exp(te0 + eta.e0)
##
DCP <- center / v
PD <- 1 - emax * DCP / (ec50 + DCP)
##
pca(0) <- e0
kin <- e0 * kout
##
d / dt(depot) <- -ktr * depot
d / dt(gut) <- ktr * depot - ka * gut
d / dt(center) <- ka * gut - cl / v * center
d / dt(pca) <- kin * PD - kout * pca
##
cp <- center / v
cmt(cp)
dvid(4, 5)
})
w2 <- warfarin
w2$dvid <- as.integer(w2$dvid)
tmp <- etTrans(w2, w, addCmt = TRUE)
expect_equal(
tmp$CMT[tmp$ID == 1],
c(
1L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 4L, 5L, 4L, 5L, 4L,
5L, 5L, 5L, 5L
)
)
## Warfarin model
inner <- rxode2({
cmt(depot)
cmt(gut)
cmt(center)
cmt(effect)
rx_expr_001 ~ -depot
rx_expr_002 ~ -center
rx_expr_003 ~ -ETA[4]
rx_expr_004 ~ -effect
rx_expr_005 ~ -2 * ETA[4]
rx_expr_006 ~ 2 * THETA[4]
rx_expr_007 ~ ETA[1] + THETA[1]
rx_expr_008 ~ ETA[2] + THETA[2]
rx_expr_009 ~ ETA[3] + THETA[3]
rx_expr_010 ~ ETA[7] + THETA[9]
rx_expr_011 ~ ETA[5] + THETA[7]
rx_expr_012 ~ ETA[6] + THETA[8]
rx_expr_013 ~ rx_expr_003 - THETA[4]
rx_expr_014 ~ ETA[8] + THETA[10]
rx_expr_015 ~ exp(rx_expr_007)
rx_expr_016 ~ exp(rx_expr_008)
rx_expr_017 ~ exp(rx_expr_009)
rx_expr_018 ~ exp(rx_expr_010)
rx_expr_019 ~ exp(rx_expr_011)
rx_expr_020 ~ exp(rx_expr_012)
rx_expr_021 ~ rx_expr_005 - rx_expr_006
rx_expr_022 ~ Rx_pow_di(center, 2)
rx_expr_023 ~ exp(rx_expr_013)
rx_expr_024 ~ exp(rx_expr_014)
rx_expr_025 ~ rx_expr_019 + 1
rx_expr_026 ~ Rx_pow_di(THETA[5], 2)
rx_expr_027 ~ gut * rx_expr_016
rx_expr_028 ~ 2 * rx_expr_026
rx_expr_029 ~ exp(rx_expr_021)
rx_expr_030 ~ depot * rx_expr_015
rx_expr_031 ~ rx_expr_001 * rx_expr_015
rx_expr_032 ~ rx_expr_002 * rx_expr_017
rx_expr_033 ~ rx_expr_004 * rx_expr_018
rx_expr_034 ~ center * rx_expr_023
rx_expr_035 ~ rx_expr_002 * rx_expr_023
rx_expr_036 ~ rx_expr_028 * center
rx_expr_037 ~ center * rx_expr_029
rx_expr_038 ~ rx_expr_023 * rx_expr_019
rx_expr_039 ~ rx__sens_gut_BY_ETA_1___ * rx_expr_016
rx_expr_040 ~ rx__sens_gut_BY_ETA_2___ * rx_expr_016
rx_expr_041 ~ rx__sens_gut_BY_ETA_3___ * rx_expr_016
rx_expr_042 ~ rx__sens_gut_BY_ETA_4___ * rx_expr_016
rx_expr_043 ~ rx__sens_gut_BY_ETA_5___ * rx_expr_016
rx_expr_044 ~ rx__sens_gut_BY_ETA_6___ * rx_expr_016
rx_expr_045 ~ rx__sens_gut_BY_ETA_7___ * rx_expr_016
rx_expr_046 ~ rx__sens_gut_BY_ETA_8___ * rx_expr_016
rx_expr_047 ~ rx__sens_depot_BY_ETA_1___ * rx_expr_015
rx_expr_048 ~ rx_expr_034 + rx_expr_020
rx_expr_049 ~ rx_expr_034 * rx_expr_019
rx_expr_050 ~ rx_expr_032 * rx_expr_023
rx_expr_051 ~ rx_expr_035 * rx_expr_019
rx_expr_052 ~ rx_expr_037 * rx_expr_019
rx_expr_053 ~ Rx_pow_di(rx_expr_048, 2)
rx_expr_054 ~ (rx_expr_048) * (rx_expr_025)
rx_expr_055 ~ rx_expr_053 * (rx_expr_025)
rx_expr_056 ~ rx_expr_038 / (rx_expr_054)
rx_expr_057 ~ rx_expr_051 / (rx_expr_054)
rx_expr_058 ~ rx_expr_057 + 1
rx_expr_059 ~ rx_expr_052 / (rx_expr_055)
rx_expr_060 ~ (rx_expr_058) * rx_expr_018
rx_expr_061 ~ rx_expr_060 * rx_expr_024
rx_expr_062 ~ rx_expr_059 - rx_expr_056
d / dt(depot) <- rx_expr_031
d / dt(gut) <- rx_expr_030 - rx_expr_027
d / dt(center) <- rx_expr_050 + rx_expr_027
effect(0) <- rx_expr_024
d / dt(effect) <- rx_expr_033 + rx_expr_061
d / dt(rx__sens_depot_BY_ETA_1___) ~ rx_expr_031 - rx_expr_047
d / dt(rx__sens_depot_BY_ETA_2___) ~ -rx__sens_depot_BY_ETA_2___ * rx_expr_015
d / dt(rx__sens_depot_BY_ETA_3___) ~ -rx__sens_depot_BY_ETA_3___ * rx_expr_015
d / dt(rx__sens_depot_BY_ETA_4___) ~ -rx__sens_depot_BY_ETA_4___ * rx_expr_015
d / dt(rx__sens_depot_BY_ETA_5___) ~ -rx__sens_depot_BY_ETA_5___ * rx_expr_015
d / dt(rx__sens_depot_BY_ETA_6___) ~ -rx__sens_depot_BY_ETA_6___ * rx_expr_015
d / dt(rx__sens_depot_BY_ETA_7___) ~ -rx__sens_depot_BY_ETA_7___ * rx_expr_015
d / dt(rx__sens_depot_BY_ETA_8___) ~ -rx__sens_depot_BY_ETA_8___ * rx_expr_015
d / dt(rx__sens_gut_BY_ETA_1___) ~ rx_expr_030 + rx_expr_047 - rx_expr_039
d / dt(rx__sens_gut_BY_ETA_2___) ~ -gut * rx_expr_016 + rx__sens_depot_BY_ETA_2___ * rx_expr_015 - rx_expr_040
