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") }) })