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authorJohannes Ranke <jranke@uni-bremen.de>2020-11-11 11:48:38 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2020-11-11 11:48:38 +0100
commit158b2f02c6778bcb1b868497c6366924ec96102d (patch)
tree0c87d22c0d71427af267d9cf1c1d32a7c6a287ac /R/saemix.R
parent0cbabc98850e436b1e0703c659cf8a00b52d7503 (diff)
Rename saemix file, option to suppress saemix messages
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diff --git a/R/saemix.R b/R/saemix.R
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-#' Fit nonlinear mixed models with SAEM
-#'
-#' This function uses [saemix::saemix()] as a backend for fitting nonlinear mixed
-#' effects models created from [mmkin] row objects using the Stochastic Approximation
-#' Expectation Maximisation algorithm (SAEM).
-#'
-#' An mmkin row object is essentially a list of mkinfit objects that have been
-#' obtained by fitting the same model to a list of datasets using [mkinfit].
-#'
-#' Starting values for the fixed effects (population mean parameters, argument
-#' psi0 of [saemix::saemixModel()] are the mean values of the parameters found
-#' using [mmkin].
-#'
-#' @param object An [mmkin] row object containing several fits of the same
-#' [mkinmod] model to different datasets
-#' @param verbose Should we print information about created objects?
-#' @param cores The number of cores to be used for multicore processing using
-#' [parallel::mclapply()]. Using more than 1 core is experimental and may
-#' lead to uncontrolled forking, apparently depending on the BLAS version
-#' used.
-#' @param suppressPlot Should we suppress any plotting that is done
-#' by the saemix function?
-#' @param control Passed to [saemix::saemix]
-#' @param \dots Further parameters passed to [saemix::saemixData]
-#' and [saemix::saemixModel].
-#' @return An S3 object of class 'saem.mmkin', containing the fitted
-#' [saemix::SaemixObject] as a list component named 'so'. The
-#' object also inherits from 'mixed.mmkin'.
-#' @seealso [summary.saem.mmkin] [plot.mixed.mmkin]
-#' @examples
-#' \dontrun{
-#' ds <- lapply(experimental_data_for_UBA_2019[6:10],
-#' function(x) subset(x$data[c("name", "time", "value")]))
-#' names(ds) <- paste("Dataset", 6:10)
-#' f_mmkin_parent_p0_fixed <- mmkin("FOMC", ds, cores = 1,
-#' state.ini = c(parent = 100), fixed_initials = "parent", quiet = TRUE)
-#' f_saem_p0_fixed <- saem(f_mmkin_parent_p0_fixed)
-#'
-#' f_mmkin_parent <- mmkin(c("SFO", "FOMC", "DFOP"), ds, quiet = TRUE)
-#' f_saem_sfo <- saem(f_mmkin_parent["SFO", ])
-#' f_saem_fomc <- saem(f_mmkin_parent["FOMC", ])
-#' f_saem_dfop <- saem(f_mmkin_parent["DFOP", ])
-#'
-#' # The returned saem.mmkin object contains an SaemixObject, therefore we can use
-#' # functions from saemix
-#' library(saemix)
-#' compare.saemix(list(f_saem_sfo$so, f_saem_fomc$so, f_saem_dfop$so))
-#' plot(f_saem_fomc$so, plot.type = "convergence")
-#' plot(f_saem_fomc$so, plot.type = "individual.fit")
-#' plot(f_saem_fomc$so, plot.type = "npde")
-#' plot(f_saem_fomc$so, plot.type = "vpc")
-#'
-#' f_mmkin_parent_tc <- update(f_mmkin_parent, error_model = "tc")
-#' 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"))
-#' # 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["DFOP-SFO", ])
-#' # We can use print, plot and summary methods to check the results
-#' print(f_saem_dfop_sfo)
-#' plot(f_saem_dfop_sfo)
-#' summary(f_saem_dfop_sfo, data = FALSE)
-#'
-#' # Using a single core, the following takes about 6 minutes as we do not have an
-#' # analytical solution. Using 10 cores it is slower instead of faster
-#' #f_saem_fomc <- saem(f_mmkin["FOMC-SFO", ], cores = 1)
-#' }
-#' @export
-saem <- function(object, control, ...) UseMethod("saem")
-
-#' @rdname saem
-#' @export
-saem.mmkin <- function(object,
- control = list(displayProgress = FALSE, print = FALSE,
- save = FALSE, save.graphs = FALSE),
- cores = 1,
- verbose = FALSE, suppressPlot = TRUE, ...)