d / dt(rx__sens_gut_BY_ETA_3___) ~ rx__sens_depot_BY_ETA_3___ * rx_expr_015 - rx_expr_041
d / dt(rx__sens_gut_BY_ETA_4___) ~ rx__sens_depot_BY_ETA_4___ * rx_expr_015 - rx_expr_042
d / dt(rx__sens_gut_BY_ETA_5___) ~ rx__sens_depot_BY_ETA_5___ * rx_expr_015 - rx_expr_043
d / dt(rx__sens_gut_BY_ETA_6___) ~ rx__sens_depot_BY_ETA_6___ * rx_expr_015 - rx_expr_044
d / dt(rx__sens_gut_BY_ETA_7___) ~ rx__sens_depot_BY_ETA_7___ * rx_expr_015 - rx_expr_045
d / dt(rx__sens_gut_BY_ETA_8___) ~ rx__sens_depot_BY_ETA_8___ * rx_expr_015 - rx_expr_046
d / dt(rx__sens_center_BY_ETA_1___) ~ -rx__sens_center_BY_ETA_1___ * rx_expr_017 * rx_expr_023 + rx_expr_039
d / dt(rx__sens_center_BY_ETA_2___) ~ rx_expr_027 - rx__sens_center_BY_ETA_2___ * rx_expr_017 * rx_expr_023 + rx_expr_040
d / dt(rx__sens_center_BY_ETA_3___) ~ rx_expr_050 - rx__sens_center_BY_ETA_3___ * rx_expr_017 * rx_expr_023 + rx_expr_041
d / dt(rx__sens_center_BY_ETA_4___) ~ center * rx_expr_017 * rx_expr_023 - rx__sens_center_BY_ETA_4___ * rx_expr_017 * rx_expr_023 + rx_expr_042
d / dt(rx__sens_center_BY_ETA_5___) ~ -rx__sens_center_BY_ETA_5___ * rx_expr_017 * rx_expr_023 + rx_expr_043
d / dt(rx__sens_center_BY_ETA_6___) ~ -rx__sens_center_BY_ETA_6___ * rx_expr_017 * rx_expr_023 + rx_expr_044
d / dt(rx__sens_center_BY_ETA_7___) ~ -rx__sens_center_BY_ETA_7___ * rx_expr_017 * rx_expr_023 + rx_expr_045
d / dt(rx__sens_center_BY_ETA_8___) ~ -rx__sens_center_BY_ETA_8___ * rx_expr_017 * rx_expr_023 + rx_expr_046
d / dt(rx__sens_effect_BY_ETA_1___) ~ rx__sens_center_BY_ETA_1___ * (rx_expr_062) * rx_expr_018 * rx_expr_024 - rx__sens_effect_BY_ETA_1___ * rx_expr_018
d / dt(rx__sens_effect_BY_ETA_2___) ~ rx__sens_center_BY_ETA_2___ * (rx_expr_062) * rx_expr_018 * rx_expr_024 - rx__sens_effect_BY_ETA_2___ * rx_expr_018
d / dt(rx__sens_effect_BY_ETA_3___) ~ rx__sens_center_BY_ETA_3___ * (rx_expr_062) * rx_expr_018 * rx_expr_024 - rx__sens_effect_BY_ETA_3___ * rx_expr_018
d / dt(rx__sens_effect_BY_ETA_4___) ~ rx__sens_center_BY_ETA_4___ * (rx_expr_062) * rx_expr_018 * rx_expr_024 - rx__sens_effect_BY_ETA_4___ * rx_expr_018 + (-rx_expr_022 * rx_expr_029 * rx_expr_019 / (rx_expr_055) + rx_expr_049 / (rx_expr_054)) * rx_expr_018 * rx_expr_024
d / dt(rx__sens_effect_BY_ETA_5___) ~ rx__sens_center_BY_ETA_5___ * (rx_expr_062) * rx_expr_018 * rx_expr_024 - rx__sens_effect_BY_ETA_5___ * rx_expr_018 + (rx_expr_057 + rx_expr_034 * exp(2 * ETA[5] + 2 * THETA[7]) / ((rx_expr_048) * Rx_pow_di(rx_expr_025, 2))) * rx_expr_018 * rx_expr_024
d / dt(rx__sens_effect_BY_ETA_6___) ~ rx_expr_049 * rx_expr_020 * rx_expr_018 * rx_expr_024 / (rx_expr_055) + rx__sens_center_BY_ETA_6___ * (rx_expr_062) * rx_expr_018 * rx_expr_024 - rx__sens_effect_BY_ETA_6___ * rx_expr_018
d / dt(rx__sens_effect_BY_ETA_7___) ~ rx_expr_033 + rx__sens_center_BY_ETA_7___ * (rx_expr_062) * rx_expr_018 * rx_expr_024 - rx__sens_effect_BY_ETA_7___ * rx_expr_018 + rx_expr_061
rx__sens_effect_BY_ETA_8___(0) <- rx_expr_024
d / dt(rx__sens_effect_BY_ETA_8___) ~ rx__sens_center_BY_ETA_8___ * (rx_expr_062) * rx_expr_018 * rx_expr_024 - rx__sens_effect_BY_ETA_8___ * rx_expr_018 + rx_expr_061
rx_yj_ ~ 2
rx_lambda_ ~ 1
if (CMT == 3) {
rx_pred_ <- rx_expr_034
rx__sens_rx_pred__BY_ETA_1___ <- rx__sens_center_BY_ETA_1___ * rx_expr_023
rx__sens_rx_pred__BY_ETA_2___ <- rx__sens_center_BY_ETA_2___ * rx_expr_023
rx__sens_rx_pred__BY_ETA_3___ <- rx__sens_center_BY_ETA_3___ * rx_expr_023
rx__sens_rx_pred__BY_ETA_4___ <- rx_expr_035 + rx__sens_center_BY_ETA_4___ * rx_expr_023
rx__sens_rx_pred__BY_ETA_5___ <- rx__sens_center_BY_ETA_5___ * rx_expr_023
rx__sens_rx_pred__BY_ETA_6___ <- rx__sens_center_BY_ETA_6___ * rx_expr_023
rx__sens_rx_pred__BY_ETA_7___ <- rx__sens_center_BY_ETA_7___ * rx_expr_023
rx__sens_rx_pred__BY_ETA_8___ <- rx__sens_center_BY_ETA_8___ * rx_expr_023
rx_r_ <- rx_expr_026 * rx_expr_022 * rx_expr_029 + Rx_pow_di(THETA[6], 2)
rx__sens_rx_r__BY_ETA_1___ <- rx_expr_036 * rx__sens_center_BY_ETA_1___ * rx_expr_029
