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Merge pull request #151 from nlmixr2/150-advan5
Initial implementation
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#' Handle the Ks for advan5/7 ode processing | ||
#' @param k This is the detected K parameter | ||
#' @return nothing called for side effects | ||
#' @noRd | ||
#' @author Matthew L. Fidler | ||
.advan5handleK <- function(k) { | ||
if (!(.nonmem2rx$advan %in% c(5L, 7L))) return(NULL) | ||
if (k %in% .nonmem2rx$advan5k) return(NULL) | ||
.reg1 <- "^[Kk]([1-9])[Tt]?([0-9])$" | ||
.reg2 <- "^[Kk]([1-9][0-9]*)[Tt]([0-9]+)$" | ||
if (grepl(.reg1, k)) { | ||
.n1 <- as.numeric(gsub(.reg1, "\\1", k)) | ||
.n2 <- as.numeric(gsub(.reg1, "\\2", k)) | ||
} else if (grepl(.reg2, k)) { | ||
.n1 <- as.numeric(gsub(.reg2, "\\1", k)) | ||
.n2 <- as.numeric(gsub(.reg2, "\\2", k)) | ||
} else { | ||
return(NULL) | ||
} | ||
.newMax <- max(.n1, .n2, .nonmem2rx$advan5max) | ||
if (.newMax > .nonmem2rx$advan5max) { | ||
.nonmem2rx$advan5 <- c(.nonmem2rx$advan5, rep("", .newMax - .nonmem2rx$advan5max)) | ||
.nonmem2rx$advan5max <- .newMax | ||
} | ||
.nonmem2rx$advan5[.n1] <- paste0(.nonmem2rx$advan5[.n1], "-", k, "*rxddta", .n1) | ||
.pushObservedDadt(.n1) | ||
.setMaxA(.n1) | ||
if (.n2 != 0) { | ||
.nonmem2rx$advan5[.n2] <- paste0(.nonmem2rx$advan5[.n2], "+", k, "*rxddta", .n1) | ||
.pushObservedDadt(.n2) | ||
.setMaxA(.n2) | ||
} | ||
.nonmem2rx$advan5k <- c(.nonmem2rx$advan5k, k) | ||
NULL | ||
} | ||
#' Get the advan5 odes | ||
#' | ||
#' @return advan5 odes if defined | ||
#' @author Matthew L. Fidler | ||
#' @noRd | ||
.advan5odes <- function() { | ||
if (!(.nonmem2rx$advan %in% c(5L, 7L))) return("") | ||
.w <- which(.nonmem2rx$advan5 == "") | ||
.ret <- paste0("d/dt(rxddta", seq_along(.nonmem2rx$advan5), ") <- ", | ||
gsub("^[+]", "", .nonmem2rx$advan5)) | ||
if (length(.w) > 0) .ret <- .ret[-.w] | ||
paste0("\n",paste(.ret, collapse="\n")) | ||
} |
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test_that("test advan5/advan7 translations", { | ||
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.a <- function(k, clear=FALSE) { | ||
if (clear) .clearNonmem2rx() | ||
.nonmem2rx$advan <- 5L | ||
.advan5handleK(k) | ||
list(advan5=.nonmem2rx$advan5, | ||
advan5k=.nonmem2rx$advan5k, | ||
advan5max=.nonmem2rx$advan5max) | ||
} | ||
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expect_equal(.a("k15", clear=TRUE), | ||
list(advan5 = c("-k15*rxddta1", "", "", "", "+k15*rxddta1"), advan5k = "k15", advan5max = 5)) | ||
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expect_equal(.a("k56"), | ||
list(advan5 = c("-k15*rxddta1", "", "", "", | ||
"+k15*rxddta1-k56*rxddta5", | ||
"+k56*rxddta5"), | ||
advan5k = c("k15", "k56"), advan5max = 6)) | ||
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expect_equal(.a("K67"), | ||
list(advan5 = c("-k15*rxddta1", "", "", "", | ||
"+k15*rxddta1-k56*rxddta5", | ||
"+k56*rxddta5-K67*rxddta6", | ||
"+K67*rxddta6"), | ||
advan5k = c("k15", "k56", "K67"), | ||
advan5max = 7)) | ||
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expect_equal(.a("K74"), | ||
list(advan5 = c("-k15*rxddta1", "", "", | ||
"+K74*rxddta7", "+k15*rxddta1-k56*rxddta5", | ||
"+k56*rxddta5-K67*rxddta6", | ||
"+K67*rxddta6-K74*rxddta7"), | ||
advan5k = c("k15", "k56", "K67", "K74"), | ||
advan5max = 7)) | ||
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expect_equal(.a("K42"), | ||
list(advan5 = c("-k15*rxddta1", "+K42*rxddta4", "", | ||
"+K74*rxddta7-K42*rxddta4", "+k15*rxddta1-k56*rxddta5", | ||