-{
- m_saemix <- saemix_model(object, cores = cores, verbose = verbose)
- d_saemix <- saemix_data(object, verbose = verbose)
- if (suppressPlot) {
- # We suppress the log-likelihood curve that saemix currently
- # produces at the end of the fit by plotting to a file
- # that we discard afterwards
- tmp <- tempfile()
- grDevices::png(tmp)
- }
- fit_time <- system.time({
- f_saemix <- saemix::saemix(m_saemix, d_saemix, control)
- 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()
- unlink(tmp)
- }
- transparms_optim <- f_saemix@results@fixed.effects
- names(transparms_optim) <- f_saemix@results@name.fixed
- bparms_optim <- backtransform_odeparms(transparms_optim,
- object[[1]]$mkinmod,
- object[[1]]$transform_rates,
- object[[1]]$transform_fractions)
-
- result <- list(
- mkinmod = object[[1]]$mkinmod,
- mmkin = object,
- solution_type = object[[1]]$solution_type,
- transform_rates = object[[1]]$transform_rates,
- transform_fractions = object[[1]]$transform_fractions,
- so = f_saemix,
- time = fit_time,
- mean_dp_start = attr(m_saemix, "mean_dp_start"),
- bparms.optim = bparms_optim,
- bparms.fixed = object[[1]]$bparms.fixed,
- data = nlme_data(object),
- err_mod = object[[1]]$err_mod,
- date.fit = date(),
- saemixversion = as.character(utils::packageVersion("saemix")),
- mkinversion = as.character(utils::packageVersion("mkin")),
- Rversion = paste(R.version$major, R.version$minor, sep=".")
- )
-
- class(result) <- c("saem.mmkin", "mixed.mmkin")
- return(result)
-}
-
-#' @export
-#' @rdname saem
-#' @param x An saem.mmkin object to print
-#' @param digits Number of digits to use for printing
-print.saem.mmkin <- function(x, digits = max(3, getOption("digits") - 3), ...) {
- cat( "Kinetic nonlinear mixed-effects model fit by SAEM" )
- cat("\nStructural model:\n")
- diffs <- x$mmkin[[1]]$mkinmod$diffs
- nice_diffs <- gsub("^(d.*) =", "\\1/dt =", diffs)
- writeLines(strwrap(nice_diffs, exdent = 11))
- cat("\nData:\n")
- cat(nrow(x$data), "observations of",
- length(unique(x$data$name)), "variable(s) grouped in",
- length(unique(x$data$ds)), "datasets\n")
-
- cat("\nLikelihood computed by importance sampling\n")
- print(data.frame(
- AIC = AIC(x$so, type = "is"),
- BIC = BIC(x$so, type = "is"),
- logLik = logLik(x$so, type = "is"),
- row.names = " "), digits = digits)
-
- cat("\nFitted parameters:\n")
- conf.int <- x$so@results@conf.int[c("estimate", "lower", "upper")]
- rownames(conf.int) <- x$so@results@conf.int[["name"]]
- print(conf.int, digits = digits)
-
- invisible(x)
-}
-
-#' @rdname saem
-#' @return An [saemix::SaemixModel] object.