rx__sens_rx_r__BY_ETA_2___ <- rx_expr_036 * rx__sens_center_BY_ETA_2___ * rx_expr_029
rx__sens_rx_r__BY_ETA_3___ <- rx_expr_036 * rx__sens_center_BY_ETA_3___ * rx_expr_029
rx__sens_rx_r__BY_ETA_4___ <- -2 * rx_expr_026 * rx_expr_022 * rx_expr_029 + rx_expr_036 * rx__sens_center_BY_ETA_4___ * rx_expr_029
rx__sens_rx_r__BY_ETA_5___ <- rx_expr_036 * rx__sens_center_BY_ETA_5___ * rx_expr_029
rx__sens_rx_r__BY_ETA_6___ <- rx_expr_036 * rx__sens_center_BY_ETA_6___ * rx_expr_029
rx__sens_rx_r__BY_ETA_7___ <- rx_expr_036 * rx__sens_center_BY_ETA_7___ * rx_expr_029
rx__sens_rx_r__BY_ETA_8___ <- rx_expr_036 * rx__sens_center_BY_ETA_8___ * rx_expr_029
}
if (CMT == 4) {
rx_pred_ <- effect
rx__sens_rx_pred__BY_ETA_1___ <- rx__sens_effect_BY_ETA_1___
rx__sens_rx_pred__BY_ETA_2___ <- rx__sens_effect_BY_ETA_2___
rx__sens_rx_pred__BY_ETA_3___ <- rx__sens_effect_BY_ETA_3___
rx__sens_rx_pred__BY_ETA_4___ <- rx__sens_effect_BY_ETA_4___
rx__sens_rx_pred__BY_ETA_5___ <- rx__sens_effect_BY_ETA_5___
rx__sens_rx_pred__BY_ETA_6___ <- rx__sens_effect_BY_ETA_6___
rx__sens_rx_pred__BY_ETA_7___ <- rx__sens_effect_BY_ETA_7___
rx__sens_rx_pred__BY_ETA_8___ <- rx__sens_effect_BY_ETA_8___
rx_r_ <- Rx_pow_di(THETA[11], 2)
rx__sens_rx_r__BY_ETA_1___ <- 0
rx__sens_rx_r__BY_ETA_2___ <- 0
rx__sens_rx_r__BY_ETA_3___ <- 0
rx__sens_rx_r__BY_ETA_4___ <- 0
rx__sens_rx_r__BY_ETA_5___ <- 0
rx__sens_rx_r__BY_ETA_6___ <- 0
rx__sens_rx_r__BY_ETA_7___ <- 0
rx__sens_rx_r__BY_ETA_8___ <- 0
}
cmt(cp)
cmt(pca)
dvid(3, 4, 5, 6)
})
# context("warfarin inner test")
data.pkpd <- warfarin
data.pkpd$dvid <- as.integer(data.pkpd$dvid)
data.pkpd$cmt <- paste(factor(data.pkpd$dvid, c(1, 2), c("center", "effect")))
data.pkpd$cmt[data.pkpd$amt > 0] <- "depot"
t2 <- etTrans(data.pkpd[, names(data.pkpd) != "dvid"], inner)
expect_equal(
t2$CMT[t2$ID == 1],
c(
1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 3L, 4L, 3L, 4L, 3L,
4L, 4L, 4L, 4L
)
)
data.pkpd$cmt <- paste(factor(data.pkpd$dvid, c(1, 2), c("cp", "pca")))
data.pkpd$cmt[data.pkpd$amt > 0] <- "depot"
t2 <- etTrans(data.pkpd[, names(data.pkpd) != "dvid"], inner)
expect_equal(
t2$CMT[t2$ID == 1],
c(
1L, 37L, 37L, 37L, 37L, 37L, 37L, 37L, 37L, 38L, 37L, 38L, 37L, 38L, 37L,
38L, 38L, 38L, 38L
)
)
data.pkpd$cmt <- factor(data.pkpd$cmt)
t2 <- etTrans(data.pkpd[, names(data.pkpd) != "dvid"], inner)
expect_equal(
t2$CMT[t2$ID == 1],
c(
1L, 37L, 37L, 37L, 37L, 37L, 37L, 37L, 37L, 38L, 37L, 38L, 37L, 38L, 37L,
38L, 38L, 38L, 38L
)
)
data.pkpd$cmt <- paste(data.pkpd$cmt)
.cmt <- data.pkpd$cmt
data.pkpd$cmt <- 1
data.pkpd$cmt[.cmt == "cp"] <- 5
data.pkpd$cmt[.cmt == "pca"] <- 6
## This skips the sensitivity equations
t2 <- etTrans(data.pkpd[, names(data.pkpd) != "dvid"], inner)
expect_equal(
t2$CMT[t2$ID == 1],
c(
1L, 37L, 37L, 37L, 37L, 37L, 37L, 37L, 37L, 38L, 37L, 38L, 37L, 38L, 37L,
38L, 38L, 38L, 38L
)
)
data.pkpd$cmt <- 1
data.pkpd$cmt[.cmt == "cp"] <- 3
data.pkpd$cmt[.cmt == "pca"] <- 4
t2 <- etTrans(data.pkpd[, names(data.pkpd) != "dvid"], inner)
expect_equal(
t2$CMT[t2$ID == 1],
c(
1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 3L, 4L, 3L, 4L, 3L,
4L, 4L, 4L, 4L
)
)
t2 <- etTrans(data.pkpd, inner)
expect_equal(
t2$CMT[t2$ID == 1],
c(
1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 3L, 4L, 3L, 4L, 3L,
4L, 4L, 4L, 4L
)
)
data.pkpd$dvid[data.pkpd$dvid == 1] <- 3
data.pkpd$dvid[data.pkpd$dvid == 2] <- 4
expect_error(etTrans(data.pkpd, inner))
t2 <- etTrans(data.pkpd[, names(data.pkpd) != "cmt"], inner, addCmt = TRUE)
expect_equal(
t2$CMT[t2$ID == 1],
c(
1L, 37L, 37L, 37L, 37L, 37L, 37L, 37L, 37L, 38L, 37L, 38L, 37L, 38L, 37L,
38L, 38L, 38L, 38L
)
)
## TEST NA cmt/dvid w/factors
## TEST NA strings for cmt/dvid
tmp <- rxode2({
d / dt(depot) <- -ka * depot
d / dt(center) <- ka * depot - cl / v * center
cp <- center / v
cp2 <- cp + nlmixr_extra_par
cmt(central)
cmt(c20)
})
expect_s3_class(tmp, "rxode2")
