diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/saemix.R | 146 | ||||
| -rw-r--r-- | R/summary.saem.mmkin.R | 2 |
2 files changed, 108 insertions, 40 deletions
@@ -40,7 +40,7 @@ #' f_saem_fomc <- saem(f_mmkin_parent["FOMC", ]) #' f_saem_dfop <- saem(f_mmkin_parent["DFOP", ]) #' -#' # The returned saem.mmkin object contains an SaemixObject, we can use +#' # The returned saem.mmkin object contains an SaemixObject, therefore we can use #' # functions from saemix #' library(saemix) #' compare.saemix(list(f_saem_sfo$so, f_saem_fomc$so, f_saem_dfop$so)) @@ -49,17 +49,26 @@ #' f_saem_fomc_tc <- saem(f_mmkin_parent_tc["FOMC", ]) #' compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so)) #' +#' sfo_sfo <- mkinmod(parent = mkinsub("SFO", "A1"), +#' A1 = mkinsub("SFO")) +#' fomc_sfo <- mkinmod(parent = mkinsub("FOMC", "A1"), +#' A1 = mkinsub("SFO")) #' dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"), #' A1 = mkinsub("SFO")) -#' f_mmkin <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE, solution_type = "analytical") -#' # This takes about 4 minutes on my system -#' f_saem <- saem(f_mmkin) +#' # The following fit uses analytical solutions for SFO-SFO and DFOP-SFO, +#' # and compiled ODEs for FOMC, both are fast +#' f_mmkin <- mmkin(list( +#' "SFO-SFO" = sfo_sfo, "FOMC-SFO" = fomc_sfo, "DFOP-SFO" = dfop_sfo), +#' ds, quiet = TRUE) +#' # These take about five seconds each on this system, as we use +#' # analytical solutions written for saemix. When using the analytical +#' # solutions written for mkin this took around four minutes +#' f_saem_sfo_sfo <- saem(f_mmkin["SFO-SFO", ]) +#' f_saem_dfop_sfo <- saem(f_mmkin["SFO-SFO", ]) #' -#' f_mmkin_des <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE, solution_type = "deSolve") #' # Using a single core, the following takes about 6 minutes, using 10 cores #' # it is slower instead of faster -#' f_saem_des <- saem(f_mmkin_des, cores = 1) -#' compare.saemix(list(f_saem$so, f_saem_des$so)) +#' f_saem_fomc <- saem(f_mmkin["FOMC-SFO", ], cores = 1) #' } #' @export saem <- function(object, control, ...) UseMethod("saem") @@ -83,7 +92,12 @@ saem.mmkin <- function(object, } fit_time <- system.time({ f_saemix <- saemix::saemix(m_saemix, d_saemix, control) - f_saemix <- try(saemix::saemix.predict(f_saemix), silent = TRUE) + f_pred <- try(saemix::saemix.predict(f_saemix), silent = TRUE) + if (!inherits(f_pred, "try-error")) { + f_saemix <- f_pred + } else { + warning("Creating predictions from the saemix model failed") + } }) if (suppressPlot) { grDevices::dev.off() @@ -145,37 +159,43 @@ saemix_model <- function(object, cores = 1, verbose = FALSE, ...) { model_function <- FALSE - if (length(mkin_model$spec) == 1 & mkin_model$use_of_ff == "max") { - parent_type <- mkin_model$spec[[1]]$type - if (length(odeini_fixed) == 1) { - if (parent_type == "SFO") { - stop("saemix needs at least two parameters to work on.") - } - if (parent_type == "FOMC") { - model_function <- function(psi, id, xidep) { - odeini_fixed / (xidep[, "time"]/exp(psi[id, 2]) + 1)^exp(psi[id, 1]) + # Model functions with analytical solutions + # Fixed parameters, use_of_ff = "min" and turning off sinks currently not supported here + # In general, we need to consider exactly how the parameters in mkinfit were specified, + # as the parameters are currently mapped by position in these solutions + sinks <- sapply(mkin_model$spec, function(x) x$sink) + if (length(odeparms_fixed) == 0 & mkin_model$use_of_ff == "max" & all(sinks)) { + # Parent only + if (length(mkin_model$spec) == 1) { + parent_type <- mkin_model$spec[[1]]$type + if (length(odeini_fixed) == 1) { + if (parent_type == "SFO") { + stop("saemix needs at least two parameters to work on.") } - } - if (parent_type == "DFOP") { - model_function <- function(psi, id, xidep) { - g <- plogis(psi[id, 3]) - t = xidep[, "time"] - odeini_fixed * (g * exp(- exp(psi[id, 1]) * t) + - (1 - g) * exp(- exp(psi[id, 2]) * t)) + if (parent_type == "FOMC") { + model_function <- function(psi, id, xidep) { + odeini_fixed / (xidep[, "time"]/exp(psi[id, 2]) + 1)^exp(psi[id, 1]) + } } - } - if (parent_type == "HS") { - model_function <- function(psi, id, xidep) { - tb <- exp(psi[id, 3]) - t = xidep[, "time"] - k1 = exp(psi[id, 1]) - odeini_fixed * ifelse(t <= tb, - exp(- k1 * t), - exp(- k1 * t) * exp(- exp(psi[id, 2]) * (t - tb))) + if (parent_type == "DFOP") { + model_function <- function(psi, id, xidep) { + g <- plogis(psi[id, 3]) + t <- xidep[, "time"] + odeini_fixed * (g * exp(- exp(psi[id, 1]) * t) + + (1 - g) * exp(- exp(psi[id, 2]) * t)) + } } - } - } else { - if (length(odeparms_fixed) == 0) { + if (parent_type == "HS") { + model_function <- function(psi, id, xidep) { + tb <- exp(psi[id, 3]) + t <- xidep[, "time"] + k1 = exp(psi[id, 1]) + odeini_fixed * ifelse(t <= tb, + exp(- k1 * t), + exp(- k1 * t) * exp(- exp(psi[id, 2]) * (t - tb))) + } + } + } else { if (parent_type == "SFO") { model_function <- function(psi, id, xidep) { psi[id, 1] * exp( - exp(psi[id, 2]) * xidep[, "time"]) @@ -189,7 +209,7 @@ saemix_model <- function(object, cores = 1, verbose = FALSE, ...) { if (parent_type == "DFOP") { model_function <- function(psi, id, xidep) { g <- plogis(psi[id, 4]) - t = xidep[, "time"] + t <- xidep[, "time"] psi[id, 1] * (g * exp(- exp(psi[id, 2]) * t) + (1 - g) * exp(- exp(psi[id, 3]) * t)) } @@ -197,7 +217,7 @@ saemix_model <- function(object, cores = 1, verbose = FALSE, ...) { if (parent_type == "HS") { model_function <- function(psi, id, xidep) { tb <- exp(psi[id, 4]) - t = xidep[, "time"] + t <- xidep[, "time"] k1 = exp(psi[id, 2]) psi[id, 1] * ifelse(t <= tb, exp(- k1 * t), @@ -206,9 +226,57 @@ saemix_model <- function(object, cores = 1, verbose = FALSE, ...) { } } } + + # Parent with one metabolite + # Parameter names used in the model functions are as in + # https://nbviewer.jupyter.org/urls/jrwb.de/nb/Symbolic%20ODE%20solutions%20for%20mkin.ipynb + if (length(mkin_model$spec) == 2) { + types <- unname(sapply(mkin_model$spec, function(x) x$type)) + # Initial value for the metabolite (n20) must be fixed + if (names(odeini_fixed) == names(mkin_model$spec)[2]) { + n20 <- odeini_fixed + parent_name <- names(mkin_model$spec)[1] + if (identical(types, c("SFO", "SFO"))) { + model_function <- function(psi, id, xidep) { + t <- xidep[, "time"] + n10 <- psi[id, 1] + k1 <- exp(psi[id, 2]) + k2 <- exp(psi[id, 3]) + f12 <- plogis(psi[id, 4]) + ifelse(xidep[, "name"] == parent_name, + n10 * exp(- k1 * t), + (((k2 - k1) * n20 - f12 * k1 * n10) * exp(- k2 * t)) / (k2 - k1) + + (f12 * k1 * n10 * exp(- k1 * t)) / (k2 - k1) + ) + } + } + if (identical(types, c("DFOP", "SFO"))) { + model_function <- function(psi, id, xidep) { + t <- xidep[, "time"] + n10 <- psi[id, 1] + k2 <- exp(psi[id, 2]) + f12 <- plogis(psi[id, 3]) + l1 <- exp(psi[id, 4]) + l2 <- exp(psi[id, 5]) + g <- plogis(psi[id, 6]) + ifelse(xidep[, "name"] == parent_name, + n10 * (g * exp(- l1 * t) + (1 - g) * exp(- l2 * t)), + ((f12 * g - f12) * l2 * n10 * exp(- l2 * t)) / (l2 - k2) - + (f12 * g * l1 * n10 * exp(- l1 * t)) / (l1 - k2) + + ((((l1 - k2) * l2 - k2 * l1 + k2^2) * n20 + + ((f12 * l1 + (f12 * g - f12) * k2) * l2 - + f12 * g * k2 * l1) * n10) * exp( - k2 * t)) / + ((l1 - k2) * l2 - k2 * l1 + k2^2) + ) + } + } + } + } } - if (!is.function(model_function)) { + if (is.function(model_function)) { + solution_type = "analytical saemix" + } else { model_function <- function(psi, id, xidep) { uid <- unique(id) diff --git a/R/summary.saem.mmkin.R b/R/summary.saem.mmkin.R index f7110dd0..4c9776a6 100644 --- a/R/summary.saem.mmkin.R +++ b/R/summary.saem.mmkin.R @@ -96,7 +96,7 @@ summary.saem.mmkin <- function(object, data = FALSE, verbose = FALSE, distimes = colnames(confint_ranef)[1] <- "est." # Error model - enames <- object$so@results@name.sigma + enames <- if (object$err_mod == "const") "a.1" else c("a.1", "b.1") confint_errmod <- as.matrix(conf.int[enames, c("estimate", "lower", "upper")]) colnames(confint_errmod)[1] <- "est." |