-#' @export
-saemix_model <- function(object, cores = 1, verbose = FALSE, ...) {
- if (nrow(object) > 1) stop("Only row objects allowed")
-
- mkin_model <- object[[1]]$mkinmod
- solution_type <- object[[1]]$solution_type
-
- degparms_optim <- mean_degparms(object)
- degparms_fixed <- object[[1]]$bparms.fixed
-
- # Transformations are done in the degradation function
- transform.par = rep(0, length(degparms_optim))
-
- odeini_optim_parm_names <- grep('_0$', names(degparms_optim), value = TRUE)
- odeini_fixed_parm_names <- grep('_0$', names(degparms_fixed), value = TRUE)
-
- odeparms_fixed_names <- setdiff(names(degparms_fixed), odeini_fixed_parm_names)
- odeparms_fixed <- degparms_fixed[odeparms_fixed_names]
-
- odeini_fixed <- degparms_fixed[odeini_fixed_parm_names]
- names(odeini_fixed) <- gsub('_0$', '', odeini_fixed_parm_names)
-
- model_function <- FALSE
-
- # 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 == "FOMC") {
- model_function <- function(psi, id, xidep) {
- odeini_fixed / (xidep[, "time"]/exp(psi[id, 2]) + 1)^exp(psi[id, 1])
- }
- }
- 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 == "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"])
- }
- }
- if (parent_type == "FOMC") {
- model_function <- function(psi, id, xidep) {
- psi[id, 1] / (xidep[, "time"]/exp(psi[id, 3]) + 1)^exp(psi[id, 2])
- }
- }
- if (parent_type == "DFOP") {
- model_function <- function(psi, id, xidep) {
- g <- plogis(psi[id, 4])
- t <- xidep[, "time"]
- psi[id, 1] * (g * exp(- exp(psi[id, 2]) * t) +
- (1 - g) * exp(- exp(psi[id, 3]) * t))
- }
- }
- if (parent_type == "HS") {
- model_function <- function(psi, id, xidep) {
- tb <- exp(psi[id, 4])
- t <- xidep[, "time"]
- k1 = exp(psi[id, 2])
- psi[id, 1] * ifelse(t <= tb,
- exp(- k1 * t),
- exp(- k1 * t) * exp(- exp(psi[id, 3]) * (t - tb)))
- }
- }
- }
- }
-
- # 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$spec)[1]
- if (identical(types, c("SFO", "SFO"))) {
- model_function <- function(psi, id, xidep) {
- t <- xidep[, "time"]
- n10 <- psi[id, 1]
- k1 <- exp(psi[id, 2])
- k2 <- exp(psi[id, 3])
- f12 <- plogis(psi[id, 4])
- ifelse(xidep[, "name"] == parent_name,
- n10 * exp(- k1 * t),
- (((k2 - k1) * n20 - f12 * k1 * n10) * exp(- k2 * t)) / (k2 - k1) +
- (f12 * k1 * n10 * exp(- k1 * t)) / (k2 - k1)
- )
- }
- }
- if (identical(types, c("DFOP", "SFO"))) {
- model_function <- function(psi, id, xidep) {
- t <- xidep[, "time"]
- n10 <- psi[id, 1]
- k2 <- exp(psi[id, 2])
- f12 <- plogis(psi[id, 3])
- l1 <- exp(psi[id, 4])
- l2 <- exp(psi[id, 5])
- g <- plogis(psi[id, 6])
- ifelse(xidep[, "name"] == parent_name,
- n10 * (g * exp(- l1 * t) + (1 - g) * exp(- l2 * t)),
- ((f12 * g - f12) * l2 * n10 * exp(- l2 * t)) / (l2 - k2) -
- (f12 * g * l1 * n10 * exp(- l1 * t)) / (l1 - k2) +
- ((((l1 - k2) * l2 - k2 * l1 + k2^2) * n20 +
- ((f12 * l1 + (f12 * g - f12) * k2) * l2 -
- f12 * g * k2 * l1) * n10) * exp( - k2 * t)) /
- ((l1 - k2) * l2 - k2 * l1 + k2^2)
- )
- }
- }
- }
- }
- }
-
- if (is.function(model_function)) {
- solution_type = "analytical saemix"
- } else {