# context("Check lhs allowed stateExtra while preserving lhs properties.")
tmp <- rxode2({
d / dt(depot) <- -ka * depot
d / dt(center) <- ka * depot - cl / v * center
cp <- center / v
cmt(cp)
})
expect_s3_class(tmp, "rxode2")
expect_equal(tmp$lhs, "cp")
expect_equal(tmp$stateExtra, "cp")
tmp <- rxode2({
d / dt(depot) <- -ka * depot
d / dt(center) <- ka * depot - cl / v * center
cmt(cp)
cp <- center / v
})
expect_s3_class(tmp, "rxode2")
expect_equal(tmp$lhs, "cp")
expect_equal(tmp$stateExtra, "cp")
tmp <- rxode2({
d / dt(depot) <- -ka * depot
d / dt(center) <- ka * depot - cl / v * center
cmt(cp)
cp <- 3
})
expect_s3_class(tmp, "rxode2")
expect_equal(tmp$lhs, "cp")
expect_equal(tmp$stateExtra, "cp")
tmp <- rxode2({
d / dt(depot) <- -ka * depot
d / dt(center) <- ka * depot - cl / v * center
cp <- 3
cmt(cp)
})
expect_s3_class(tmp, "rxode2")
expect_equal(tmp$lhs, "cp")
expect_equal(tmp$stateExtra, "cp")
})
test_that("cmt() and hidden lhs variables", {
tmp <- rxode2({
d / dt(depot) ~ -ka * depot
d / dt(center) ~ ka * depot - cl / v * center
cp ~ 3
cmt(cp)
})
expect_s3_class(tmp, "rxode2")
expect_equal(tmp$lhs, character(0))
expect_equal(tmp$stateExtra, "cp")
})
test_that("compartment ordering does not affect c-code generation #785",
{
f1 <- function() {
ini({
TVCL <- c(0, 0.0308628127403366)
TVV1 <- c(0, 0.132584062223269)
TVQ <- c(0, 0.0107718034646091)
TVV2 <- c(0, 0.0613517707801907)
TVR0 <- c(0, 3.94111989610973)
TVKON <- c(0, 1.31095109796496)
TVKOFF <- c(0, 0.0758072298659602)
TVKDEG <- c(0, 1.07290072658165)
TVKINT <- c(0, 3.49422759360926)
ADD.ERR.PK <- c(0, 0.446231462752061)
ETA.CL ~ 0.0499998244205031
})
model({
CL <- TVCL * exp(ETA.CL)
V1 <- TVV1
Q <- TVQ
V2 <- TVV2
R0 <- TVR0
KON <- TVKON
KOFF <- TVKOFF
KDEG <- TVKDEG
KINT <- TVKINT
KEL <- CL/V1
K12 <- Q/V1
K21 <- Q/V2
KD <- KOFF/KON
KSYN <- R0 * KDEG
A3(0) <- R0
KEL <- 0
d/dt(A1) = -(K12 + KEL) * A1 + K21 * A2 - KON * A1 *
A3 + KOFF * A4 * V1
d/dt(A2) = K12 * A1 - K21 * A2
d/dt(A3) = KSYN - KDEG * A3 - KON * (A1/V1) * A3 + KOFF *
A4
d/dt(A4) = KON * (A1/V1) * A3 - (KINT + KOFF) * A4
CFREE = A1/V1
CTOT = CFREE + A4
CP = log(CTOT)
CP ~ add(ADD.ERR.PK)
SPEC.OUT <- SPEC
DGRP.OUT <- DGRP
BW.OUT <- BW
})
}
f1 <- f1 %>% zeroRe("omega")
f2 <- function() {
ini({
TVCL <- c(0, 0.0308628127403366)
TVV1 <- c(0, 0.132584062223269)
TVQ <- c(0, 0.0107718034646091)
TVV2 <- c(0, 0.0613517707801907)
TVR0 <- c(0, 3.94111989610973)
TVKON <- c(0, 1.31095109796496)
TVKOFF <- c(0, 0.0758072298659602)
TVKDEG <- c(0, 1.07290072658165)
TVKINT <- c(0, 3.49422759360926)
ADD.ERR.PK <- c(0, 0.446231462752061)
ETA.CL ~ 0.0499998244205031
})
model({
cmt(A1)
cmt(A2)
cmt(A3)
cmt(A4)
CL <- TVCL * exp(ETA.CL)
V1 <- TVV1
Q <- TVQ
V2 <- TVV2
R0 <- TVR0
KON <- TVKON
KOFF <- TVKOFF
KDEG <- TVKDEG
KINT <- TVKINT
KEL <- CL/V1
K12 <- Q/V1
K21 <- Q/V2
KD <- KOFF/KON
KSYN <- R0 * KDEG
A3(0) <- R0
KEL <- 0
d/dt(A1) = -(K12 + KEL) * A1 + K21 * A2 - KON * A1 *
A3 + KOFF * A4 * V1
d/dt(A2) = K12 * A1 - K21 * A2
d/dt(A3) = KSYN - KDEG * A3 - KON * (A1/V1) * A3 + KOFF *
A4
d/dt(A4) = KON * (A1/V1) * A3 - (KINT + KOFF) * A4
CFREE = A1/V1
CTOT = CFREE + A4
CP = log(CTOT)
CP ~ add(ADD.ERR.PK)
SPEC.OUT <- SPEC
DGRP.OUT <- DGRP
BW.OUT <- BW
})
}
f2 <- f2 %>% zeroRe("omega")
ev <- eventTable()
mybw <- 70
mymw <- 150000
mydgrp <- 50
ev$add.dosing(dose=mydgrp*mybw*1000000/mymw ,nbr.doses= 13, dosing.interval= 7)
ev$add.sampling(seq(0,13*7,length.out=7))
ev2 <- ev %>% as.data.frame() %>%
dplyr::mutate(BW=mybw, DGRP=mydgrp, SPEC=4)
s2 <- rxSolve(f2, ev2, returnType="data.frame")
s1 <- rxSolve(f1, ev2, returnType="data.frame")
expect_equal(s1[,c("A1", "A2", "A3", "A4")],
s2[,c("A1", "A2", "A3", "A4")])
})
})
nlmixr2/rxode2 documentation built on Jan. 11, 2025, 8:48 a.m.
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rxTest({
warfarin <- nlmixr2data::warfarin
test_that("cmt() syntax makes sense", {
mod <- rxode2({
a <- 6
b <- 0.6
cmt(blood) # cmt = 1 now
d / dt(intestine) <- -a * intestine
d / dt(blood) <- a * intestine - b * blood
})
expect_equal(c("blood", "intestine"), rxState(mod))
mod <- rxode2({
a <- 6
b <- 0.6
d / dt(intestine) <- -a * intestine
d / dt(blood) <- a * intestine - b * blood
})
expect_equal(c("intestine", "blood"), rxState(mod))
expect_output(
expect_error(expect_message(rxode2({
a <- 6
b <- 0.6
cmt(matt) # cmt = 1 now
d/dt(intestine) <- -a * intestine
d/dt(blood) <- a * intestine - b * blood
}))),
regexp = "compartment 'matt' needs differential equations defined"
)
tmp <- rxode2({
a <- 6
b <- 0.6
cmt(blood) # cmt = 1 now
cmt(intestine) # cmt = 2 now
cmt(matt)
d / dt(intestine) <- -a * intestine
d / dt(blood) <- a * intestine - b * blood
})
expect_equal(tmp$stateExtra, "matt")
})
test_that("Compartment melding with dvid", {
w <- rxode2({
ktr <- exp(tktr + eta.ktr)
ka <- exp(tka + eta.ka)
cl <- exp(tcl + eta.cl)
##
logit <- exp(poplogit + eta.emax)
emax <- logit / (1 + logit)