"+k56*rxddta5-K67*rxddta6", "+K67*rxddta6-K74*rxddta7"), | ||
advan5k = c("k15", "k56", "K67", "K74", "K42"), | ||
advan5max = 7)) | ||
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expect_equal(.a("K42"), | ||
list(advan5 = c("-k15*rxddta1", "+K42*rxddta4", "", | ||
"+K74*rxddta7-K42*rxddta4", "+k15*rxddta1-k56*rxddta5", | ||
"+k56*rxddta5-K67*rxddta6", "+K67*rxddta6-K74*rxddta7"), | ||
advan5k = c("k15", "k56", "K67", "K74", "K42"), | ||
advan5max = 7)) | ||
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expect_equal(.a("K40"), | ||
list(advan5 = c("-k15*rxddta1", "+K42*rxddta4", "", | ||
"+K74*rxddta7-K42*rxddta4-K40*rxddta4", | ||
"+k15*rxddta1-k56*rxddta5", "+k56*rxddta5-K67*rxddta6", | ||
"+K67*rxddta6-K74*rxddta7"), | ||
advan5k = c("k15", "k56", "K67", "K74", "K42", "K40"), advan5max =7)) | ||
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expect_equal(.a("K24"), | ||
list(advan5 = c("-k15*rxddta1", "+K42*rxddta4-K24*rxddta2", "", | ||
"+K74*rxddta7-K42*rxddta4-K40*rxddta4+K24*rxddta2", | ||
"+k15*rxddta1-k56*rxddta5", "+k56*rxddta5-K67*rxddta6", | ||
"+K67*rxddta6-K74*rxddta7"), | ||
advan5k = c("k15", "k56", "K67", "K74", "K42", "K40", "K24"), advan5max = 7)) | ||
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expect_equal(.a("K24"), | ||
list(advan5 = c("-k15*rxddta1", "+K42*rxddta4-K24*rxddta2", "", | ||
"+K74*rxddta7-K42*rxddta4-K40*rxddta4+K24*rxddta2", | ||
"+k15*rxddta1-k56*rxddta5", "+k56*rxddta5-K67*rxddta6", | ||
"+K67*rxddta6-K74*rxddta7"), | ||
advan5k = c("k15", "k56", "K67", "K74", "K42", "K40", "K24"), advan5max = 7)) | ||
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expect_equal(.a("K23"), | ||
list(advan5 = | ||
c("-k15*rxddta1", | ||
"+K42*rxddta4-K24*rxddta2-K23*rxddta2", | ||
"+K23*rxddta2", "+K74*rxddta7-K42*rxddta4-K40*rxddta4+K24*rxddta2", | ||
"+k15*rxddta1-k56*rxddta5", "+k56*rxddta5-K67*rxddta6", | ||
"+K67*rxddta6-K74*rxddta7"), | ||
advan5k = c("k15", "k56", "K67", "K74", "K42", "K40", "K24", "K23"), advan5max = 7)) | ||
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expect_equal(.a("K32"), | ||
list(advan5 = c("-k15*rxddta1", "+K42*rxddta4-K24*rxddta2-K23*rxddta2+K32*rxddta3", | ||
"+K23*rxddta2-K32*rxddta3", "+K74*rxddta7-K42*rxddta4-K40*rxddta4+K24*rxddta2", | ||
"+k15*rxddta1-k56*rxddta5", "+k56*rxddta5-K67*rxddta6", "+K67*rxddta6-K74*rxddta7"), | ||
advan5k = c("k15", "k56", "K67", "K74", "K42", "K40", "K24", "K23", "K32"), advan5max = 7)) | ||
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expect_equal(.a("K10T0"), | ||
list(advan5 = c("-k15*rxddta1", "+K42*rxddta4-K24*rxddta2-K23*rxddta2+K32*rxddta3", | ||
"+K23*rxddta2-K32*rxddta3", "+K74*rxddta7-K42*rxddta4-K40*rxddta4+K24*rxddta2", | ||
"+k15*rxddta1-k56*rxddta5", "+k56*rxddta5-K67*rxddta6", "+K67*rxddta6-K74*rxddta7", | ||
"", "", "-K10T0*rxddta10"), | ||
advan5k = c("k15", "k56", "K67", "K74", "K42", "K40", "K24", "K23", "K32", "K10T0"), | ||
advan5max = 10)) | ||
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expect_equal(.advan5odes(), | ||
"\nd/dt(rxddta1) <- -k15*rxddta1\nd/dt(rxddta2) <- K42*rxddta4-K24*rxddta2-K23*rxddta2+K32*rxddta3\nd/dt(rxddta3) <- K23*rxddta2-K32*rxddta3\nd/dt(rxddta4) <- K74*rxddta7-K42*rxddta4-K40*rxddta4+K24*rxddta2\nd/dt(rxddta5) <- k15*rxddta1-k56*rxddta5\nd/dt(rxddta6) <- k56*rxddta5-K67*rxddta6\nd/dt(rxddta7) <- K67*rxddta6-K74*rxddta7\nd/dt(rxddta10) <- -K10T0*rxddta10") | ||
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}) |
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