- model_function <- function(psi, id, xidep) {
-
- uid <- unique(id)
-
- res_list <- parallel::mclapply(uid, function(i) {
- transparms_optim <- psi[i, ]
- names(transparms_optim) <- names(degparms_optim)
-
- odeini_optim <- transparms_optim[odeini_optim_parm_names]
- names(odeini_optim) <- gsub('_0$', '', odeini_optim_parm_names)
-
- odeini <- c(odeini_optim, odeini_fixed)[names(mkin_model$diffs)]
-
- ode_transparms_optim_names <- setdiff(names(transparms_optim), odeini_optim_parm_names)
- odeparms_optim <- backtransform_odeparms(transparms_optim[ode_transparms_optim_names], mkin_model,
- transform_rates = object[[1]]$transform_rates,
- transform_fractions = object[[1]]$transform_fractions)
- odeparms <- c(odeparms_optim, odeparms_fixed)
-
- xidep_i <- subset(xidep, id == i)
-
- if (solution_type == "analytical") {
- out_values <- mkin_model$deg_func(xidep_i, odeini, odeparms)
- } else {
-
- i_time <- xidep_i$time
- i_name <- xidep_i$name
-
- out_wide <- mkinpredict(mkin_model,
- odeparms = odeparms, odeini = odeini,
- solution_type = solution_type,
- outtimes = sort(unique(i_time)),
- na_stop = FALSE
- )
-
- out_index <- cbind(as.character(i_time), as.character(i_name))
- out_values <- out_wide[out_index]
- }
- return(out_values)
- }, mc.cores = cores)
- res <- unlist(res_list)
- return(res)
- }
- }
-
- error.model <- switch(object[[1]]$err_mod,
- const = "constant",
- tc = "combined",
- obs = "constant")
-
- if (object[[1]]$err_mod == "obs") {
- warning("The error model 'obs' (variance by variable) can currently not be transferred to an saemix model")
- }
-
- error.init <- switch(object[[1]]$err_mod,
- const = c(a = mean(sapply(object, function(x) x$errparms)), b = 1),
- tc = c(a = mean(sapply(object, function(x) x$errparms[1])),
- b = mean(sapply(object, function(x) x$errparms[2]))),
- obs = c(a = mean(sapply(object, function(x) x$errparms)), b = 1))
-
- psi0_matrix <- matrix(degparms_optim, nrow = 1)
- colnames(psi0_matrix) <- names(degparms_optim)
-
- res <- saemix::saemixModel(model_function,
- psi0 = psi0_matrix,
- "Mixed model generated from mmkin object",
- transform.par = transform.par,
- error.model = error.model,
- verbose = verbose
- )
- attr(res, "mean_dp_start") <- degparms_optim
- return(res)
-}
-
-#' @rdname saem
-#' @return An [saemix::SaemixData] object.
-#' @export
-saemix_data <- function(object, verbose = FALSE, ...) {
- if (nrow(object) > 1) stop("Only row objects allowed")
- ds_names <- colnames(object)
-
- ds_list <- lapply(object, function(x) x$data[c("time", "variable", "observed")])
- names(ds_list) <- ds_names
- ds_saemix_all <- purrr::map_dfr(ds_list, function(x) x, .id = "ds")
- ds_saemix <- data.frame(ds = ds_saemix_all$ds,
- name = as.character(ds_saemix_all$variable),
- time = ds_saemix_all$time,
- value = ds_saemix_all$observed,
- stringsAsFactors = FALSE)
-
- res <- saemix::saemixData(ds_saemix,
- name.group = "ds",
- name.predictors = c("time", "name"),
- name.response = "value",
- verbose = verbose,
- ...)
- return(res)
-}

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