ec50 <- exp(tec50 + eta.ec50)
kout <- exp(tkout + eta.kout)
e0 <- exp(te0 + eta.e0)
##
DCP <- center / v
PD <- 1 - emax * DCP / (ec50 + DCP)
##
pca(0) <- e0
kin <- e0 * kout
##
d / dt(depot) <- -ktr * depot
d / dt(gut) <- ktr * depot - ka * gut
d / dt(center) <- ka * gut - cl / v * center
d / dt(pca) <- kin * PD - kout * pca
##
cp <- center / v
cmt(cp)
## These dvid w/ negative values are counted backward from the last
dvid(-1, 4)
})
w2 <- warfarin
tmp <- etTrans(w2, w, addCmt = TRUE)
expect_equal(
tmp$CMT[tmp$ID == 1],
c(
1L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 4L, 5L, 4L, 5L, 4L, 5L,
4L, 4L, 4L, 4L
)
)
w <- rxode2({
ktr <- exp(tktr + eta.ktr)
ka <- exp(tka + eta.ka)
cl <- exp(tcl + eta.cl)
##
logit <- exp(poplogit + eta.emax)
emax <- logit / (1 + logit)
ec50 <- exp(tec50 + eta.ec50)
kout <- exp(tkout + eta.kout)
e0 <- exp(te0 + eta.e0)
##
DCP <- center / v
PD <- 1 - emax * DCP / (ec50 + DCP)
##
pca(0) <- e0
kin <- e0 * kout
##
d / dt(depot) <- -ktr * depot
d / dt(gut) <- ktr * depot - ka * gut
d / dt(center) <- ka * gut - cl / v * center
d / dt(pca) <- kin * PD - kout * pca
##
cp <- center / v
cmt(cp)
dvid(5, 4)
})
w2 <- warfarin
tmp <- etTrans(w2, w, addCmt = TRUE)
expect_equal(
tmp$CMT[tmp$ID == 1],
c(
1L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 4L, 5L, 4L, 5L, 4L, 5L,
4L, 4L, 4L, 4L
)
)
w2$dvid <- paste(w2$dvid)
tmp <- etTrans(w2, w, addCmt = TRUE)
expect_equal(
tmp$CMT[tmp$ID == 1],
c(
1L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 4L, 5L, 4L, 5L, 4L, 5L,
4L, 4L, 4L, 4L
)
)
w2 <- warfarin
w2$dvid <- as.integer(w2$dvid)
tmp <- etTrans(w2, w, addCmt = TRUE)
expect_equal(
tmp$CMT[tmp$ID == 1],
c(
1L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 4L, 5L, 4L, 5L, 4L, 5L,
4L, 4L, 4L, 4L
)
)
w2 <- warfarin
w2$dvid <- as.integer(w2$dvid) * 10
expect_warning(tmp <- etTrans(w2, w, addCmt = TRUE))
expect_equal(
tmp$CMT[tmp$ID == 1],
c(
1L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 4L, 5L, 4L, 5L, 4L, 5L,
4L, 4L, 4L, 4L
)
)
w <- rxode2({
ktr <- exp(tktr + eta.ktr)
ka <- exp(tka + eta.ka)
cl <- exp(tcl + eta.cl)
##
logit <- exp(poplogit + eta.emax)
emax <- logit / (1 + logit)
ec50 <- exp(tec50 + eta.ec50)
kout <- exp(tkout + eta.kout)
e0 <- exp(te0 + eta.e0)
##
DCP <- center / v
PD <- 1 - emax * DCP / (ec50 + DCP)
##
pca(0) <- e0
kin <- e0 * kout
##
d / dt(depot) <- -ktr * depot
d / dt(gut) <- ktr * depot - ka * gut
d / dt(center) <- ka * gut - cl / v * center
d / dt(pca) <- kin * PD - kout * pca
##
cp <- center / v
cmt(cp)
dvid(5)
})
w2 <- warfarin
w2$dvid <- as.integer(w2$dvid) * 10
expect_warning(tmp <- etTrans(w2, w, addCmt = TRUE))
expect_equal(
tmp$CMT[tmp$ID == 1],
c(
1L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 1L, 5L, 1L, 5L, 1L, 5L,
1L, 1L, 1L, 1L
)
)
w <- rxode2({
ktr <- exp(tktr + eta.ktr)
ka <- exp(tka + eta.ka)
cl <- exp(tcl + eta.cl)
##
logit <- exp(poplogit + eta.emax)
emax <- logit / (1 + logit)
ec50 <- exp(tec50 + eta.ec50)
kout <- exp(tkout + eta.kout)
e0 <- exp(te0 + eta.e0)
##
DCP <- center / v
PD <- 1 - emax * DCP / (ec50 + DCP)
##
pca(0) <- e0
kin <- e0 * kout
##
d / dt(depot) <- -ktr * depot
d / dt(gut) <- ktr * depot - ka * gut
d / dt(center) <- ka * gut - cl / v * center
d / dt(pca) <- kin * PD - kout * pca
##
cp <- center / v
cmt(cp)
dvid(4, 5)
})
w2 <- warfarin
w2$dvid <- as.integer(w2$dvid)
tmp <- etTrans(w2, w, addCmt = TRUE)
expect_equal(
tmp$CMT[tmp$ID == 1],
c(
1L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 4L, 5L, 4L, 5L, 4L,
5L, 5L, 5L, 5L
)
)
## Warfarin model
inner <- rxode2({
cmt(depot)
cmt(gut)
cmt(center)
cmt(effect)
rx_expr_001 ~ -depot
rx_expr_002 ~ -center
rx_expr_003 ~ -ETA[4]
rx_expr_004 ~ -effect
rx_expr_005 ~ -2 * ETA[4]
rx_expr_006 ~ 2 * THETA[4]
rx_expr_007 ~ ETA[1] + THETA[1]
rx_expr_008 ~ ETA[2] + THETA[2]
rx_expr_009 ~ ETA[3] + THETA[3]
rx_expr_010 ~ ETA[7] + THETA[9]
rx_expr_011 ~ ETA[5] + THETA[7]
rx_expr_012 ~ ETA[6] + THETA[8]
rx_expr_013 ~ rx_expr_003 - THETA[4]
rx_expr_014 ~ ETA[8] + THETA[10]
rx_expr_015 ~ exp(rx_expr_007)
rx_expr_016 ~ exp(rx_expr_008)
rx_expr_017 ~ exp(rx_expr_009)
rx_expr_018 ~ exp(rx_expr_010)
rx_expr_019 ~ exp(rx_expr_011)
rx_expr_020 ~ exp(rx_expr_012)
rx_expr_021 ~ rx_expr_005 - rx_expr_006
rx_expr_022 ~ Rx_pow_di(center, 2)
rx_expr_023 ~ exp(rx_expr_013)
rx_expr_024 ~ exp(rx_expr_014)
rx_expr_025 ~ rx_expr_019 + 1
rx_expr_026 ~ Rx_pow_di(THETA[5], 2)
rx_expr_027 ~ gut * rx_expr_016
rx_expr_028 ~ 2 * rx_expr_026
rx_expr_029 ~ exp(rx_expr_021)
rx_expr_030 ~ depot * rx_expr_015
rx_expr_031 ~ rx_expr_001 * rx_expr_015
rx_expr_032 ~ rx_expr_002 * rx_expr_017
rx_expr_033 ~ rx_expr_004 * rx_expr_018
rx_expr_034 ~ center * rx_expr_023
rx_expr_035 ~ rx_expr_002 * rx_expr_023
rx_expr_036 ~ rx_expr_028 * center
rx_expr_037 ~ center * rx_expr_029
rx_expr_038 ~ rx_expr_023 * rx_expr_019
rx_expr_039 ~ rx__sens_gut_BY_ETA_1___ * rx_expr_016
rx_expr_040 ~ rx__sens_gut_BY_ETA_2___ * rx_expr_016
rx_expr_041 ~ rx__sens_gut_BY_ETA_3___ * rx_expr_016
rx_expr_042 ~ rx__sens_gut_BY_ETA_4___ * rx_expr_016
rx_expr_043 ~ rx__sens_gut_BY_ETA_5___ * rx_expr_016
rx_expr_044 ~ rx__sens_gut_BY_ETA_6___ * rx_expr_016
rx_expr_045 ~ rx__sens_gut_BY_ETA_7___ * rx_expr_016
rx_expr_046 ~ rx__sens_gut_BY_ETA_8___ * rx_expr_016
rx_expr_047 ~ rx__sens_depot_BY_ETA_1___ * rx_expr_015
rx_expr_048 ~ rx_expr_034 + rx_expr_020
rx_expr_049 ~ rx_expr_034 * rx_expr_019
rx_expr_050 ~ rx_expr_032 * rx_expr_023
rx_expr_051 ~ rx_expr_035 * rx_expr_019
rx_expr_052 ~ rx_expr_037 * rx_expr_019
rx_expr_053 ~ Rx_pow_di(rx_expr_048, 2)
rx_expr_054 ~ (rx_expr_048) * (rx_expr_025)
rx_expr_055 ~ rx_expr_053 * (rx_expr_025)
rx_expr_056 ~ rx_expr_038 / (rx_expr_054)
rx_expr_057 ~ rx_expr_051 / (rx_expr_054)
rx_expr_058 ~ rx_expr_057 + 1
rx_expr_059 ~ rx_expr_052 / (rx_expr_055)
rx_expr_060 ~ (rx_expr_058) * rx_expr_018
rx_expr_061 ~ rx_expr_060 * rx_expr_024
rx_expr_062 ~ rx_expr_059 - rx_expr_056
d / dt(depot) <- rx_expr_031
d / dt(gut) <- rx_expr_030 - rx_expr_027
d / dt(center) <- rx_expr_050 + rx_expr_027
effect(0) <- rx_expr_024
d / dt(effect) <- rx_expr_033 + rx_expr_061
d / dt(rx__sens_depot_BY_ETA_1___) ~ rx_expr_031 - rx_expr_047
d / dt(rx__sens_depot_BY_ETA_2___) ~ -rx__sens_depot_BY_ETA_2___ * rx_expr_015
d / dt(rx__sens_depot_BY_ETA_3___) ~ -rx__sens_depot_BY_ETA_3___ * rx_expr_015
d / dt(rx__sens_depot_BY_ETA_4___) ~ -rx__sens_depot_BY_ETA_4___ * rx_expr_015
d / dt(rx__sens_depot_BY_ETA_5___) ~ -rx__sens_depot_BY_ETA_5___ * rx_expr_015
d / dt(rx__sens_depot_BY_ETA_6___) ~ -rx__sens_depot_BY_ETA_6___ * rx_expr_015
d / dt(rx__sens_depot_BY_ETA_7___) ~ -rx__sens_depot_BY_ETA_7___ * rx_expr_015
d / dt(rx__sens_depot_BY_ETA_8___) ~ -rx__sens_depot_BY_ETA_8___ * rx_expr_015
d / dt(rx__sens_gut_BY_ETA_1___) ~ rx_expr_030 + rx_expr_047 - rx_expr_039
d / dt(rx__sens_gut_BY_ETA_2___) ~ -gut * rx_expr_016 + rx__sens_depot_BY_ETA_2___ * rx_expr_015 - rx_expr_040
d / dt(rx__sens_gut_BY_ETA_3___) ~ rx__sens_depot_BY_ETA_3___ * rx_expr_015 - rx_expr_041
d / dt(rx__sens_gut_BY_ETA_4___) ~ rx__sens_depot_BY_ETA_4___ * rx_expr_015 - rx_expr_042
d / dt(rx__sens_gut_BY_ETA_5___) ~ rx__sens_depot_BY_ETA_5___ * rx_expr_015 - rx_expr_043
d / dt(rx__sens_gut_BY_ETA_6___) ~ rx__sens_depot_BY_ETA_6___ * rx_expr_015 - rx_expr_044
d / dt(rx__sens_gut_BY_ETA_7___) ~ rx__sens_depot_BY_ETA_7___ * rx_expr_015 - rx_expr_045
d / dt(rx__sens_gut_BY_ETA_8___) ~ rx__sens_depot_BY_ETA_8___ * rx_expr_015 - rx_expr_046
d / dt(rx__sens_center_BY_ETA_1___) ~ -rx__sens_center_BY_ETA_1___ * rx_expr_017 * rx_expr_023 + rx_expr_039
d / dt(rx__sens_center_BY_ETA_2___) ~ rx_expr_027 - rx__sens_center_BY_ETA_2___ * rx_expr_017 * rx_expr_023 + rx_expr_040
d / dt(rx__sens_center_BY_ETA_3___) ~ rx_expr_050 - rx__sens_center_BY_ETA_3___ * rx_expr_017 * rx_expr_023 + rx_expr_041
d / dt(rx__sens_center_BY_ETA_4___) ~ center * rx_expr_017 * rx_expr_023 - rx__sens_center_BY_ETA_4___ * rx_expr_017 * rx_expr_023 + rx_expr_042
d / dt(rx__sens_center_BY_ETA_5___) ~ -rx__sens_center_BY_ETA_5___ * rx_expr_017 * rx_expr_023 + rx_expr_043
d / dt(rx__sens_center_BY_ETA_6___) ~ -rx__sens_center_BY_ETA_6___ * rx_expr_017 * rx_expr_023 + rx_expr_044
d / dt(rx__sens_center_BY_ETA_7___) ~ -rx__sens_center_BY_ETA_7___ * rx_expr_017 * rx_expr_023 + rx_expr_045
d / dt(rx__sens_center_BY_ETA_8___) ~ -rx__sens_center_BY_ETA_8___ * rx_expr_017 * rx_expr_023 + rx_expr_046
d / dt(rx__sens_effect_BY_ETA_1___) ~ rx__sens_center_BY_ETA_1___ * (rx_expr_062) * rx_expr_018 * rx_expr_024 - rx__sens_effect_BY_ETA_1___ * rx_expr_018
d / dt(rx__sens_effect_BY_ETA_2___) ~ rx__sens_center_BY_ETA_2___ * (rx_expr_062) * rx_expr_018 * rx_expr_024 - rx__sens_effect_BY_ETA_2___ * rx_expr_018
d / dt(rx__sens_effect_BY_ETA_3___) ~ rx__sens_center_BY_ETA_3___ * (rx_expr_062) * rx_expr_018 * rx_expr_024 - rx__sens_effect_BY_ETA_3___ * rx_expr_018
d / dt(rx__sens_effect_BY_ETA_4___) ~ rx__sens_center_BY_ETA_4___ * (rx_expr_062) * rx_expr_018 * rx_expr_024 - rx__sens_effect_BY_ETA_4___ * rx_expr_018 + (-rx_expr_022 * rx_expr_029 * rx_expr_019 / (rx_expr_055) + rx_expr_049 / (rx_expr_054)) * rx_expr_018 * rx_expr_024
d / dt(rx__sens_effect_BY_ETA_5___) ~ rx__sens_center_BY_ETA_5___ * (rx_expr_062) * rx_expr_018 * rx_expr_024 - rx__sens_effect_BY_ETA_5___ * rx_expr_018 + (rx_expr_057 + rx_expr_034 * exp(2 * ETA[5] + 2 * THETA[7]) / ((rx_expr_048) * Rx_pow_di(rx_expr_025, 2))) * rx_expr_018 * rx_expr_024
d / dt(rx__sens_effect_BY_ETA_6___) ~ rx_expr_049 * rx_expr_020 * rx_expr_018 * rx_expr_024 / (rx_expr_055) + rx__sens_center_BY_ETA_6___ * (rx_expr_062) * rx_expr_018 * rx_expr_024 - rx__sens_effect_BY_ETA_6___ * rx_expr_018
d / dt(rx__sens_effect_BY_ETA_7___) ~ rx_expr_033 + rx__sens_center_BY_ETA_7___ * (rx_expr_062) * rx_expr_018 * rx_expr_024 - rx__sens_effect_BY_ETA_7___ * rx_expr_018 + rx_expr_061
rx__sens_effect_BY_ETA_8___(0) <- rx_expr_024
d / dt(rx__sens_effect_BY_ETA_8___) ~ rx__sens_center_BY_ETA_8___ * (rx_expr_062) * rx_expr_018 * rx_expr_024 - rx__sens_effect_BY_ETA_8___ * rx_expr_018 + rx_expr_061
rx_yj_ ~ 2
rx_lambda_ ~ 1
if (CMT == 3) {
rx_pred_ <- rx_expr_034
rx__sens_rx_pred__BY_ETA_1___ <- rx__sens_center_BY_ETA_1___ * rx_expr_023
rx__sens_rx_pred__BY_ETA_2___ <- rx__sens_center_BY_ETA_2___ * rx_expr_023
rx__sens_rx_pred__BY_ETA_3___ <- rx__sens_center_BY_ETA_3___ * rx_expr_023
rx__sens_rx_pred__BY_ETA_4___ <- rx_expr_035 + rx__sens_center_BY_ETA_4___ * rx_expr_023
rx__sens_rx_pred__BY_ETA_5___ <- rx__sens_center_BY_ETA_5___ * rx_expr_023
rx__sens_rx_pred__BY_ETA_6___ <- rx__sens_center_BY_ETA_6___ * rx_expr_023
rx__sens_rx_pred__BY_ETA_7___ <- rx__sens_center_BY_ETA_7___ * rx_expr_023
rx__sens_rx_pred__BY_ETA_8___ <- rx__sens_center_BY_ETA_8___ * rx_expr_023
rx_r_ <- rx_expr_026 * rx_expr_022 * rx_expr_029 + Rx_pow_di(THETA[6], 2)
rx__sens_rx_r__BY_ETA_1___ <- rx_expr_036 * rx__sens_center_BY_ETA_1___ * rx_expr_029
rx__sens_rx_r__BY_ETA_2___ <- rx_expr_036 * rx__sens_center_BY_ETA_2___ * rx_expr_029
rx__sens_rx_r__BY_ETA_3___ <- rx_expr_036 * rx__sens_center_BY_ETA_3___ * rx_expr_029
rx__sens_rx_r__BY_ETA_4___ <- -2 * rx_expr_026 * rx_expr_022 * rx_expr_029 + rx_expr_036 * rx__sens_center_BY_ETA_4___ * rx_expr_029
rx__sens_rx_r__BY_ETA_5___ <- rx_expr_036 * rx__sens_center_BY_ETA_5___ * rx_expr_029
rx__sens_rx_r__BY_ETA_6___ <- rx_expr_036 * rx__sens_center_BY_ETA_6___ * rx_expr_029
rx__sens_rx_r__BY_ETA_7___ <- rx_expr_036 * rx__sens_center_BY_ETA_7___ * rx_expr_029
rx__sens_rx_r__BY_ETA_8___ <- rx_expr_036 * rx__sens_center_BY_ETA_8___ * rx_expr_029
}
if (CMT == 4) {
rx_pred_ <- effect
rx__sens_rx_pred__BY_ETA_1___ <- rx__sens_effect_BY_ETA_1___
rx__sens_rx_pred__BY_ETA_2___ <- rx__sens_effect_BY_ETA_2___
rx__sens_rx_pred__BY_ETA_3___ <- rx__sens_effect_BY_ETA_3___
rx__sens_rx_pred__BY_ETA_4___ <- rx__sens_effect_BY_ETA_4___
rx__sens_rx_pred__BY_ETA_5___ <- rx__sens_effect_BY_ETA_5___
rx__sens_rx_pred__BY_ETA_6___ <- rx__sens_effect_BY_ETA_6___
rx__sens_rx_pred__BY_ETA_7___ <- rx__sens_effect_BY_ETA_7___
rx__sens_rx_pred__BY_ETA_8___ <- rx__sens_effect_BY_ETA_8___
rx_r_ <- Rx_pow_di(THETA[11], 2)
rx__sens_rx_r__BY_ETA_1___ <- 0
rx__sens_rx_r__BY_ETA_2___ <- 0
rx__sens_rx_r__BY_ETA_3___ <- 0
rx__sens_rx_r__BY_ETA_4___ <- 0
rx__sens_rx_r__BY_ETA_5___ <- 0
rx__sens_rx_r__BY_ETA_6___ <- 0
rx__sens_rx_r__BY_ETA_7___ <- 0
rx__sens_rx_r__BY_ETA_8___ <- 0
}
cmt(cp)
cmt(pca)
dvid(3, 4, 5, 6)
})
# context("warfarin inner test")
data.pkpd <- warfarin
data.pkpd$dvid <- as.integer(data.pkpd$dvid)
data.pkpd$cmt <- paste(factor(data.pkpd$dvid, c(1, 2), c("center", "effect")))
data.pkpd$cmt[data.pkpd$amt > 0] <- "depot"
t2 <- etTrans(data.pkpd[, names(data.pkpd) != "dvid"], inner)
expect_equal(
t2$CMT[t2$ID == 1],
c(
1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 3L, 4L, 3L, 4L, 3L,
4L, 4L, 4L, 4L
)
)
data.pkpd$cmt <- paste(factor(data.pkpd$dvid, c(1, 2), c("cp", "pca")))
data.pkpd$cmt[data.pkpd$amt > 0] <- "depot"
t2 <- etTrans(data.pkpd[, names(data.pkpd) != "dvid"], inner)
expect_equal(
t2$CMT[t2$ID == 1],
c(
1L, 37L, 37L, 37L, 37L, 37L, 37L, 37L, 37L, 38L, 37L, 38L, 37L, 38L, 37L,
38L, 38L, 38L, 38L
)
)
data.pkpd$cmt <- factor(data.pkpd$cmt)
t2 <- etTrans(data.pkpd[, names(data.pkpd) != "dvid"], inner)
expect_equal(
t2$CMT[t2$ID == 1],
c(
1L, 37L, 37L, 37L, 37L, 37L, 37L, 37L, 37L, 38L, 37L, 38L, 37L, 38L, 37L,
38L, 38L, 38L, 38L
)
)
data.pkpd$cmt <- paste(data.pkpd$cmt)
.cmt <- data.pkpd$cmt
data.pkpd$cmt <- 1
data.pkpd$cmt[.cmt == "cp"] <- 5
data.pkpd$cmt[.cmt == "pca"] <- 6
## This skips the sensitivity equations
t2 <- etTrans(data.pkpd[, names(data.pkpd) != "dvid"], inner)
expect_equal(
t2$CMT[t2$ID == 1],
c(
1L, 37L, 37L, 37L, 37L, 37L, 37L, 37L, 37L, 38L, 37L, 38L, 37L, 38L, 37L,
38L, 38L, 38L, 38L
)
)
data.pkpd$cmt <- 1
data.pkpd$cmt[.cmt == "cp"] <- 3
data.pkpd$cmt[.cmt == "pca"] <- 4
t2 <- etTrans(data.pkpd[, names(data.pkpd) != "dvid"], inner)
expect_equal(
t2$CMT[t2$ID == 1],
c(
1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 3L, 4L, 3L, 4L, 3L,
4L, 4L, 4L, 4L
)
)
t2 <- etTrans(data.pkpd, inner)
expect_equal(
t2$CMT[t2$ID == 1],
c(
1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 3L, 4L, 3L, 4L, 3L,
4L, 4L, 4L, 4L
)
)
data.pkpd$dvid[data.pkpd$dvid == 1] <- 3
data.pkpd$dvid[data.pkpd$dvid == 2] <- 4
expect_error(etTrans(data.pkpd, inner))
t2 <- etTrans(data.pkpd[, names(data.pkpd) != "cmt"], inner, addCmt = TRUE)
expect_equal(
t2$CMT[t2$ID == 1],
c(
1L, 37L, 37L, 37L, 37L, 37L, 37L, 37L, 37L, 38L, 37L, 38L, 37L, 38L, 37L,
38L, 38L, 38L, 38L
)
)
## TEST NA cmt/dvid w/factors
## TEST NA strings for cmt/dvid
tmp <- rxode2({
d / dt(depot) <- -ka * depot
d / dt(center) <- ka * depot - cl / v * center
cp <- center / v
cp2 <- cp + nlmixr_extra_par
cmt(central)
cmt(c20)
})
expect_s3_class(tmp, "rxode2")
# context("Check lhs allowed stateExtra while preserving lhs properties.")
tmp <- rxode2({
d / dt(depot) <- -ka * depot
d / dt(center) <- ka * depot - cl / v * center
cp <- center / v
cmt(cp)
})
expect_s3_class(tmp, "rxode2")
expect_equal(tmp$lhs, "cp")
expect_equal(tmp$stateExtra, "cp")
tmp <- rxode2({
d / dt(depot) <- -ka * depot
d / dt(center) <- ka * depot - cl / v * center
cmt(cp)
cp <- center / v
})
expect_s3_class(tmp, "rxode2")
expect_equal(tmp$lhs, "cp")
expect_equal(tmp$stateExtra, "cp")
tmp <- rxode2({
d / dt(depot) <- -ka * depot
d / dt(center) <- ka * depot - cl / v * center
cmt(cp)
cp <- 3
})
expect_s3_class(tmp, "rxode2")
expect_equal(tmp$lhs, "cp")
expect_equal(tmp$stateExtra, "cp")
tmp <- rxode2({
d / dt(depot) <- -ka * depot
d / dt(center) <- ka * depot - cl / v * center
cp <- 3
cmt(cp)
})
expect_s3_class(tmp, "rxode2")
expect_equal(tmp$lhs, "cp")
expect_equal(tmp$stateExtra, "cp")
})
test_that("cmt() and hidden lhs variables", {
tmp <- rxode2({
d / dt(depot) ~ -ka * depot
d / dt(center) ~ ka * depot - cl / v * center
cp ~ 3
cmt(cp)
})
expect_s3_class(tmp, "rxode2")
expect_equal(tmp$lhs, character(0))
expect_equal(tmp$stateExtra, "cp")
})
test_that("compartment ordering does not affect c-code generation #785",
{
f1 <- function() {
ini({
TVCL <- c(0, 0.0308628127403366)
TVV1 <- c(0, 0.132584062223269)
TVQ <- c(0, 0.0107718034646091)
TVV2 <- c(0, 0.0613517707801907)
TVR0 <- c(0, 3.94111989610973)
TVKON <- c(0, 1.31095109796496)
TVKOFF <- c(0, 0.0758072298659602)
TVKDEG <- c(0, 1.07290072658165)
TVKINT <- c(0, 3.49422759360926)
ADD.ERR.PK <- c(0, 0.446231462752061)
ETA.CL ~ 0.0499998244205031
})
model({
CL <- TVCL * exp(ETA.CL)
V1 <- TVV1
Q <- TVQ
V2 <- TVV2
R0 <- TVR0
KON <- TVKON
KOFF <- TVKOFF
KDEG <- TVKDEG
KINT <- TVKINT
KEL <- CL/V1
K12 <- Q/V1
K21 <- Q/V2
KD <- KOFF/KON
KSYN <- R0 * KDEG
A3(0) <- R0
KEL <- 0
d/dt(A1) = -(K12 + KEL) * A1 + K21 * A2 - KON * A1 *
A3 + KOFF * A4 * V1
d/dt(A2) = K12 * A1 - K21 * A2
d/dt(A3) = KSYN - KDEG * A3 - KON * (A1/V1) * A3 + KOFF *
A4
d/dt(A4) = KON * (A1/V1) * A3 - (KINT + KOFF) * A4
CFREE = A1/V1
CTOT = CFREE + A4
CP = log(CTOT)
CP ~ add(ADD.ERR.PK)
SPEC.OUT <- SPEC
DGRP.OUT <- DGRP
BW.OUT <- BW
})
}
f1 <- f1 %>% zeroRe("omega")
f2 <- function() {
ini({
TVCL <- c(0, 0.0308628127403366)
TVV1 <- c(0, 0.132584062223269)
TVQ <- c(0, 0.0107718034646091)
TVV2 <- c(0, 0.0613517707801907)
TVR0 <- c(0, 3.94111989610973)
TVKON <- c(0, 1.31095109796496)
TVKOFF <- c(0, 0.0758072298659602)
TVKDEG <- c(0, 1.07290072658165)
TVKINT <- c(0, 3.49422759360926)
ADD.ERR.PK <- c(0, 0.446231462752061)
ETA.CL ~ 0.0499998244205031
})
model({
cmt(A1)
cmt(A2)
cmt(A3)
cmt(A4)
CL <- TVCL * exp(ETA.CL)
V1 <- TVV1
Q <- TVQ
V2 <- TVV2
R0 <- TVR0
KON <- TVKON
KOFF <- TVKOFF
KDEG <- TVKDEG
KINT <- TVKINT
KEL <- CL/V1
K12 <- Q/V1
K21 <- Q/V2
KD <- KOFF/KON
KSYN <- R0 * KDEG
A3(0) <- R0
KEL <- 0
d/dt(A1) = -(K12 + KEL) * A1 + K21 * A2 - KON * A1 *
A3 + KOFF * A4 * V1
d/dt(A2) = K12 * A1 - K21 * A2
d/dt(A3) = KSYN - KDEG * A3 - KON * (A1/V1) * A3 + KOFF *
A4
d/dt(A4) = KON * (A1/V1) * A3 - (KINT + KOFF) * A4
CFREE = A1/V1
CTOT = CFREE + A4
CP = log(CTOT)
CP ~ add(ADD.ERR.PK)
SPEC.OUT <- SPEC
DGRP.OUT <- DGRP
BW.OUT <- BW
})
}
f2 <- f2 %>% zeroRe("omega")
ev <- eventTable()
mybw <- 70
mymw <- 150000
mydgrp <- 50
ev$add.dosing(dose=mydgrp*mybw*1000000/mymw ,nbr.doses= 13, dosing.interval= 7)
ev$add.sampling(seq(0,13*7,length.out=7))
ev2 <- ev %>% as.data.frame() %>%
dplyr::mutate(BW=mybw, DGRP=mydgrp, SPEC=4)
s2 <- rxSolve(f2, ev2, returnType="data.frame")
s1 <- rxSolve(f1, ev2, returnType="data.frame")
expect_equal(s1[,c("A1", "A2", "A3", "A4")],
s2[,c("A1", "A2", "A3", "A4")])
})
})
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